diff --git a/DESCRIPTION b/DESCRIPTION index 9a860edd0..3faba99e6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: singleCellTK Type: Package Title: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data -Version: 2.16.0 +Version: 2.16.1 Authors@R: c(person(given="Yichen", family="Wang", email="wangych@bu.edu", role=c("aut"), comment = c(ORCID = "0000-0003-4347-5199")), person(given="Irzam", family="Sarfraz", email="isarfraz@bu.edu", role=c("aut"), diff --git a/docs/404.html b/docs/404.html index 51a131a57..285f09d3f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -6,7 +6,7 @@ Page not found (404) • singleCellTK - + @@ -19,7 +19,7 @@ - +
@@ -42,7 +42,7 @@
  • - +
  • @@ -51,7 +51,7 @@
    • - +
    @@ -268,16 +268,16 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 951e07615..3b6c19d20 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -1,9 +1,9 @@ -License • singleCellTKLicense • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -202,26 +202,7 @@

    License

    YEAR: 2016
-COPYRIGHT HOLDER: David Jenkins and W. Evan Johnson
-
-The MIT License (MIT) (http://opensource.org/licenses/MIT)
-
-Permission is hereby granted, free of charge, to any person obtaining a copy of
-this software and associated documentation files (the "Software"), to deal in
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
-the Software, and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
-FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
-IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+COPYRIGHT HOLDER: David Jenkins, W. Evan Johnson, and Joshua D. Campbell
    @@ -239,15 +220,15 @@

    License

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/01_import_and_qc_tutorial.html b/docs/articles/01_import_and_qc_tutorial.html index 205ccfb0a..c94bc7d59 100644 --- a/docs/articles/01_import_and_qc_tutorial.html +++ b/docs/articles/01_import_and_qc_tutorial.html @@ -6,21 +6,20 @@ Importing and Quality Control Tutorial - PBMC3K • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -603,9 +602,7 @@

    Filtering - -

    +
    @@ -618,16 +615,16 @@

    Filtering

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotPerCellQC-1.png b/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotPerCellQC-1.png index d6f2fd8d5..aae7ab32b 100644 Binary files a/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotPerCellQC-1.png and b/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotPerCellQC-1.png differ diff --git a/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotScDblFinder-1.png b/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotScDblFinder-1.png index e1760a359..5c0d64de5 100644 Binary files a/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotScDblFinder-1.png and b/docs/articles/01_import_and_qc_tutorial_files/figure-html/plotScDblFinder-1.png differ diff --git a/docs/articles/01_import_and_qc_tutorial_files/figure-html/plottDecontX-1.png b/docs/articles/01_import_and_qc_tutorial_files/figure-html/plottDecontX-1.png index 142c22a89..472a6bab3 100644 Binary files a/docs/articles/01_import_and_qc_tutorial_files/figure-html/plottDecontX-1.png and b/docs/articles/01_import_and_qc_tutorial_files/figure-html/plottDecontX-1.png differ diff --git a/docs/articles/02_a_la_carte_workflow.html b/docs/articles/02_a_la_carte_workflow.html index bb44f1a58..63b3cac2d 100644 --- a/docs/articles/02_a_la_carte_workflow.html +++ b/docs/articles/02_a_la_carte_workflow.html @@ -6,21 +6,20 @@ A La Carte Workflow Tutorial - PBMC3K • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -699,23 +698,25 @@

    Marker Detection maxCtrlExprPerc = 0.5, minMeanExpr = 0) topMarkers

    ##           Gene   Log2_FC        Pvalue           FDR cluster clusterExprPerc
-## 8764      IL7R 0.7697338  9.053691e-69  2.279998e-65       1       0.7212885
-## 1956    S100A9 4.3853548 2.397248e-207 3.924055e-203       2       0.9977064
-## 269581    CCR7 0.6150976  1.881449e-41  9.332559e-39       3       0.5688312
-## 106781 HLA-DRA 3.2752984 1.682895e-182 2.754731e-178       4       1.0000000
-## 26825     CCL5 3.0878935 2.507059e-148 8.207610e-144       5       0.9712644
-## 106091    LST1 2.8683989  1.038405e-98  1.133177e-94       6       1.0000000
-## 310761    NKG7 4.2435780  8.853054e-82  2.898313e-77       7       1.0000000
-## 288182    CST3 3.2975861  2.221917e-16  1.039159e-12       8       1.0000000
-## 7697      PPBP 5.9620589  9.423341e-07  2.504757e-03       9       1.0000000
+## 1956    S100A9 4.3918388 1.231801e-205 2.016334e-201       1       0.9976852
+## 26958     CCR7 0.6107894  7.062217e-41  3.400042e-38       2       0.5662338
+## 87641     IL7R 0.6949784  1.462605e-36  1.294129e-33       3       0.7493404
+## 26825     CCL5 3.0724416 1.407334e-149 4.607331e-145       4       0.9715909
+## 106781 HLA-DRA 3.2851089 6.201038e-183 1.015048e-178       5       1.0000000
+## 16364      CD2 0.5344754  6.223183e-26  2.263717e-22       6       0.6377246
+## 106091    LST1 2.8798261 3.464220e-101  3.780388e-97       7       1.0000000
+## 310761    NKG7 4.2518808  8.025412e-81  2.627359e-76       8       1.0000000
+## 288182    CST3 3.2975861  2.221917e-16  1.039159e-12       9       1.0000000
+## 7697      PPBP 5.9620589  9.423341e-07  2.504757e-03      10       1.0000000
 ##        ControlExprPerc clusterAveExpr
-## 8764        0.28698380      1.1880037
-## 1956        0.23094477      4.7335694
-## 269581      0.13380910      0.7705352
-## 106781      0.49538867      4.4065968
-## 26825       0.21676174      3.4664459
-## 106091      0.30477759      3.4541085
-## 310761      0.25717752      4.7869642
+## 1956        0.23234624      4.7456645
+## 26958       0.13425513      0.7668583
+## 87641       0.34697509      1.2221913
+## 26825       0.21538462      3.4483627
+## 106781      0.49561018      4.4163508
+## 16364       0.27387702      0.8940661
+## 106091      0.30363036      3.4602852
+## 310761      0.25777778      4.7980173
 ## 288182      0.39113680      4.3717555
 ## 7697        0.02406417      5.9894455

    For visualization, SCTK has a specific heatmap plotting function for @@ -970,20 +971,6 @@

    Differential Abundance 1 -707 -729 -0 -151 -0.492340 -0.508 -0.00000 -1.000 -Inf -6.28e-42 -2.83e-41 - - -2 1 1435 0 @@ -996,8 +983,8 @@

    Differential Abundance1.00e+00 1.00e+00 - -3 + +2 378 1058 1 @@ -1008,10 +995,38 @@

    Differential Abundance0.993 53.54253 9.54e-18 -2.86e-17 +3.18e-17 + + +3 +373 +1063 +0 +151 +0.259749 +0.740 +0.00000 +1.000 +Inf +4.63e-19 +2.31e-18 4 +327 +1109 +20 +131 +0.227716 +0.772 +0.13245 +0.868 +1.93065 +6.86e-03 +1.37e-02 + + +5 4 1432 0 @@ -1024,22 +1039,22 @@

    Differential Abundance1.00e+00 1.00e+00 - -5 -324 -1112 -19 -132 -0.225627 -0.774 -0.12583 -0.874 -2.02348 -3.55e-03 -7.99e-03 - 6 +332 +1104 +0 +151 +0.231198 +0.769 +0.00000 +1.000 +Inf +7.12e-17 +1.78e-16 + + +7 0 1436 0 @@ -1052,22 +1067,22 @@

    Differential Abundance1.00e+00 1.00e+00 - -7 -22 -1414 -131 -20 -0.015320 -0.985 -0.86755 -0.132 -0.00242 -7.29e-145 -6.56e-144 - 8 +21 +1415 +130 +21 +0.014624 +0.985 +0.86093 +0.139 +0.00244 +6.26e-144 +6.26e-143 + + +9 0 1436 0 @@ -1080,8 +1095,8 @@

    Differential Abundance1.00e+00 1.00e+00 - -9 + +10 0 1436 0 @@ -1253,9 +1268,7 @@

    Performing DE Analysi +

    @@ -1268,16 +1281,16 @@

    Performing DE Analysi

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/deHeatmap-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/deHeatmap-1.png index fb1f79a8c..8cec088b9 100644 Binary files a/docs/articles/02_a_la_carte_workflow_files/figure-html/deHeatmap-1.png and b/docs/articles/02_a_la_carte_workflow_files/figure-html/deHeatmap-1.png differ diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/markerHeatmap-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/markerHeatmap-1.png index 99e3c8d05..580b5531e 100644 Binary files a/docs/articles/02_a_la_carte_workflow_files/figure-html/markerHeatmap-1.png and b/docs/articles/02_a_la_carte_workflow_files/figure-html/markerHeatmap-1.png differ diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/pathwayDEHeatmap-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/pathwayDEHeatmap-1.png index 883101a4f..8a6e9170e 100644 Binary files a/docs/articles/02_a_la_carte_workflow_files/figure-html/pathwayDEHeatmap-1.png and b/docs/articles/02_a_la_carte_workflow_files/figure-html/pathwayDEHeatmap-1.png differ diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/plotCluster-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/plotCluster-1.png index a23fb448c..aa41a3087 100644 Binary files a/docs/articles/02_a_la_carte_workflow_files/figure-html/plotCluster-1.png and b/docs/articles/02_a_la_carte_workflow_files/figure-html/plotCluster-1.png differ diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/plotClusterAbundance-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/plotClusterAbundance-1.png index 02af7dd4a..446b305f8 100644 Binary files a/docs/articles/02_a_la_carte_workflow_files/figure-html/plotClusterAbundance-1.png and b/docs/articles/02_a_la_carte_workflow_files/figure-html/plotClusterAbundance-1.png differ diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/plotUMAP-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/plotUMAP-1.png index 03cd2e044..1a40b679b 100644 Binary files a/docs/articles/02_a_la_carte_workflow_files/figure-html/plotUMAP-1.png and b/docs/articles/02_a_la_carte_workflow_files/figure-html/plotUMAP-1.png differ diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/singleRUMAP-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/singleRUMAP-1.png index 5b712bebe..a3b37f61e 100644 Binary files a/docs/articles/02_a_la_carte_workflow_files/figure-html/singleRUMAP-1.png and b/docs/articles/02_a_la_carte_workflow_files/figure-html/singleRUMAP-1.png differ diff --git a/docs/articles/02_a_la_carte_workflow_files/figure-html/visVAM-1.png b/docs/articles/02_a_la_carte_workflow_files/figure-html/visVAM-1.png index ef4d3c824..882cb8cbc 100644 Binary files a/docs/articles/02_a_la_carte_workflow_files/figure-html/visVAM-1.png and b/docs/articles/02_a_la_carte_workflow_files/figure-html/visVAM-1.png differ diff --git a/docs/articles/2d_embedding.html b/docs/articles/2d_embedding.html index 0d6c3253c..14f443697 100644 --- a/docs/articles/2d_embedding.html +++ b/docs/articles/2d_embedding.html @@ -6,21 +6,20 @@ 2D Embedding • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -469,9 +468,7 @@

    References - -

    +
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    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/2d_embedding_files/figure-html/dm_console_example-1.png b/docs/articles/2d_embedding_files/figure-html/dm_console_example-1.png index a1b4a8b98..3232b52de 100644 Binary files a/docs/articles/2d_embedding_files/figure-html/dm_console_example-1.png and b/docs/articles/2d_embedding_files/figure-html/dm_console_example-1.png differ diff --git a/docs/articles/batch_correction.html b/docs/articles/batch_correction.html index 8a6fc5e2d..680bca2a8 100644 --- a/docs/articles/batch_correction.html +++ b/docs/articles/batch_correction.html @@ -6,21 +6,20 @@ Batch Correction • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -462,10 +461,10 @@

    Workflow Guide## dim: 800 800 ## metadata(1): assayType ## assays(2): counts logcounts -## rownames(800): CHPT1 SLC15A4 ... ZFAND2B LINC01473 +## rownames(800): MRPS16 POLR2L ... TP53INP2 ABT1 ## rowData names(5): rownames ENSEMBL_ID Symbol_TENx Symbol expPerc -## colnames(800): pbmc6k_ACGTTACTAGCCAT-1 pbmc8k_ATTGGACTCTCGAGTA-1 ... -## pbmc8k_GCAAACTCAGGTCCAC-1 pbmc6k_GCGAGCACCTCAAG-1 +## colnames(800): pbmc8k_TGTGTTTTCTACTCAT-1 pbmc8k_CTGGTCTGTGCCTTGG-1 ... +## pbmc8k_GGAATAATCATGCTCC-1 pbmc6k_AATTACGAACCTTT-1 ## colData names(14): rownames Sample ... sample sizeFactor ## reducedDimNames(0): ## mainExpName: NULL @@ -487,10 +486,10 @@

    Workflow Guide## dim: 800 800 ## metadata(2): assayType batchCorr ## assays(3): counts logcounts LIMMA -## rownames(800): CHPT1 SLC15A4 ... ZFAND2B LINC01473 +## rownames(800): MRPS16 POLR2L ... TP53INP2 ABT1 ## rowData names(5): rownames ENSEMBL_ID Symbol_TENx Symbol expPerc -## colnames(800): pbmc6k_ACGTTACTAGCCAT-1 pbmc8k_ATTGGACTCTCGAGTA-1 ... -## pbmc8k_GCAAACTCAGGTCCAC-1 pbmc6k_GCGAGCACCTCAAG-1 +## colnames(800): pbmc8k_TGTGTTTTCTACTCAT-1 pbmc8k_CTGGTCTGTGCCTTGG-1 ... +## pbmc8k_GGAATAATCATGCTCC-1 pbmc6k_AATTACGAACCTTT-1 ## colData names(14): rownames Sample ... sample sizeFactor ## reducedDimNames(0): ## mainExpName: NULL @@ -733,9 +732,7 @@

    References - -

    +
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    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/batch_correction_files/figure-html/batchVarAfter-1.png b/docs/articles/batch_correction_files/figure-html/batchVarAfter-1.png index 274c0808f..1679b3192 100644 Binary files a/docs/articles/batch_correction_files/figure-html/batchVarAfter-1.png and b/docs/articles/batch_correction_files/figure-html/batchVarAfter-1.png differ diff --git a/docs/articles/batch_correction_files/figure-html/batchVarBefore-1.png b/docs/articles/batch_correction_files/figure-html/batchVarBefore-1.png index 353ddca76..afbd9bc4b 100644 Binary files a/docs/articles/batch_correction_files/figure-html/batchVarBefore-1.png and b/docs/articles/batch_correction_files/figure-html/batchVarBefore-1.png differ diff --git a/docs/articles/batch_correction_files/figure-html/umapAfter-1.png b/docs/articles/batch_correction_files/figure-html/umapAfter-1.png index c741d6db8..fee5e2e66 100644 Binary files a/docs/articles/batch_correction_files/figure-html/umapAfter-1.png and b/docs/articles/batch_correction_files/figure-html/umapAfter-1.png differ diff --git a/docs/articles/batch_correction_files/figure-html/umapBefore-1.png b/docs/articles/batch_correction_files/figure-html/umapBefore-1.png index c113d7217..76a9d3fdd 100644 Binary files a/docs/articles/batch_correction_files/figure-html/umapBefore-1.png and b/docs/articles/batch_correction_files/figure-html/umapBefore-1.png differ diff --git a/docs/articles/celda_curated_workflow.html b/docs/articles/celda_curated_workflow.html index 3a0a686ef..c98d3e805 100644 --- a/docs/articles/celda_curated_workflow.html +++ b/docs/articles/celda_curated_workflow.html @@ -6,21 +6,20 @@ Celda Curated Workflow • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
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    • - +
    @@ -550,9 +549,7 @@

    References - -

    +
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    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/cell_type_labeling.html b/docs/articles/cell_type_labeling.html index 62602e29d..38d08e3f1 100644 --- a/docs/articles/cell_type_labeling.html +++ b/docs/articles/cell_type_labeling.html @@ -6,21 +6,20 @@ Cell Type Labeling • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -462,9 +461,7 @@

    References - -

    +
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    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/cell_type_labeling_files/figure-html/visualization-1.png b/docs/articles/cell_type_labeling_files/figure-html/visualization-1.png index 44c9684a4..c0b5ff5b7 100644 Binary files a/docs/articles/cell_type_labeling_files/figure-html/visualization-1.png and b/docs/articles/cell_type_labeling_files/figure-html/visualization-1.png differ diff --git a/docs/articles/clustering.html b/docs/articles/clustering.html index 43b178a42..4ea7789db 100644 --- a/docs/articles/clustering.html +++ b/docs/articles/clustering.html @@ -6,21 +6,20 @@ Clustering • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
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    • - +
    @@ -560,7 +559,7 @@

    Workflow Guidepca <- reducedDim(sce, "PCA")[,1:10] rownames(pca) <- gsub("_", "-", rownames(pca)) stdev <- as.numeric(attr(pca, "percentVar")) -new_pca <- CreateDimReducObject(embeddings = pca, assay = "RNA", stdev = stdev, key = "PC_") +new_pca <- CreateDimReducObject(embeddings = pca, assay = "RNA", stdev = stdev, key = "PC_") # Then we can take the Seurat Curated Workflow independent dimension # reduction as an input. sce <- runSeuratFindClusters(sce, externalReduction = new_pca) @@ -634,9 +633,7 @@

    References - -

    +
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    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/clustering_files/figure-html/clst_prep-1.png b/docs/articles/clustering_files/figure-html/clst_prep-1.png index ae19eac65..10380accc 100644 Binary files a/docs/articles/clustering_files/figure-html/clst_prep-1.png and b/docs/articles/clustering_files/figure-html/clst_prep-1.png differ diff --git a/docs/articles/cmd_qc.html b/docs/articles/cmd_qc.html index 7d7b2fb72..ca7987772 100644 --- a/docs/articles/cmd_qc.html +++ b/docs/articles/cmd_qc.html @@ -6,21 +6,20 @@ Generation of comprehensive quality control metrics with SCTK • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
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    • - +
    @@ -345,12 +344,12 @@

    Installing dockerRunning SCTK-QC pipeline using docker image

    The Docker image can be obtained by running:

    -
    docker pull campbio/sctk_qc:2.14.0
    +
    docker pull campbio/sctk_qc:2.16.1

    The usage of each argument is the same as running command line analysis. Here is an example code to perform QC on CellRangerV3 data with SCTK docker:

    docker run --rm -v /path/to/data:/SCTK_docker \
-  -it campbio/sctk_qc:2.14.0 \
+  -it campbio/sctk_qc:2.16.1 \
   -b /SCTK_docker/cellranger_folder \
   -P CellRangerV3 \
   -s SampleName \
@@ -377,7 +376,7 @@ 
    Running SCTK-QC
 before can install it following the instruction here.
 The Singularity image for SCTK-QC can be easily built using Docker Hub
 as a source:
    
-
    singularity pull docker://campbio/sctk_qc:2.14.0
    
+
    singularity pull docker://campbio/sctk_qc:2.16.1
    
 
    The usage of singleCellTK Singularity image is very similar to that
 of Docker. In Singularity 3.0+, the mount volume is automatically
 overlaid.
    
@@ -396,7 +395,7 @@ 
    Running SCTK-QC
 used to store the output of QC pipeline. The example is shown as
 below:
    
 
    singularity run --home=/PathToSanitizedHome \
-  --bind /PathToData:/data sctk_qc_2.14.0.sif \
+  --bind /PathToData:/data sctk_qc_2.16.1.sif \
   -b /SCTK_docker/cellranger_folder \
   -P CellRangerV3 \
   -s SampleName \
@@ -426,7 +425,7 @@ 
    Important note about docker imageAmbient RNA detection
 
-        
-
    +
    @@ -1168,16 +1165,16 @@

    Ambient RNA detection

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/cnsl_cellqc.html b/docs/articles/cnsl_cellqc.html index 37eb363dd..32d0cbfe4 100644 --- a/docs/articles/cnsl_cellqc.html +++ b/docs/articles/cnsl_cellqc.html @@ -6,21 +6,20 @@ Quality Control for cell-level data • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -369,7 +368,7 @@

    Run CellQC## Overall doublet rate: ## Expected = 10.0% ## Estimated = 3.0% -## Elapsed time: 2.6 seconds +## Elapsed time: 3.7 seconds ## Preprocessing... ## Simulating doublets... ## Embedding transcriptomes using PCA... @@ -380,7 +379,7 @@

    Run CellQC## Overall doublet rate: ## Expected = 10.0% ## Estimated = 4.8% -## Elapsed time: 6.6 seconds +## Elapsed time: 7.4 seconds


    If users choose to only run a specific set of algorithms, they can specify which to run with the algorithms parameter. By default, the     runCellQC() will run "QCMetrics", @@ -610,13 +609,13 @@

    Run CellQC -0.0573566 +0.0463075 -0.7966514 +0.7311433 -0.1272208 +0.1416335 0.0138889 @@ -741,13 +740,13 @@

    Run CellQC -0.4663909 +0.2857276 -0.5632351 +0.5029756 -0.3518394 +0.3474459 0.1527778 @@ -970,8 +969,8 @@

    Generating a summary statistic tab ## Median features detected 817.0000 716.0000 ## Scrublet - Number of doublets 0.0000 0.0000 ## Scrublet - Percentage of doublets 0.0000 0.0000 -## scDblFinder - Number of doublets 95.0000 263.0000 -## scDblFinder - Percentage of doublets 3.5200 4.8500 +## scDblFinder - Number of doublets 121.0000 248.0000 +## scDblFinder - Percentage of doublets 4.4800 4.5800 ## DoubletFinder - Number of doublets, Resolution 1.5 202.0000 406.0000 ## DoubletFinder - Percentage of doublets, Resolution 1.5 7.4800 7.4900 ## CXDS - Number of doublets 132.0000 294.0000 @@ -990,8 +989,8 @@

    Generating a summary statistic tab ## Median features detected 750.0000 ## Scrublet - Number of doublets 0.0000 ## Scrublet - Percentage of doublets 0.0000 -## scDblFinder - Number of doublets 358.0000 -## scDblFinder - Percentage of doublets 4.4100 +## scDblFinder - Number of doublets 369.0000 +## scDblFinder - Percentage of doublets 4.5400 ## DoubletFinder - Number of doublets, Resolution 1.5 608.0000 ## DoubletFinder - Percentage of doublets, Resolution 1.5 7.4900 ## CXDS - Number of doublets 426.0000 @@ -1473,13 +1472,13 @@

    Filtering the dataset
    Session Information -
    ## R version 4.3.3 (2024-02-29)
-## Platform: x86_64-apple-darwin20 (64-bit)
-## Running under: macOS Sonoma 14.4.1
+
    ## R version 4.4.2 (2024-10-31)
+## Platform: x86_64-apple-darwin20
+## Running under: macOS Sequoia 15.3
 ## 
 ## Matrix products: default
-## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
-## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
+## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
+## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
 ## 
 ## locale:
 ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
@@ -1492,123 +1491,126 @@ 
    Filtering the dataset## [8] base     
 ## 
 ## other attached packages:
-##  [1] TENxPBMCData_1.20.0         HDF5Array_1.30.1           
-##  [3] rhdf5_2.46.1                dplyr_1.1.4                
-##  [5] singleCellTK_2.14.0         DelayedArray_0.28.0        
-##  [7] SparseArray_1.2.4           S4Arrays_1.2.1             
-##  [9] abind_1.4-5                 Matrix_1.6-5               
-## [11] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
-## [13] Biobase_2.62.0              GenomicRanges_1.54.1       
-## [15] GenomeInfoDb_1.38.8         IRanges_2.36.0             
-## [17] S4Vectors_0.40.2            BiocGenerics_0.48.1        
-## [19] MatrixGenerics_1.14.0       matrixStats_1.3.0          
+##  [1] TENxPBMCData_1.24.0         HDF5Array_1.34.0           
+##  [3] rhdf5_2.50.2                dplyr_1.1.4                
+##  [5] singleCellTK_2.16.1         DelayedArray_0.32.0        
+##  [7] SparseArray_1.6.1           S4Arrays_1.6.0             
+##  [9] abind_1.4-8                 Matrix_1.7-2               
+## [11] SingleCellExperiment_1.28.1 SummarizedExperiment_1.36.0
+## [13] Biobase_2.66.0              GenomicRanges_1.58.0       
+## [15] GenomeInfoDb_1.42.3         IRanges_2.40.1             
+## [17] S4Vectors_0.44.0            BiocGenerics_0.52.0        
+## [19] MatrixGenerics_1.18.1       matrixStats_1.5.0          
 ## 
 ## loaded via a namespace (and not attached):
-##   [1] spatstat.sparse_3.0-3         fs_1.6.4                     
-##   [3] bitops_1.0-7                  doParallel_1.0.17            
-##   [5] httr_1.4.7                    RColorBrewer_1.1-3           
-##   [7] sctransform_0.4.1             tools_4.3.3                  
-##   [9] utf8_1.2.4                    R6_2.5.1                     
-##  [11] lazyeval_0.2.2                uwot_0.2.2                   
-##  [13] rhdf5filters_1.14.1           withr_3.0.0                  
-##  [15] sp_2.1-4                      gridExtra_2.3                
-##  [17] progressr_0.14.0              cli_3.6.2                    
-##  [19] textshaping_0.3.7             spatstat.explore_3.2-7       
-##  [21] fastDummies_1.7.3             enrichR_3.2                  
-##  [23] labeling_0.4.3                eds_1.4.0                    
-##  [25] sass_0.4.9                    Seurat_5.0.3                 
-##  [27] spatstat.data_3.0-4           ggridges_0.5.6               
-##  [29] pbapply_1.7-2                 pkgdown_2.0.7                
-##  [31] Rsamtools_2.18.0              systemfonts_1.0.6            
-##  [33] dbscan_1.1-12                 svglite_2.1.3                
-##  [35] R.utils_2.12.3                scater_1.30.1                
-##  [37] WriteXLS_6.5.0                parallelly_1.37.1            
-##  [39] maps_3.4.2                    limma_3.58.1                 
-##  [41] rstudioapi_0.16.0             RSQLite_2.3.6                
-##  [43] FNN_1.1.4                     generics_0.1.3               
-##  [45] BiocIO_1.12.0                 combinat_0.0-8               
-##  [47] spatstat.random_3.2-3         ica_1.0-3                    
-##  [49] ggbeeswarm_0.7.2              fansi_1.0.6                  
-##  [51] R.methodsS3_1.8.2             lifecycle_1.0.4              
-##  [53] SoupX_1.6.2                   yaml_2.3.8                   
-##  [55] edgeR_4.0.16                  BiocFileCache_2.10.2         
-##  [57] Rtsne_0.17                    grid_4.3.3                   
-##  [59] blob_1.2.4                    promises_1.3.0               
-##  [61] dqrng_0.3.2                   ExperimentHub_2.10.0         
-##  [63] crayon_1.5.2                  miniUI_0.1.1.1               
-##  [65] lattice_0.22-5                beachmat_2.18.1              
-##  [67] cowplot_1.1.3                 annotate_1.80.0              
-##  [69] KEGGREST_1.42.0               pillar_1.9.0                 
-##  [71] knitr_1.46                    metapod_1.10.1               
-##  [73] rjson_0.2.21                  celda_1.19.1                 
-##  [75] xgboost_1.7.7.1               future.apply_1.11.2          
-##  [77] codetools_0.2-19              leiden_0.4.3.1               
-##  [79] glue_1.7.0                    data.table_1.15.4            
-##  [81] vctrs_0.6.5                   png_0.1-8                    
-##  [83] spam_2.10-0                   gtable_0.3.5                 
-##  [85] cachem_1.0.8                  xfun_0.43                    
-##  [87] mime_0.12                     DropletUtils_1.22.0          
-##  [89] RcppEigen_0.3.4.0.0           GSVAdata_1.38.0              
-##  [91] survival_3.5-8                iterators_1.0.14             
-##  [93] fields_15.2                   statmod_1.5.0                
-##  [95] bluster_1.12.0                interactiveDisplayBase_1.40.0
-##  [97] fitdistrplus_1.1-11           ROCR_1.0-11                  
-##  [99] nlme_3.1-164                  bit64_4.0.5                  
-## [101] scds_1.18.0                   filelock_1.0.3               
-## [103] RcppAnnoy_0.0.22              rprojroot_2.0.4              
-## [105] bslib_0.7.0                   irlba_2.3.5.1                
-## [107] vipor_0.4.7                   KernSmooth_2.23-22           
-## [109] colorspace_2.1-0              DBI_1.2.2                    
-## [111] tidyselect_1.2.1              bit_4.0.5                    
-## [113] compiler_4.3.3                curl_5.2.1                   
-## [115] graph_1.80.0                  BiocNeighbors_1.20.2         
-## [117] xml2_1.3.6                    desc_1.4.3                   
-## [119] plotly_4.10.4                 rtracklayer_1.62.0           
-## [121] scales_1.3.0                  lmtest_0.9-40                
-## [123] rappdirs_0.3.3                goftest_1.2-3                
-## [125] stringr_1.5.1                 digest_0.6.35                
-## [127] spatstat.utils_3.0-4          rmarkdown_2.26               
-## [129] XVector_0.42.0                htmltools_0.5.8.1            
-## [131] pkgconfig_2.0.3               sparseMatrixStats_1.14.0     
-## [133] highr_0.10                    dbplyr_2.5.0                 
-## [135] fastmap_1.1.1                 rlang_1.1.3                  
-## [137] htmlwidgets_1.6.4             shiny_1.8.1.1                
-## [139] DelayedMatrixStats_1.24.0     farver_2.1.1                 
-## [141] jquerylib_0.1.4               zoo_1.8-12                   
-## [143] jsonlite_1.8.8                BiocParallel_1.36.0          
-## [145] R.oo_1.26.0                   BiocSingular_1.18.0          
-## [147] RCurl_1.98-1.14               magrittr_2.0.3               
-## [149] kableExtra_1.4.0              scuttle_1.12.0               
-## [151] GenomeInfoDbData_1.2.11       dotCall64_1.1-1              
-## [153] patchwork_1.2.0               Rhdf5lib_1.24.2              
-## [155] munsell_0.5.1                 Rcpp_1.0.12                  
-## [157] viridis_0.6.5                 reticulate_1.36.1            
-## [159] pROC_1.18.5                   stringi_1.8.3                
-## [161] MCMCprecision_0.4.0           zlibbioc_1.48.2              
-## [163] MASS_7.3-60.0.1               AnnotationHub_3.10.1         
-## [165] plyr_1.8.9                    parallel_4.3.3               
-## [167] listenv_0.9.1                 ggrepel_0.9.5                
-## [169] deldir_2.0-4                  scDblFinder_1.16.0           
-## [171] Biostrings_2.70.3             splines_4.3.3                
-## [173] tensor_1.5                    locfit_1.5-9.9               
-## [175] igraph_2.0.3                  spatstat.geom_3.2-9          
-## [177] RcppHNSW_0.6.0                reshape2_1.4.4               
-## [179] ScaledMatrix_1.10.0           BiocVersion_3.18.1           
-## [181] XML_3.99-0.16.1               evaluate_0.23                
-## [183] SeuratObject_5.0.1            scran_1.30.2                 
-## [185] BiocManager_1.30.22           foreach_1.5.2                
-## [187] httpuv_1.6.15                 polyclip_1.10-6              
-## [189] tidyr_1.3.1                   RANN_2.6.1                   
-## [191] purrr_1.0.2                   scattermore_1.2              
-## [193] future_1.33.2                 ggplot2_3.5.1                
-## [195] rsvd_1.0.5                    xtable_1.8-4                 
-## [197] restfulr_0.0.15               RSpectra_0.16-1              
-## [199] later_1.3.2                   viridisLite_0.4.2            
-## [201] ragg_1.3.0                    tibble_3.2.1                 
-## [203] memoise_2.0.1                 beeswarm_0.4.0               
-## [205] AnnotationDbi_1.64.1          GenomicAlignments_1.38.2     
-## [207] cluster_2.1.6                 globals_0.16.3               
-## [209] GSEABase_1.64.0               here_1.0.1
    
+##   [1] spatstat.sparse_3.1-0     fs_1.6.5                 
+##   [3] bitops_1.0-9              httr_1.4.7               
+##   [5] RColorBrewer_1.1-3        doParallel_1.0.17        
+##   [7] sctransform_0.4.1         tools_4.4.2              
+##   [9] R6_2.6.0                  lazyeval_0.2.2           
+##  [11] uwot_0.2.2                rhdf5filters_1.18.0      
+##  [13] GetoptLong_1.0.5          withr_3.0.2              
+##  [15] sp_2.2-0                  gridExtra_2.3            
+##  [17] progressr_0.15.1          cli_3.6.3                
+##  [19] textshaping_1.0.0         spatstat.explore_3.3-4   
+##  [21] fastDummies_1.7.5         enrichR_3.4              
+##  [23] labeling_0.4.3            eds_1.8.0                
+##  [25] sass_0.4.9                Seurat_5.2.1             
+##  [27] spatstat.data_3.1-4       ggridges_0.5.6           
+##  [29] pbapply_1.7-2             pkgdown_2.1.1            
+##  [31] Rsamtools_2.22.0          systemfonts_1.2.1        
+##  [33] dbscan_1.2.2              svglite_2.1.3            
+##  [35] R.utils_2.12.3            scater_1.34.0            
+##  [37] WriteXLS_6.7.0            parallelly_1.42.0        
+##  [39] maps_3.4.2.1              limma_3.62.2             
+##  [41] rstudioapi_0.17.1         RSQLite_2.3.9            
+##  [43] FNN_1.1.4.1               generics_0.1.3           
+##  [45] shape_1.4.6.1             BiocIO_1.16.0            
+##  [47] combinat_0.0-8            spatstat.random_3.3-2    
+##  [49] ica_1.0-3                 dendextend_1.19.0        
+##  [51] ggbeeswarm_0.7.2          R.methodsS3_1.8.2        
+##  [53] lifecycle_1.0.4           SoupX_1.6.2              
+##  [55] yaml_2.3.10               edgeR_4.4.2              
+##  [57] BiocFileCache_2.14.0      Rtsne_0.17               
+##  [59] grid_4.4.2                blob_1.2.4               
+##  [61] promises_1.3.2            dqrng_0.4.1              
+##  [63] ExperimentHub_2.14.0      crayon_1.5.3             
+##  [65] miniUI_0.1.1.1            lattice_0.22-6           
+##  [67] beachmat_2.22.0           cowplot_1.1.3            
+##  [69] annotate_1.84.0           KEGGREST_1.46.0          
+##  [71] pillar_1.10.1             knitr_1.49               
+##  [73] ComplexHeatmap_2.22.0     metapod_1.14.0           
+##  [75] rjson_0.2.23              celda_1.22.1             
+##  [77] xgboost_1.7.8.1           future.apply_1.11.3      
+##  [79] codetools_0.2-20          glue_1.8.0               
+##  [81] spatstat.univar_3.1-1     data.table_1.16.4        
+##  [83] vctrs_0.6.5               png_0.1-8                
+##  [85] spam_2.11-1               gtable_0.3.6             
+##  [87] cachem_1.1.0              xfun_0.50                
+##  [89] mime_0.12                 DropletUtils_1.26.0      
+##  [91] RcppEigen_0.3.4.0.2       GSVAdata_1.42.0          
+##  [93] survival_3.8-3            iterators_1.0.14         
+##  [95] fields_16.3               statmod_1.5.0            
+##  [97] bluster_1.16.0            fitdistrplus_1.2-2       
+##  [99] ROCR_1.0-11               nlme_3.1-167             
+## [101] bit64_4.6.0-1             scds_1.22.0              
+## [103] filelock_1.0.3            RcppAnnoy_0.0.22         
+## [105] rprojroot_2.0.4           bslib_0.9.0              
+## [107] irlba_2.3.5.1             vipor_0.4.7              
+## [109] KernSmooth_2.23-26        colorspace_2.1-1         
+## [111] DBI_1.2.3                 tidyselect_1.2.1         
+## [113] bit_4.5.0.1               compiler_4.4.2           
+## [115] curl_6.2.0                graph_1.84.1             
+## [117] BiocNeighbors_2.0.1       xml2_1.3.6               
+## [119] ggdendro_0.2.0            plotly_4.10.4            
+## [121] desc_1.4.3                rtracklayer_1.66.0       
+## [123] scales_1.3.0              lmtest_0.9-40            
+## [125] rappdirs_0.3.3            goftest_1.2-3            
+## [127] stringr_1.5.1             digest_0.6.37            
+## [129] spatstat.utils_3.1-2      rmarkdown_2.29           
+## [131] XVector_0.46.0            htmltools_0.5.8.1        
+## [133] pkgconfig_2.0.3           sparseMatrixStats_1.18.0 
+## [135] dbplyr_2.5.0              fastmap_1.2.0            
+## [137] rlang_1.1.5               GlobalOptions_0.1.2      
+## [139] htmlwidgets_1.6.4         UCSC.utils_1.2.0         
+## [141] shiny_1.10.0              DelayedMatrixStats_1.28.1
+## [143] farver_2.1.2              jquerylib_0.1.4          
+## [145] zoo_1.8-12                jsonlite_1.8.9           
+## [147] BiocParallel_1.40.0       R.oo_1.27.0              
+## [149] BiocSingular_1.22.0       RCurl_1.98-1.16          
+## [151] magrittr_2.0.3            kableExtra_1.4.0         
+## [153] scuttle_1.16.0            GenomeInfoDbData_1.2.13  
+## [155] dotCall64_1.2             patchwork_1.3.0          
+## [157] Rhdf5lib_1.28.0           munsell_0.5.1            
+## [159] Rcpp_1.0.14               viridis_0.6.5            
+## [161] reticulate_1.40.0         pROC_1.18.5              
+## [163] stringi_1.8.4             MCMCprecision_0.4.0      
+## [165] zlibbioc_1.52.0           MASS_7.3-64              
+## [167] AnnotationHub_3.14.0      plyr_1.8.9               
+## [169] parallel_4.4.2            listenv_0.9.1            
+## [171] ggrepel_0.9.6             deldir_2.0-4             
+## [173] scDblFinder_1.20.0        Biostrings_2.74.1        
+## [175] splines_4.4.2             tensor_1.5               
+## [177] circlize_0.4.16           locfit_1.5-9.11          
+## [179] igraph_2.1.4              spatstat.geom_3.3-5      
+## [181] RcppHNSW_0.6.0            reshape2_1.4.4           
+## [183] ScaledMatrix_1.14.0       BiocVersion_3.20.0       
+## [185] XML_3.99-0.18             evaluate_1.0.3           
+## [187] SeuratObject_5.0.2        scran_1.34.0             
+## [189] BiocManager_1.30.25       foreach_1.5.2            
+## [191] httpuv_1.6.15             polyclip_1.10-7          
+## [193] RANN_2.6.2                tidyr_1.3.1              
+## [195] purrr_1.0.4               scattermore_1.2          
+## [197] future_1.34.0             clue_0.3-66              
+## [199] ggplot2_3.5.1             rsvd_1.0.5               
+## [201] xtable_1.8-4              restfulr_0.0.15          
+## [203] RSpectra_0.16-2           later_1.4.1              
+## [205] viridisLite_0.4.2         ragg_1.3.3               
+## [207] tibble_3.2.1              memoise_2.0.1            
+## [209] beeswarm_0.4.0            AnnotationDbi_1.68.0     
+## [211] GenomicAlignments_1.42.0  cluster_2.1.8            
+## [213] globals_0.16.3            GSEABase_1.68.0          
+## [215] here_1.0.1

    @@ -1616,9 +1618,7 @@

    Filtering the dataset - - + @@ -1631,16 +1631,16 @@

    Filtering the dataset

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/cnsl_cellqc_files/figure-html/plot_umap_scrublet-1.png b/docs/articles/cnsl_cellqc_files/figure-html/plot_umap_scrublet-1.png index 53721a85f..1206f8985 100644 Binary files a/docs/articles/cnsl_cellqc_files/figure-html/plot_umap_scrublet-1.png and b/docs/articles/cnsl_cellqc_files/figure-html/plot_umap_scrublet-1.png differ diff --git a/docs/articles/cnsl_cellqc_files/figure-html/plots_umap_decontx-1.png b/docs/articles/cnsl_cellqc_files/figure-html/plots_umap_decontx-1.png index cfe636b58..7703056ab 100644 Binary files a/docs/articles/cnsl_cellqc_files/figure-html/plots_umap_decontx-1.png and b/docs/articles/cnsl_cellqc_files/figure-html/plots_umap_decontx-1.png differ diff --git a/docs/articles/cnsl_cellqc_files/figure-html/plots_umap_soupx-1.png b/docs/articles/cnsl_cellqc_files/figure-html/plots_umap_soupx-1.png index 4fccea038..a2ba8b102 100644 Binary files a/docs/articles/cnsl_cellqc_files/figure-html/plots_umap_soupx-1.png and b/docs/articles/cnsl_cellqc_files/figure-html/plots_umap_soupx-1.png differ diff --git a/docs/articles/cnsl_cellqc_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/cnsl_cellqc_files/figure-html/unnamed-chunk-3-1.png index 005d124f1..406a501a1 100644 Binary files a/docs/articles/cnsl_cellqc_files/figure-html/unnamed-chunk-3-1.png and b/docs/articles/cnsl_cellqc_files/figure-html/unnamed-chunk-3-1.png differ diff --git a/docs/articles/cnsl_dropletqc.html b/docs/articles/cnsl_dropletqc.html index 9e9f192f2..d4a00a066 100644 --- a/docs/articles/cnsl_dropletqc.html +++ b/docs/articles/cnsl_dropletqc.html @@ -6,21 +6,20 @@ Quality Control for droplet data • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -333,10 +332,10 @@

    runDropletQC
     pbmc4k.droplet <- runDropletQC(pbmc4k.droplet)

    -
    ## Fri May  3 07:50:08 2024 ... Running 'perCellQCMetrics'
    -
    ## Fri May  3 07:50:08 2024 ...... Attempting to find mitochondrial genes by identifying features in 'rownames' that match mitochondrial genes from reference 'human' and ID type 'ensembl'.
    -
    ## Fri May  3 07:50:11 2024 ... Running 'emptyDrops'
    -
    ## Fri May  3 07:50:29 2024 ... Running 'barcodeRanks'
    +
    ## Thu Feb 13 11:08:32 2025 ... Running 'perCellQCMetrics'
    +
    ## Thu Feb 13 11:08:32 2025 ...... Attempting to find mitochondrial genes by identifying features in 'rownames' that match mitochondrial genes from reference 'human' and ID type 'ensembl'.
    +
    ## Thu Feb 13 11:08:36 2025 ... Running 'emptyDrops'
    +
    ## Thu Feb 13 11:08:57 2025 ... Running 'barcodeRanks'

    If users choose to only run a specific set of algorithms, they can specify which to run with the algorithms parameter.

    After running QC functions with SCTK, the output will be stored in @@ -347,67 +346,67 @@

    runDropletQC## DataFrame with 5 rows and 19 columns ## sample Barcode sum detected ## <character> <character> <numeric> <integer> -## CTCCTAGTCTATGTGG-1 pbmc4k CTCCTAGTCTATGTGG-1 2 2 -## CTCTACGGTAAATGAC-1 pbmc4k CTCTACGGTAAATGAC-1 1 1 -## TACTCGCCACAGATTC-1 pbmc4k TACTCGCCACAGATTC-1 1 1 -## GCGCGATCACAGGAGT-1 pbmc4k GCGCGATCACAGGAGT-1 1 1 -## GATTCAGGTAGTACCT-1 pbmc4k GATTCAGGTAGTACCT-1 0 0 +## TTTCCTCAGAGCTGGT-1 pbmc4k TTTCCTCAGAGCTGGT-1 0 0 +## CGCGTTTGTCAAACTC-1 pbmc4k CGCGTTTGTCAAACTC-1 0 0 +## CTACGTCTCAGGCAAG-1 pbmc4k CTACGTCTCAGGCAAG-1 0 0 +## CGATCGGCACCATGTA-1 pbmc4k CGATCGGCACCATGTA-1 0 0 +## AGTGTCACAAGTTAAG-1 pbmc4k AGTGTCACAAGTTAAG-1 1 1 ## percent.top_50 percent.top_100 percent.top_200 ## <numeric> <numeric> <numeric> -## CTCCTAGTCTATGTGG-1 100 100 100 -## CTCTACGGTAAATGAC-1 100 100 100 -## TACTCGCCACAGATTC-1 100 100 100 -## GCGCGATCACAGGAGT-1 100 100 100 -## GATTCAGGTAGTACCT-1 NaN NaN NaN +## TTTCCTCAGAGCTGGT-1 NaN NaN NaN +## CGCGTTTGTCAAACTC-1 NaN NaN NaN +## CTACGTCTCAGGCAAG-1 NaN NaN NaN +## CGATCGGCACCATGTA-1 NaN NaN NaN +## AGTGTCACAAGTTAAG-1 100 100 100 ## percent.top_500 mito_sum mito_detected mito_percent ## <numeric> <numeric> <integer> <numeric> -## CTCCTAGTCTATGTGG-1 100 0 0 0 -## CTCTACGGTAAATGAC-1 100 0 0 0 -## TACTCGCCACAGATTC-1 100 0 0 0 -## GCGCGATCACAGGAGT-1 100 0 0 0 -## GATTCAGGTAGTACCT-1 NaN 0 0 NaN +## TTTCCTCAGAGCTGGT-1 NaN 0 0 NaN +## CGCGTTTGTCAAACTC-1 NaN 0 0 NaN +## CTACGTCTCAGGCAAG-1 NaN 0 0 NaN +## CGATCGGCACCATGTA-1 NaN 0 0 NaN +## AGTGTCACAAGTTAAG-1 100 0 0 0 ## total dropletUtils_emptyDrops_total ## <numeric> <integer> -## CTCCTAGTCTATGTGG-1 2 2 -## CTCTACGGTAAATGAC-1 1 1 -## TACTCGCCACAGATTC-1 1 1 -## GCGCGATCACAGGAGT-1 1 1 -## GATTCAGGTAGTACCT-1 0 0 +## TTTCCTCAGAGCTGGT-1 0 0 +## CGCGTTTGTCAAACTC-1 0 0 +## CTACGTCTCAGGCAAG-1 0 0 +## CGATCGGCACCATGTA-1 0 0 +## AGTGTCACAAGTTAAG-1 1 1 ## dropletUtils_emptyDrops_logprob ## <numeric> -## CTCCTAGTCTATGTGG-1 NA -## CTCTACGGTAAATGAC-1 NA -## TACTCGCCACAGATTC-1 NA -## GCGCGATCACAGGAGT-1 NA -## GATTCAGGTAGTACCT-1 NA +## TTTCCTCAGAGCTGGT-1 NA +## CGCGTTTGTCAAACTC-1 NA +## CTACGTCTCAGGCAAG-1 NA +## CGATCGGCACCATGTA-1 NA +## AGTGTCACAAGTTAAG-1 NA ## dropletUtils_emptyDrops_pvalue ## <numeric> -## CTCCTAGTCTATGTGG-1 NA -## CTCTACGGTAAATGAC-1 NA -## TACTCGCCACAGATTC-1 NA -## GCGCGATCACAGGAGT-1 NA -## GATTCAGGTAGTACCT-1 NA +## TTTCCTCAGAGCTGGT-1 NA +## CGCGTTTGTCAAACTC-1 NA +## CTACGTCTCAGGCAAG-1 NA +## CGATCGGCACCATGTA-1 NA +## AGTGTCACAAGTTAAG-1 NA ## dropletUtils_emptyDrops_limited dropletUtils_emptyDrops_fdr ## <logical> <numeric> -## CTCCTAGTCTATGTGG-1 NA NA -## CTCTACGGTAAATGAC-1 NA NA -## TACTCGCCACAGATTC-1 NA NA -## GCGCGATCACAGGAGT-1 NA NA -## GATTCAGGTAGTACCT-1 NA NA +## TTTCCTCAGAGCTGGT-1 NA NA +## CGCGTTTGTCAAACTC-1 NA NA +## CTACGTCTCAGGCAAG-1 NA NA +## CGATCGGCACCATGTA-1 NA NA +## AGTGTCACAAGTTAAG-1 NA NA ## dropletUtils_BarcodeRank_Knee ## <integer> -## CTCCTAGTCTATGTGG-1 0 -## CTCTACGGTAAATGAC-1 0 -## TACTCGCCACAGATTC-1 0 -## GCGCGATCACAGGAGT-1 0 -## GATTCAGGTAGTACCT-1 0 +## TTTCCTCAGAGCTGGT-1 0 +## CGCGTTTGTCAAACTC-1 0 +## CTACGTCTCAGGCAAG-1 0 +## CGATCGGCACCATGTA-1 0 +## AGTGTCACAAGTTAAG-1 0 ## dropletUtils_BarcodeRank_Inflection ## <integer> -## CTCCTAGTCTATGTGG-1 0 -## CTCTACGGTAAATGAC-1 0 -## TACTCGCCACAGATTC-1 0 -## GCGCGATCACAGGAGT-1 0 -## GATTCAGGTAGTACCT-1 0 +## TTTCCTCAGAGCTGGT-1 0 +## CGCGTTTGTCAAACTC-1 0 +## CTACGTCTCAGGCAAG-1 0 +## CGATCGGCACCATGTA-1 0 +## AGTGTCACAAGTTAAG-1 0
    @@ -474,31 +473,31 @@

    runDropletQC -CTCCTAGTCTATGTGG-1 +TTTCCTCAGAGCTGGT-1

    - + @@ -499,7 +498,7 @@

    Workflow GuidePON2;HES1;SOX4

    - + @@ -512,7 +511,7 @@

    Workflow GuideHES1;SOX4

    - + @@ -525,7 +524,7 @@

    Workflow GuidePON2;HES1;SOX4

    - + @@ -538,7 +537,7 @@

    Workflow GuideHES1;SOX4

    - + @@ -551,7 +550,7 @@

    Workflow GuidePON2;HES1;SOX4

    - + @@ -596,9 +595,7 @@

    References - - + @@ -611,16 +608,16 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/export_data.html b/docs/articles/export_data.html index d2eb0c063..f2e5b8063 100644 --- a/docs/articles/export_data.html +++ b/docs/articles/export_data.html @@ -6,21 +6,20 @@ Export Data • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -402,9 +401,7 @@

    Workflow Guide - -

    +
    @@ -417,16 +414,16 @@

    Workflow Guide

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/feature_selection.html b/docs/articles/feature_selection.html index 448a9b7b7..e7141d00b 100644 --- a/docs/articles/feature_selection.html +++ b/docs/articles/feature_selection.html @@ -6,21 +6,20 @@ Feature Selection • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -492,9 +491,7 @@

    References - -

    +
    @@ -507,16 +504,16 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/filtering.html b/docs/articles/filtering.html index 5c260e185..a12715f4d 100644 --- a/docs/articles/filtering.html +++ b/docs/articles/filtering.html @@ -6,21 +6,20 @@ Filtering the datasets • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -371,9 +370,7 @@

    Workflow Guide - -

    +
    @@ -386,16 +383,16 @@

    Workflow Guide

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/find_marker.html b/docs/articles/find_marker.html index e09c6ee3f..1d650f8a5 100644 --- a/docs/articles/find_marker.html +++ b/docs/articles/find_marker.html @@ -6,21 +6,20 @@ Find Marker • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -452,23 +451,25 @@

    Workflow Guide
     getFindMarkerTopTable(sce, log2fcThreshold = 0, minClustExprPerc = 0.5, topN = 1)

    ##           Gene   Log2_FC        Pvalue           FDR cluster clusterExprPerc
-## 8764      IL7R 0.7697338  9.053691e-69  2.279998e-65       1       0.7212885
-## 1956    S100A9 4.3853548 2.397248e-207 3.924055e-203       2       0.9977064
-## 269581    CCR7 0.6150976  1.881449e-41  9.332559e-39       3       0.5688312
-## 106781 HLA-DRA 3.2752984 1.682895e-182 2.754731e-178       4       1.0000000
-## 26825     CCL5 3.0878935 2.507059e-148 8.207610e-144       5       0.9712644
-## 106091    LST1 2.8683989  1.038405e-98  1.133177e-94       6       1.0000000
-## 310761    NKG7 4.2435780  8.853054e-82  2.898313e-77       7       1.0000000
-## 288182    CST3 3.2975861  2.221917e-16  1.039159e-12       8       1.0000000
-## 7697      PPBP 5.9620589  9.423341e-07  2.504757e-03       9       1.0000000
+## 1956    S100A9 4.3918388 1.231801e-205 2.016334e-201       1       0.9976852
+## 26958     CCR7 0.6107894  7.062217e-41  3.400042e-38       2       0.5662338
+## 87641     IL7R 0.6949784  1.462605e-36  1.294129e-33       3       0.7493404
+## 26825     CCL5 3.0724416 1.407334e-149 4.607331e-145       4       0.9715909
+## 106781 HLA-DRA 3.2851089 6.201038e-183 1.015048e-178       5       1.0000000
+## 16364      CD2 0.5344754  6.223183e-26  2.263717e-22       6       0.6377246
+## 106091    LST1 2.8798261 3.464220e-101  3.780388e-97       7       1.0000000
+## 310761    NKG7 4.2518808  8.025412e-81  2.627359e-76       8       1.0000000
+## 288182    CST3 3.2975861  2.221917e-16  1.039159e-12       9       1.0000000
+## 7697      PPBP 5.9620589  9.423341e-07  2.504757e-03      10       1.0000000
 ##        ControlExprPerc clusterAveExpr
-## 8764        0.28698380      1.1880037
-## 1956        0.23094477      4.7335694
-## 269581      0.13380910      0.7705352
-## 106781      0.49538867      4.4065968
-## 26825       0.21676174      3.4664459
-## 106091      0.30477759      3.4541085
-## 310761      0.25717752      4.7869642
+## 1956        0.23234624      4.7456645
+## 26958       0.13425513      0.7668583
+## 87641       0.34697509      1.2221913
+## 26825       0.21538462      3.4483627
+## 106781      0.49561018      4.4163508
+## 16364       0.27387702      0.8940661
+## 106091      0.30363036      3.4602852
+## 310761      0.25777778      4.7980173
 ## 288182      0.39113680      4.3717555
 ## 7697        0.02406417      5.9894455

    Similarly to the Differential Expression section, we also provide a @@ -490,9 +491,7 @@

    Workflow Guide - -

    + @@ -505,16 +504,16 @@

    Workflow Guide

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/find_marker_files/figure-html/de_prep_plot-1.png b/docs/articles/find_marker_files/figure-html/de_prep_plot-1.png index fbb68238d..aa41a3087 100644 Binary files a/docs/articles/find_marker_files/figure-html/de_prep_plot-1.png and b/docs/articles/find_marker_files/figure-html/de_prep_plot-1.png differ diff --git a/docs/articles/find_marker_files/figure-html/plotMarkers-1.png b/docs/articles/find_marker_files/figure-html/plotMarkers-1.png index d070a6a77..7b9d43017 100644 Binary files a/docs/articles/find_marker_files/figure-html/plotMarkers-1.png and b/docs/articles/find_marker_files/figure-html/plotMarkers-1.png differ diff --git a/docs/articles/heatmap.html b/docs/articles/heatmap.html index 58ca5a06e..32367e826 100644 --- a/docs/articles/heatmap.html +++ b/docs/articles/heatmap.html @@ -6,21 +6,20 @@ Heatmap Visualization • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -448,6 +447,12 @@

    Workflow Guide

    To present the usage of plotSCEHeatmap(), we would like to use a small example provided with SCTK.

    +

    “Raw” plotting

    +

    The minimum setting for plotSCEHeatmap() is the input +SCE object and the data matrix to plot (default +"logcounts"). In this way, all cells and features will be +presented while no annotation or legend (except the main color scheme) +will be shown.

     library(singleCellTK)
 data("scExample") # This imports SCE object "sce"
@@ -465,15 +470,17 @@ 
    Workflow Guide## reducedDimNames(0):
 ## mainExpName: NULL
 ## altExpNames(0):
    -

    “Raw” plotting

    -

    The minimum setting for plotSCEHeatmap() is the input -SCE object and the data matrix to plot (default -"logcounts"). In this way, all cells and features will be -presented while no annotation or legend (except the main color scheme) -will be shown.

    -plotSCEHeatmap(sce, useAssay = "counts")
    -

    +# QC - Remove empty droplets +sce2<-subsetSCECols(sce, colData = c("type != 'EmptyDroplet'")) + +# Normalize the counts +sce2<-runNormalization(sce2, useAssay = "counts", outAssayName = "logcounts", + normalizationMethod = "logNormCounts",scale = TRUE) + +# plot the data +plotSCEHeatmap(sce2,useAssay = "logcounts",cluster_rows = TRUE, cluster_columns = TRUE)
    +

    Subsetting

    SCTK allows relatively flexible approaches to select the cells/features to plot.

    @@ -482,13 +489,9 @@

    Workflow GuidecellIndex, including numeric, and logical vectors, which are widely used, and character vector containing the row/col names. Of course, -user can directly use a subsetted SCE object as input.

    -
    -# Make up random downsampling numeric vector
-featureSubset <- sample(nrow(sce), 50)
-cellSubset <- sample(ncol(sce), 50)
-
-plotSCEHeatmap(inSCE = sce, useAssay = "counts", featureIndex = featureSubset, cellIndex = cellSubset)
    +user can directly use a subsetted SCE object as input. First let’s run a +simple clustering workflow to identify clusters and find DE genes for +each cluster. We can subset the heatmap using this list of DE genes

    Using Identifiers in rowData/colData

    In a more complex situation, where users might only have a set of @@ -498,10 +501,10 @@

    Workflow GuidefeatureIndexBy or cellIndexBy. This specification allows directly giving one column name of rowData or colData.

    -
    -subsetFeatureName <- sample(rowData(sce)$feature_name, 50)
-subsetCellBarcode <- sample(sce$cell_barcode, 50)
-plotSCEHeatmap(inSCE = sce, useAssay = "counts", featureIndex = subsetFeatureName, featureIndexBy = "feature_name", cellIndex = subsetCellBarcode, cellIndexBy = "cell_barcode")
    +
    +list_of_FIDs<-c("ENSG00000251562","ENSG00000205542","ENSG00000177954","ENSG00000166710")
+
+plotSCEHeatmap(inSCE = sce2, useAssay = "logcounts", featureIndexBy = "feature_ID",  featureIndex = list_of_FIDs, cluster_rows = TRUE, cluster_columns = TRUE, rowLabel = TRUE)

    Adding Annotations

    As introduced before, we allow directly using column names of @@ -509,16 +512,12 @@

    Workflow Guidecharacter vector to rowDataName or colDataName.

    -
    -# Make up arbitrary annotation, 
-rowRandLabel <- c(rep('aa', 100), rep('bb', 100))
-rowData(sce)$randLabel <- rowRandLabel
-colRandLabel <- c(rep('cc', 195), rep('dd', 195))
-colData(sce)$randLabel <- colRandLabel
-plotSCEHeatmap(inSCE = sce, useAssay = "counts", featureIndex = featureSubset, cellIndex = cellSubset, rowDataName = "randLabel", colDataName = c("type", "randLabel"))
    +
    +# Creat new annotation for markers 
+plotSCEHeatmap(inSCE = sce2, useAssay = "logcounts", featureIndex = topMarkers$Gene, colDataName = c( "scranSNN_PCA"),rowLabel = TRUE, cluster_rows = TRUE, cluster_columns = TRUE)

    Customized Annotation

    Fully customized annotation is also supported, though it can be -complexed for users. For the labeling, it is more recommanded to insert +complex for users. For the labeling, it is more recommended to insert the information into rowData or colData and then make use. For coloring, information should be passed to featureAnnotationColor or cellAnnotationColor. @@ -535,9 +534,56 @@

    Workflow GuiderowSplitBy or colSplitBy, and the arguments must be a character vector that is a subset of the specified annotation.

    -
    -plotSCEHeatmap(inSCE = sce, useAssay = "counts", featureIndex = featureSubset, cellIndex = cellSubset, rowDataName = "randLabel", colDataName = c("type", "randLabel"), rowSplitBy = "randLabel", colSplitBy = "type")
    +
    +# Create a new label in the rowData using the cluster markers
+library(dplyr)
    +
    ## 
+## Attaching package: 'dplyr'
    +
    ## The following object is masked from 'package:Biobase':
+## 
+##     combine
    +
    ## The following objects are masked from 'package:GenomicRanges':
+## 
+##     intersect, setdiff, union
    +
    ## The following object is masked from 'package:GenomeInfoDb':
+## 
+##     intersect
    +
    ## The following objects are masked from 'package:IRanges':
+## 
+##     collapse, desc, intersect, setdiff, slice, union
    +
    ## The following objects are masked from 'package:S4Vectors':
+## 
+##     first, intersect, rename, setdiff, setequal, union
    +
    ## The following objects are masked from 'package:BiocGenerics':
+## 
+##     combine, intersect, setdiff, union
    +
    ## The following object is masked from 'package:matrixStats':
+## 
+##     count
    +
    ## The following objects are masked from 'package:stats':
+## 
+##     filter, lag
    +
    ## The following objects are masked from 'package:base':
+## 
+##     intersect, setdiff, setequal, union
    +
    +data.frame(rowData(sce2)) %>% 
+  left_join(topMarkers, by = c("feature_name" = "Gene")) %>%
+  rename("cluster_markers" = "scranSNN_PCA") -> new_row_data
+rowData(sce2)$cluster_markers <-new_row_data$cluster_markers
+
+plotSCEHeatmap(inSCE = sce2, useAssay = "logcounts", featureIndex = topMarkers$Gene, colDataName = c("type"), aggregateCol = "scranSNN_PCA", rowGap = grid::unit(2, 'mm'),rowLabel = TRUE, rowDataName = "cluster_markers", rowSplitBy = "cluster_markers")

    +
    +# Adding a summary 
+
+data.frame(colData(sce2)) %>% 
+  mutate(summary_col = sample(5,n(), replace = TRUE)) -> new_col_data
+
+colData(sce2)<-DataFrame(new_col_data)
+
+plotSCEHeatmap(inSCE = sce2, useAssay = "logcounts", featureIndex = topMarkers$Gene, colDataName = c("type"), aggregateCol = "scranSNN_PCA", rowGap = grid::unit(2, 'mm'),rowLabel = TRUE, rowDataName = "cluster_markers", rowSplitBy = "cluster_markers", addCellSummary = "summary_col" )
    +

    2. Cell/Feature Labeling Text labels of features or cells can be added via rowLabel or colLabel. Use TRUE or FALSE to specify whether to show @@ -554,8 +600,8 @@

    Workflow Guide"Genes") and column title ("Cells") can be changed or removed by passing a string or NULL to rowTitle or colTitle, respectively.

    -
    -plotSCEHeatmap(inSCE = sce, useAssay = "counts", featureIndex = featureSubset, cellIndex = cellSubset, rowLabel = "feature_name", colLabel = seq(ncol(sce)), colDend = FALSE, rowTitle = "Downsampled features")
    +
    +plotSCEHeatmap(inSCE = sce2, useAssay = "logcounts", featureIndex = topMarkers$Gene, rowGap = grid::unit(2, 'mm'),rowLabel = TRUE,  rowTitle = "Markers",colTitle = "Clusters", cluster_columns = TRUE, cluster_rows = TRUE)

    There are still some parameters not mentioned here, but they are not frequently used. Please refer to ?plotSCEHeatmap as well as @@ -583,9 +629,7 @@

    References - -

    +
    @@ -598,16 +642,16 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/heatmap_files/figure-html/colRowAnn-1.png b/docs/articles/heatmap_files/figure-html/colRowAnn-1.png index 3fe3fcbd7..b3fe1deb7 100644 Binary files a/docs/articles/heatmap_files/figure-html/colRowAnn-1.png and b/docs/articles/heatmap_files/figure-html/colRowAnn-1.png differ diff --git a/docs/articles/heatmap_files/figure-html/idxSubset-1.png b/docs/articles/heatmap_files/figure-html/idxSubset-1.png index 8dfcb3546..f79872fd1 100644 Binary files a/docs/articles/heatmap_files/figure-html/idxSubset-1.png and b/docs/articles/heatmap_files/figure-html/idxSubset-1.png differ diff --git a/docs/articles/heatmap_files/figure-html/indexBy-1.png b/docs/articles/heatmap_files/figure-html/indexBy-1.png index 81aeca46d..9596db695 100644 Binary files a/docs/articles/heatmap_files/figure-html/indexBy-1.png and b/docs/articles/heatmap_files/figure-html/indexBy-1.png differ diff --git a/docs/articles/heatmap_files/figure-html/label-1.png b/docs/articles/heatmap_files/figure-html/label-1.png index d77ead89b..7dbcc133d 100644 Binary files a/docs/articles/heatmap_files/figure-html/label-1.png and b/docs/articles/heatmap_files/figure-html/label-1.png differ diff --git a/docs/articles/heatmap_files/figure-html/split-1.png b/docs/articles/heatmap_files/figure-html/split-1.png index a1a905826..2c4ad1b4f 100644 Binary files a/docs/articles/heatmap_files/figure-html/split-1.png and b/docs/articles/heatmap_files/figure-html/split-1.png differ diff --git a/docs/articles/heatmap_files/figure-html/split-2.png b/docs/articles/heatmap_files/figure-html/split-2.png index f78cd2476..4ea52906c 100644 Binary files a/docs/articles/heatmap_files/figure-html/split-2.png and b/docs/articles/heatmap_files/figure-html/split-2.png differ diff --git a/docs/articles/import_annotation.html b/docs/articles/import_annotation.html index ad5d3bc90..14d133d54 100644 --- a/docs/articles/import_annotation.html +++ b/docs/articles/import_annotation.html @@ -6,21 +6,20 @@ Manage Annotation of Cell and Features • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -457,9 +456,7 @@

    Workflow Guide - -

    +
    @@ -472,16 +469,16 @@

    Workflow Guide

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/import_data.html b/docs/articles/import_data.html index ec291afc6..93ddd131f 100644 --- a/docs/articles/import_data.html +++ b/docs/articles/import_data.html @@ -6,21 +6,20 @@ Import Data • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -606,9 +605,7 @@

    References - -

    +
    @@ -621,16 +618,16 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/import_genesets.html b/docs/articles/import_genesets.html index 74ab8e98e..5c2d21d7c 100644 --- a/docs/articles/import_genesets.html +++ b/docs/articles/import_genesets.html @@ -6,21 +6,20 @@ Import Genesets • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -383,9 +382,7 @@

    References - -

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    References

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    Site built with pkgdown 2.0.7.

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    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/index.html b/docs/articles/index.html index a91a00a57..67b87fe16 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,9 +1,9 @@ -Articles • singleCellTKArticles • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -259,6 +259,8 @@

    All vignettes

    Seurat Curated Workflow
    +
    Introduction to singleCellTK
    +
    Trajectory Analysis with TSCAN
    Using the UI to generate QC metrics
    @@ -267,8 +269,6 @@

    All vignettes

    SCTK Web Application
    -
    Introduction to singleCellTK
    -
    @@ -279,15 +279,15 @@

    All vignettes

    -

    Site built with pkgdown 2.0.7.

    +

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    - - + + diff --git a/docs/articles/installation.html b/docs/articles/installation.html index 9cb020345..9ccf66fb0 100644 --- a/docs/articles/installation.html +++ b/docs/articles/installation.html @@ -6,21 +6,20 @@ Installation • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -502,9 +501,7 @@

    Develop singleCellTK - -

    +
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    Develop singleCellTK

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/normalization.html b/docs/articles/normalization.html index 78af12e9d..11b425882 100644 --- a/docs/articles/normalization.html +++ b/docs/articles/normalization.html @@ -6,21 +6,20 @@ Normalization • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
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    • - +
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    References - -

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    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/pathwayAnalysis.html b/docs/articles/pathwayAnalysis.html index 991ac0286..d8e2ed810 100644 --- a/docs/articles/pathwayAnalysis.html +++ b/docs/articles/pathwayAnalysis.html @@ -6,21 +6,20 @@ Pathway Analysis • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
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    • - +
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    References - -

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    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/pathwayAnalysis_files/figure-html/pathVis-1.png b/docs/articles/pathwayAnalysis_files/figure-html/pathVis-1.png index b213b4333..1f142cf3f 100644 Binary files a/docs/articles/pathwayAnalysis_files/figure-html/pathVis-1.png and b/docs/articles/pathwayAnalysis_files/figure-html/pathVis-1.png differ diff --git a/docs/articles/scanpy_curated_workflow.html b/docs/articles/scanpy_curated_workflow.html index 0962665d3..5376eb550 100644 --- a/docs/articles/scanpy_curated_workflow.html +++ b/docs/articles/scanpy_curated_workflow.html @@ -6,21 +6,20 @@ Scanpy Curated Workflow • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
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    • - +
    @@ -574,13 +573,13 @@

    Workflow Guide 
     print(head(metadata(sce)[["scanpyMarkersTable"]]))
    -
    ##        Gene findMarker_cluster  Log2_FC        Pvalue   zscore
-## 01     CD74                  0 4.057573  0.000000e+00 78.69228
-## 02  HLA-DRA                  0 4.877226  0.000000e+00 74.43016
-## 03    CD79A                  0 7.735484 2.272841e-165 52.24474
-## 04 HLA-DPB1                  0 4.021307 4.142218e-253 51.94960
-## 05 HLA-DRB1                  0 3.864657 3.225850e-229 47.71487
-## 06    CD79B                  0 5.529685 1.860679e-150 44.38144
    +
    ##      Gene findMarker_cluster   Log2_FC        Pvalue   zscore
+## 01  RPS12                  0 0.8089651 2.093646e-105 25.08269
+## 02  RPS25                  0 0.8680546  6.748015e-95 23.33849
+## 03   RPS6                  0 0.7139596  2.935386e-91 23.30149
+## 04  RPS27                  0 0.7877940  2.479621e-88 22.71698
+## 05  RPL31                  0 0.8843585  2.715709e-83 21.65312
+## 06 MALAT1                  0 0.7837504  4.076034e-79 21.44774

    Expression of individual marker genes can be visualized in Feature plots, Dot plots, Violin plots, Matrix plots and via a Heatmap:

    @@ -603,9 +602,7 @@ 
    Workflow Guide
 
-        
-
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    Workflow Guide

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/seurat_curated_workflow.html b/docs/articles/seurat_curated_workflow.html index 48a1c4982..6ebd136c7 100644 --- a/docs/articles/seurat_curated_workflow.html +++ b/docs/articles/seurat_curated_workflow.html @@ -6,21 +6,20 @@ Seurat Curated Workflow • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - - - - -
    + +

    Seurat Curated Workflow

    @@ -486,7 +482,7 @@

    Workflow Guide## metadata(3): sctk scDblFinder.threshold assayType ## assays(2): counts decontXcounts ## rownames(32738): MIR1302-10 FAM138A ... AC002321.2 AC002321.1 -## rowData names(3): ENSEMBL_ID Symbol_TENx Symbol +## rowData names(4): ENSEMBL_ID Symbol_TENx Symbol subsets_mito ## colnames(2627): pbmc3k_AAACATACAACCAC-1 pbmc3k_AAACATTGAGCTAC-1 ... ## pbmc3k_TTTGCATGAGAGGC-1 pbmc3k_TTTGCATGCCTCAC-1 ## colData names(29): Sample Barcode ... decontX_contamination @@ -547,8 +543,8 @@

    Workflow Guide
     # Plot Elbowplot
 plotSeuratElbow(inSCE = sce)

    -
    - -
    ##         gene.id         p_val avg_log2FC pct.1 pct.2     p_val_adj cluster1
-## 9952     FCER1A 2.437284e-245   7.894711 0.871 0.011 7.979180e-241        9
-## 2030 AC079767.4  1.403770e-60   7.704734 0.124 0.001  4.595661e-56        2
-## 6494       VMO1  4.036596e-73   7.614426 0.149 0.001  1.321501e-68        6
-## 2012      IGLL5  1.647933e-88   7.526822 0.236 0.011  5.395003e-84        2
-## 1983  LINC00926 1.065847e-252   7.078343 0.537 0.010 3.489370e-248        2
-## 1985     VPREB3 3.103973e-225   6.882444 0.472 0.007 1.016179e-220        2
-##      cluster2
-## 9952      all
-## 2030      all
-## 6494      all
-## 2012      all
-## 1983      all
-## 1985      all
    +
    ##          gene.id         p_val avg_log2FC pct.1 pct.2     p_val_adj cluster1
+## 6569       LYPD2  1.218958e-52   8.799225 0.101 0.000  3.990626e-48        6
+## 10024     FCER1A 2.437284e-245   7.894711 0.871 0.011 7.979180e-241        9
+## 2039  AC079767.4  5.726383e-61   7.714132 0.124 0.001  1.874703e-56        2
+## 6521        VMO1  2.048582e-75   7.659427 0.154 0.001  6.706649e-71        6
+## 2021       IGLL5  3.956645e-89   7.536220 0.237 0.011  1.295326e-84        2
+## 1992   LINC00926 2.141923e-254   7.087741 0.540 0.010 7.012228e-250        2
+##       cluster2
+## 6569       all
+## 10024      all
+## 2039       all
+## 6521       all
+## 2021       all
+## 1992       all

    The marker genes identified can be visualized through one of the available plots from ridge plot, violin plot, feature plot, dot plot and @@ -712,9 +708,7 @@

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    @@ -43,7 +42,7 @@
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    • - +
    @@ -390,13 +389,13 @@

    Vignettes

    Session info

    -
    ## R version 4.3.3 (2024-02-29)
-## Platform: x86_64-apple-darwin20 (64-bit)
-## Running under: macOS Sonoma 14.4.1
+
    ## R version 4.4.2 (2024-10-31)
+## Platform: x86_64-apple-darwin20
+## Running under: macOS Sequoia 15.3
 ## 
 ## Matrix products: default
-## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
-## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
+## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
+## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
 ## 
 ## locale:
 ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
@@ -408,28 +407,25 @@ 
    Session info## [1] stats     graphics  grDevices utils     datasets  methods   base     
 ## 
 ## other attached packages:
-## [1] BiocStyle_2.30.0
+## [1] BiocStyle_2.34.0
 ## 
 ## loaded via a namespace (and not attached):
-##  [1] vctrs_0.6.5         cli_3.6.2           knitr_1.46         
-##  [4] rlang_1.1.3         xfun_0.43           purrr_1.0.2        
-##  [7] textshaping_0.3.7   jsonlite_1.8.8      htmltools_0.5.8.1  
-## [10] ragg_1.3.0          sass_0.4.9          rmarkdown_2.26     
-## [13] evaluate_0.23       jquerylib_0.1.4     fastmap_1.1.1      
-## [16] yaml_2.3.8          lifecycle_1.0.4     memoise_2.0.1      
-## [19] bookdown_0.37       BiocManager_1.30.22 compiler_4.3.3     
-## [22] fs_1.6.4            systemfonts_1.0.6   digest_0.6.35      
-## [25] R6_2.5.1            magrittr_2.0.3      bslib_0.7.0        
-## [28] tools_4.3.3         pkgdown_2.0.7       cachem_1.0.8       
-## [31] desc_1.4.3
    
+##  [1] digest_0.6.37       desc_1.4.3          R6_2.6.0           
+##  [4] bookdown_0.42       fastmap_1.2.0       xfun_0.50          
+##  [7] cachem_1.1.0        knitr_1.49          htmltools_0.5.8.1  
+## [10] rmarkdown_2.29      lifecycle_1.0.4     cli_3.6.3          
+## [13] sass_0.4.9          pkgdown_2.1.1       textshaping_1.0.0  
+## [16] jquerylib_0.1.4     systemfonts_1.2.1   compiler_4.4.2     
+## [19] rstudioapi_0.17.1   tools_4.4.2         ragg_1.3.3         
+## [22] bslib_0.9.0         evaluate_1.0.3      yaml_2.3.10        
+## [25] BiocManager_1.30.25 jsonlite_1.8.9      rlang_1.1.5        
+## [28] fs_1.6.5            htmlwidgets_1.6.4

    + @@ -442,16 +438,16 @@

    Session info

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/trajectoryAnalysis.html b/docs/articles/trajectoryAnalysis.html index cb6663cf6..d7a633156 100644 --- a/docs/articles/trajectoryAnalysis.html +++ b/docs/articles/trajectoryAnalysis.html @@ -6,21 +6,20 @@ Trajectory Analysis with TSCAN • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
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    • - +
    @@ -571,7 +570,7 @@

    Workflow Guide 
     tableList$`6`
    -
    ## DataFrame with 0 rows and 3 columns
    +
    ## NULL
    Show recomputed pseudotime rooting from the cluster
     plotTSCANClusterPseudo(sce, useCluster = useCluster, useReducedDim = "UMAP")

    @@ -601,9 +600,7 @@

    References - -

    +
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    References

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    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDEG-1.png b/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDEG-1.png index 79ec00eed..564234b33 100644 Binary files a/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDEG-1.png and b/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDEG-1.png differ diff --git a/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDEG-2.png b/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDEG-2.png index 9f9486942..08e94c5f8 100644 Binary files a/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDEG-2.png and b/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDEG-2.png differ diff --git a/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDimReduceFeatures-1.png b/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDimReduceFeatures-1.png index 1bca23c29..75223271a 100644 Binary files a/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDimReduceFeatures-1.png and b/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANDimReduceFeatures-1.png differ diff --git a/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANResults-1.png b/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANResults-1.png index 6c025a148..ede0e5841 100644 Binary files a/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANResults-1.png and b/docs/articles/trajectoryAnalysis_files/figure-html/plotTSCANResults-1.png differ diff --git a/docs/articles/trajectoryAnalysis_files/figure-html/tscanClusterPseudo-1.png b/docs/articles/trajectoryAnalysis_files/figure-html/tscanClusterPseudo-1.png index fddd03ea6..942b42266 100644 Binary files a/docs/articles/trajectoryAnalysis_files/figure-html/tscanClusterPseudo-1.png and b/docs/articles/trajectoryAnalysis_files/figure-html/tscanClusterPseudo-1.png differ diff --git a/docs/articles/trajectoryAnalysis_files/figure-html/tscan_prep_plot-1.png b/docs/articles/trajectoryAnalysis_files/figure-html/tscan_prep_plot-1.png index 061fca2f5..aa41a3087 100644 Binary files a/docs/articles/trajectoryAnalysis_files/figure-html/tscan_prep_plot-1.png and b/docs/articles/trajectoryAnalysis_files/figure-html/tscan_prep_plot-1.png differ diff --git a/docs/articles/ui_qc.html b/docs/articles/ui_qc.html index dbb0f38c3..e88be74c9 100644 --- a/docs/articles/ui_qc.html +++ b/docs/articles/ui_qc.html @@ -6,21 +6,20 @@ Using the UI to generate QC metrics • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -348,9 +347,7 @@

    Filtering poor quality data - -

    +
    @@ -363,16 +360,16 @@

    Filtering poor quality data

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/visualization.html b/docs/articles/visualization.html index 458b94f0c..582ccc321 100644 --- a/docs/articles/visualization.html +++ b/docs/articles/visualization.html @@ -6,21 +6,20 @@ Visualization • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -439,9 +438,7 @@

    Workflow Guide - -

    +
    @@ -454,16 +451,16 @@

    Workflow Guide

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/visualization_files/figure-html/groupby-1.png b/docs/articles/visualization_files/figure-html/groupby-1.png index 74102e296..5f5914ccc 100644 Binary files a/docs/articles/visualization_files/figure-html/groupby-1.png and b/docs/articles/visualization_files/figure-html/groupby-1.png differ diff --git a/docs/articles/visualization_files/figure-html/sample-1.png b/docs/articles/visualization_files/figure-html/sample-1.png index 4dcc14cd1..0e3912692 100644 Binary files a/docs/articles/visualization_files/figure-html/sample-1.png and b/docs/articles/visualization_files/figure-html/sample-1.png differ diff --git a/docs/articles/visualization_files/figure-html/sample-2.png b/docs/articles/visualization_files/figure-html/sample-2.png index 34535347d..7729be475 100644 Binary files a/docs/articles/visualization_files/figure-html/sample-2.png and b/docs/articles/visualization_files/figure-html/sample-2.png differ diff --git a/docs/authors.html b/docs/authors.html index b09e7e226..c58c143bc 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,9 +1,9 @@ -Authors and Citation • singleCellTKAuthors and Citation • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    -

    Authors

    +

    Authors and Citation

    - +

    • Yichen Wang. Author.

      @@ -212,19 +212,19 @@

      Authors

    • -

      Rui Hong. Author. +

      Rui Hong. Author.

    • -

      Yusuke Koga. Author. +

      Yusuke Koga. Author.

    • -

      Salam Alabdullatif. Author. +

      Salam Alabdullatif. Author.

    • -

      Nida Pervaiz. Author. +

      Nida Pervaiz. Author.

    • @@ -232,31 +232,31 @@

      Authors

    • -

      Vidya Akavoor. Author. +

      Vidya Akavoor. Author.

    • -

      Xinyun Cao. Author. +

      Xinyun Cao. Author.

    • -

      Shruthi Bandyadka. Author. +

      Shruthi Bandyadka. Author.

    • -

      Anastasia Leshchyk. Author. +

      Anastasia Leshchyk. Author.

    • -

      Tyler Faits. Author. +

      Tyler Faits. Author.

    • -

      Mohammed Muzamil Khan. Author. +

      Mohammed Muzamil Khan. Author.

    • -

      Zhe Wang. Author. +

      Zhe Wang. Author.

    • @@ -264,7 +264,7 @@

      Authors

    • -

      Ming Liu. Author. +

      Ming Liu. Author.

    • @@ -280,15 +280,15 @@

      Citation

    -

    Wang Y, Sarfraz I, Hong R, Koga Y, Alabdullatif S, Pervaiz N, Jenkins D, Akavoor V, Cao X, Bandyadka S, Leshchyk A, Faits T, Khan MM, Wang Z, Johnson WE, Liu M, Campbell JD (2024). +

    Wang Y, Sarfraz I, Hong R, Koga Y, Alabdullatif S, Pervaiz N, Jenkins D, Akavoor V, Cao X, Bandyadka S, Leshchyk A, Faits T, Khan MM, Wang Z, Johnson WE, Liu M, Campbell JD (2025). singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data. -R package version 2.14.0, https://www.camplab.net/sctk/. +R package version 2.16.1, https://www.camplab.net/sctk/. 

    @Manual{,
   title = {singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data},
   author = {Yichen Wang and Irzam Sarfraz and Rui Hong and Yusuke Koga and Salam Alabdullatif and Nida Pervaiz and David Jenkins and Vidya Akavoor and Xinyun Cao and Shruthi Bandyadka and Anastasia Leshchyk and Tyler Faits and Mohammed Muzamil Khan and Zhe Wang and W. Evan Johnson and Ming Liu and Joshua David Campbell},
-  year = {2024},
-  note = {R package version 2.14.0},
+  year = {2025},
+  note = {R package version 2.16.1},
   url = {https://www.camplab.net/sctk/},
 }
    @@ -303,15 +303,15 @@

    Citation

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/index.html b/docs/index.html index cb1e7e944..954191643 100644 --- a/docs/index.html +++ b/docs/index.html @@ -6,7 +6,7 @@ Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data • singleCellTK - + @@ -20,7 +20,7 @@ - +
    @@ -43,7 +43,7 @@
  • - +
  • @@ -52,7 +52,7 @@
    • - +
    @@ -373,16 +373,16 @@

    Developers

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/news/index.html b/docs/news/index.html index d68ae7cbc..d388e74a0 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,9 +1,9 @@ -Changelog • singleCellTKChangelog • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -202,10 +202,20 @@

    Changelog

    Source: NEWS.md
    +
    +

    Changes in Version 2.16.1 (2024-02-12)

    +
    • Fixed decontX/soupX webapp error
      • +
    • Fixed error in reportCellQC
      • +
    • Fixed additional bugs with Seurat V5 integration
      • +
    +
    +

    Changes in Version 2.16.0 (2024-10-29)

    +
    • Updated version to match Bioconductor 3.20
      • +

    Changes in Version 2.14.0 (2024-05-03)

    • Updated version to match Bioconductor 3.19
      • -
    • Update runGSVA fucntion to work with newer GSVA package
      • +
    • Update runGSVA function to work with newer GSVA package

    Changes in Version 2.12.2 (2024-01-28)

    @@ -421,15 +431,15 @@

    Change

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 3eeffeedf..dcd191606 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,38 +1,37 @@ -pandoc: 3.1.11.1 -pkgdown: 2.0.7 +pandoc: '3.2' +pkgdown: 2.1.1 pkgdown_sha: ~ articles: - 01_import_and_qc_tutorial: 01_import_and_qc_tutorial.html - 02_a_la_carte_workflow: 02_a_la_carte_workflow.html - 2d_embedding: 2d_embedding.html - batch_correction: batch_correction.html - celda_curated_workflow: celda_curated_workflow.html - cell_type_labeling: cell_type_labeling.html - clustering: clustering.html - cmd_qc: cmd_qc.html - cnsl_cellqc: cnsl_cellqc.html - cnsl_dropletqc: cnsl_dropletqc.html - delete_data: delete_data.html - differential_expression: differential_expression.html - dimensionality_reduction: dimensionality_reduction.html - enrichR: enrichR.html - export_data: export_data.html - feature_selection: feature_selection.html - filtering: filtering.html - find_marker: find_marker.html - heatmap: heatmap.html - import_annotation: import_annotation.html - import_data: import_data.html - import_genesets: import_genesets.html - installation: installation.html - normalization: normalization.html - pathwayAnalysis: pathwayAnalysis.html - scanpy_curated_workflow: scanpy_curated_workflow.html - seurat_curated_workflow: seurat_curated_workflow.html - trajectoryAnalysis: trajectoryAnalysis.html - ui_qc: ui_qc.html - visualization: visualization.html - webApp: webApp.html + articles/01_import_and_qc_tutorial: 01_import_and_qc_tutorial.html + articles/02_a_la_carte_workflow: 02_a_la_carte_workflow.html + articles/2d_embedding: 2d_embedding.html + articles/batch_correction: batch_correction.html + articles/celda_curated_workflow: celda_curated_workflow.html + articles/cell_type_labeling: cell_type_labeling.html + articles/clustering: clustering.html + articles/cmd_qc: cmd_qc.html + articles/cnsl_cellqc: cnsl_cellqc.html + articles/cnsl_dropletqc: cnsl_dropletqc.html + articles/delete_data: delete_data.html + articles/differential_expression: differential_expression.html + articles/dimensionality_reduction: dimensionality_reduction.html + articles/enrichR: enrichR.html + articles/export_data: export_data.html + articles/feature_selection: feature_selection.html + articles/filtering: filtering.html + articles/find_marker: find_marker.html + articles/heatmap: heatmap.html + articles/import_annotation: import_annotation.html + articles/import_data: import_data.html + articles/import_genesets: import_genesets.html + articles/installation: installation.html + articles/normalization: normalization.html + articles/pathwayAnalysis: pathwayAnalysis.html + articles/scanpy_curated_workflow: scanpy_curated_workflow.html + articles/seurat_curated_workflow: seurat_curated_workflow.html singleCellTK: singleCellTK.html -last_built: 2024-05-03T11:13Z - + articles/trajectoryAnalysis: trajectoryAnalysis.html + articles/ui_qc: ui_qc.html + articles/visualization: visualization.html + articles/webApp: webApp.html +last_built: 2025-02-13T15:26Z diff --git a/docs/reference/MitoGenes.html b/docs/reference/MitoGenes.html index 5b91c1978..fd51e6b1e 100644 --- a/docs/reference/MitoGenes.html +++ b/docs/reference/MitoGenes.html @@ -1,12 +1,12 @@ -List of mitochondrial genes of multiple reference — MitoGenes • singleCellTKList of mitochondrial genes of multiple reference — MitoGenes • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -209,7 +209,7 @@

    List of mitochondrial genes of multiple reference

    A list of gene set that contains mitochondrial genes of multiple reference (hg38, hg19, mm10 and mm9). It contains multiple types of gene identifier: -gene symbol, entrez ID, ensemble ID and ensemble transcript ID. It's used +gene symbol, entrez ID, ensemble ID and ensemble transcript ID. It's used for the function 'importMitoGeneSet'.

    @@ -223,9 +223,7 @@

    Format

    Value

    - - -

    List of mitochondrial genes of multiple reference

    +

    List of mitochondrial genes of multiple reference

    @@ -245,15 +243,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/SEG.html b/docs/reference/SEG.html index 11ee94120..6b0d7fa08 100644 --- a/docs/reference/SEG.html +++ b/docs/reference/SEG.html @@ -1,9 +1,9 @@ -Stably Expressed Gene (SEG) list obect, with SEG sets for human and mouse. — SEG • singleCellTKStably Expressed Gene (SEG) list obect, with SEG sets for human and mouse. — SEG • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -222,9 +222,7 @@

    Source

    Value

    - - -

    Stably Expressed Gene (SEG) list obect, with SEG sets for human and mouse.

    +

    Stably Expressed Gene (SEG) list obect, with SEG sets for human and mouse.

    @@ -245,15 +243,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/calcEffectSizes.html b/docs/reference/calcEffectSizes.html index 0c705cd75..73b61b190 100644 --- a/docs/reference/calcEffectSizes.html +++ b/docs/reference/calcEffectSizes.html @@ -1,12 +1,10 @@ -Finds the effect sizes for all genes in the original dataset, regardless of -significance. — calcEffectSizes • singleCellTKFinds the effect sizes for all genes in the original dataset, regardless of significance. — calcEffectSizes • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    Finds the effect sizes for all genes in the original dataset, regardless of -significance.

    +

    Finds the effect sizes for all genes in the original dataset, regardless of significance.

    Source: R/DownsampleMatrix.R
    @@ -218,11 +215,13 @@

    Finds the effect sizes for all genes in the original dataset, regardless of

    Arguments

    -
    countMatrix
    + + +
    countMatrix

    Matrix. A simulated counts matrix, sans labels.

    -
    condition
    +
    condition

    Factor. The condition labels for the simulated cells. If more than 2 conditions are given, the first will be compared to all others by default.

    @@ -230,9 +229,7 @@

    Arguments

    Value

    - - -

    A vector of cohen's d effect sizes for each gene.

    +

    A vector of cohen's d effect sizes for each gene.

    @@ -255,15 +252,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/combineSCE.html b/docs/reference/combineSCE.html index e726c1064..5235e45aa 100644 --- a/docs/reference/combineSCE.html +++ b/docs/reference/combineSCE.html @@ -1,9 +1,9 @@ -Combine a list of SingleCellExperiment objects as one SingleCellExperiment object — combineSCE • singleCellTKCombine a list of SingleCellExperiment objects as one SingleCellExperiment object — combineSCE • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,34 +213,34 @@

    Combine a list of SingleCellExperiment objects as one SingleCellExperiment o

    Arguments

    -
    sceList
    + + +
    sceList

    A list contains SingleCellExperiment objects. Currently, combineSCE function only support combining SCE objects with assay in dgCMatrix format. It does not support combining SCE with assay in delayedArray format.

    -
    by.r
    -

    Specifications of the columns used for merging rowData. If set as NULL, +

    by.r
    +

    Specifications of the columns used for merging rowData. If set as NULL, the rownames of rowData tables will be used to merging rowData. Default is NULL.

    -
    by.c
    -

    Specifications of the columns used for merging colData. If set as NULL, +

    by.c
    +

    Specifications of the columns used for merging colData. If set as NULL, the rownames of colData tables will be used to merging colData. Default is NULL.

    -
    combined
    -

    logical; if TRUE, it will combine the list of SingleCellExperiment objects +

    combined
    +

    logical; if TRUE, it will combine the list of SingleCellExperiment objects and return a SingleCellExperiment. If FALSE, it will return a list of SingleCellExperiment whose -rowData, colData, assay and reducedDim data slot are compatible within SCE objects in the list. +rowData, colData, assay and reducedDim data slot are compatible within SCE objects in the list. Default is TRUE.

    Value

    - - -

    A SingleCellExperiment object which combines all +

    A SingleCellExperiment object which combines all objects in sceList. The colData is merged.

    @@ -262,15 +262,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/computeHeatmap.html b/docs/reference/computeHeatmap.html index c5f01eff0..e7e7e1199 100644 --- a/docs/reference/computeHeatmap.html +++ b/docs/reference/computeHeatmap.html @@ -1,14 +1,12 @@ -Computes heatmap for a set of features against dimensionality reduction -components — computeHeatmap • singleCellTKComputes heatmap for a set of features against dimensionality reduction components — computeHeatmap • singleCellTK - +
    @@ -30,7 +28,7 @@
    - +
    -

    Computes heatmap for a set of features against dimensionality reduction -components

    +

    Computes heatmap for a set of features against dimensionality reduction components

    Source: R/computeHeatmap.R
    @@ -234,56 +231,58 @@

    Computes heatmap for a set of features against dimensionality reduction

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Specify the name of the assay that will be scaled by this function for the features that are used in the heatmap.

    -
    dims
    +
    dims

    Specify the number of dimensions to use for heatmap. Default 10.

    -
    nfeatures
    +
    nfeatures

    Specify the number of features to use for heatmap. Default is 30.

    -
    cells
    +
    cells

    Specify the samples/cells to use for heatmap computation. Default is NULL which will utilize all samples in the assay.

    -
    reduction
    +
    reduction

    Specify the reduction slot in the input object. Default is "pca".

    -
    disp.min
    +
    disp.min

    Specify the minimum dispersion value to use for floor clipping of assay values. Default is -2.5.

    -
    disp.max
    +
    disp.max

    Specify the maximum dispersion value to use for ceiling clipping of assay values. Default is 2.5.

    -
    balanced
    +
    balanced

    Specify if the number of of up-regulated and down-regulated features should be balanced. Default is TRUE.

    -
    nCol
    +
    nCol

    Specify the number of columns in the output plot. Default is NULL which will auto-compute the number of columns.

    -
    externalReduction
    +
    externalReduction

    Specify an external reduction if not present in the input object. This external reduction should be created using CreateDimReducObject function.

    @@ -291,9 +290,7 @@

    Arguments

    Value

    - - -

    Heatmap plot object.

    +

    Heatmap plot object.

    @@ -308,15 +305,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/computeZScore.html b/docs/reference/computeZScore.html index c9dc37738..86bac5be6 100644 --- a/docs/reference/computeZScore.html +++ b/docs/reference/computeZScore.html @@ -1,5 +1,5 @@ -Compute Z-Score — computeZScore • singleCellTKCompute Z-Score — computeZScore • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -221,15 +221,15 @@

    Compute Z-Score

    Arguments

    -
    counts
    + + +
    counts

    matrix (base matrix, dgCMatrix or DelayedMatrix)

    Value

    - - -

    z-score computed counts matrix (DelayedMatrix)

    +

    z-score computed counts matrix (DelayedMatrix)

    @@ -250,15 +250,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/constructSCE.html b/docs/reference/constructSCE.html index 0ff528cca..80a482666 100644 --- a/docs/reference/constructSCE.html +++ b/docs/reference/constructSCE.html @@ -1,9 +1,9 @@ -Create SingleCellExperiment object from csv or txt input — constructSCE • singleCellTKCreate SingleCellExperiment object from csv or txt input — constructSCE • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,19 +213,19 @@

    Create SingleCellExperiment object from csv or txt input

    Arguments

    -
    data
    -

    A data.table object containing the count matrix.

    -
    samplename
    +
    data
    +

    A data.table object containing the count matrix.

    + + +
    samplename

    The sample name of the data.

    Value

    - - -

    A SingleCellExperiment object containing +

    A SingleCellExperiment object containing the count matrix.

    @@ -241,15 +241,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/convertSCEToSeurat.html b/docs/reference/convertSCEToSeurat.html index 5adfabe5b..ae65b1f25 100644 --- a/docs/reference/convertSCEToSeurat.html +++ b/docs/reference/convertSCEToSeurat.html @@ -1,12 +1,10 @@ -convertSCEToSeurat -Converts sce object to seurat while retaining all assays and metadata — convertSCEToSeurat • singleCellTKconvertSCEToSeurat Converts sce object to seurat while retaining all assays and metadata — convertSCEToSeurat • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    convertSCEToSeurat -Converts sce object to seurat while retaining all assays and metadata

    +

    convertSCEToSeurat Converts sce object to seurat while retaining all assays and metadata

    Source: R/seuratFunctions.R
    @@ -230,42 +227,44 @@

    convertSCEToSeurat

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object to convert to a Seurat object.

    -
    countsAssay
    +
    countsAssay

    Which assay to use from sce object for raw counts. Default NULL.

    -
    normAssay
    +
    normAssay

    Which assay to use from sce object for normalized data. Default NULL.

    -
    scaledAssay
    +
    scaledAssay

    Which assay to use from sce object for scaled data. Default NULL.

    -
    copyColData
    +
    copyColData

    Boolean. Whether copy 'colData' of SCE object to the 'meta.data' of Seurat object. Default FALSE.

    -
    copyReducedDim
    +
    copyReducedDim

    Boolean. Whether copy 'reducedDims' of the SCE object to the 'reductions' of Seurat object. Default FALSE.

    -
    copyDecontX
    +
    copyDecontX

    Boolean. Whether copy 'decontXcounts' assay of the SCE object to the 'assays' of Seurat object. Default TRUE.

    -
    pcaReducedDim
    +
    pcaReducedDim

    Specify a character value indicating the name of the reducedDim to store as default pca computation in the output seurat object. Default is NULL which will not store any reducedDim as the @@ -273,7 +272,7 @@

    Arguments

    set to TRUE.

    -
    icaReducedDim
    +
    icaReducedDim

    Specify a character value indicating the name of the reducedDim to store as default ica computation in the output seurat object. Default is NULL which will not store any reducedDim as the @@ -281,7 +280,7 @@

    Arguments

    set to TRUE.

    -
    tsneReducedDim
    +
    tsneReducedDim

    Specify a character value indicating the name of the reducedDim to store as default tsne computation in the output seurat object. Default is NULL which will not store any reducedDim as the @@ -289,7 +288,7 @@

    Arguments

    set to TRUE.

    -
    umapReducedDim
    +
    umapReducedDim

    Specify a character value indicating the name of the reducedDim to store as default umap computation in the output seurat object. Default is NULL which will not store any reducedDim as the @@ -299,9 +298,7 @@

    Arguments

    Value

    - - -

    Updated seurat object that contains all data from the input sce +

    Updated seurat object that contains all data from the input sce object

    @@ -323,15 +320,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/convertSeuratToSCE.html b/docs/reference/convertSeuratToSCE.html index 7c77c6611..97f6db6a3 100644 --- a/docs/reference/convertSeuratToSCE.html +++ b/docs/reference/convertSeuratToSCE.html @@ -1,12 +1,10 @@ -convertSeuratToSCE -Converts the input seurat object to a sce object — convertSeuratToSCE • singleCellTKconvertSeuratToSCE Converts the input seurat object to a sce object — convertSeuratToSCE • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    convertSeuratToSCE -Converts the input seurat object to a sce object

    +

    convertSeuratToSCE Converts the input seurat object to a sce object

    Source: R/seuratFunctions.R
    @@ -222,25 +219,25 @@

    convertSeuratToSCE

    Arguments

    -
    seuratObject
    + + +
    seuratObject

    Input Seurat object

    -
    normAssayName
    +
    normAssayName

    Name of assay to store the normalized data. Default "seuratNormData".

    -
    scaledAssayName
    +
    scaledAssayName

    Name of assay to store the scaled data. Default "seuratScaledData".

    Value

    - - -

    SingleCellExperiment output object

    +

    SingleCellExperiment output object

    @@ -263,15 +260,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/dedupRowNames.html b/docs/reference/dedupRowNames.html index e5021d571..45515c1a8 100644 --- a/docs/reference/dedupRowNames.html +++ b/docs/reference/dedupRowNames.html @@ -1,11 +1,11 @@ -Deduplicate the rownames of a matrix or SingleCellExperiment object — dedupRowNames • singleCellTKDeduplicate the rownames of a matrix or SingleCellExperiment object — dedupRowNames • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -217,33 +217,31 @@

    Deduplicate the rownames of a matrix or SingleCellExperiment object

    Arguments

    -
    x
    -

    A matrix like or /linkS4classSingleCellExperiment object, on which + + +

    x
    +

    A matrix like or SingleCellExperiment object, on which we can apply rownames() to and has duplicated rownames.

    -
    as.rowData
    +
    as.rowData

    Only applicable when x is a -/linkS4classSingleCellExperiment object. When set to TRUE, will +SingleCellExperiment object. When set to TRUE, will insert a new column called "rownames.uniq" to rowData(x), with the deduplicated rownames.

    -
    return.list
    +
    return.list

    When set to TRUE, will return a character vector of the deduplicated rownames.

    Value

    - - -

    By default, a matrix or /linkS4classSingleCellExperiment object +

    By default, a matrix or SingleCellExperiment object with rownames deduplicated. -When x is a /linkS4classSingleCellExperiment and as.rowData

    - - -

    is set to TRUE, will return x with rowData updated. +When x is a SingleCellExperiment and as.rowData +is set to TRUE, will return x with rowData updated. When return.list is set to TRUE, will return a character vector with the deduplicated rownames.

    @@ -266,15 +264,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/detectCellOutlier.html b/docs/reference/detectCellOutlier.html index 8e30be89a..d377b4f97 100644 --- a/docs/reference/detectCellOutlier.html +++ b/docs/reference/detectCellOutlier.html @@ -1,10 +1,10 @@ -Detecting outliers within the SingleCellExperiment object. — detectCellOutlier • singleCellTKDetecting outliers within the SingleCellExperiment object. — detectCellOutlier • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -223,20 +223,22 @@

    Detecting outliers within the SingleCellExperiment object.

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    slotName
    +
    slotName

    Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata", "reducedDims". Required.

    -
    itemName
    +
    itemName

    Desired vector within the slot used for plotting. Required.

    -
    sample
    +
    sample

    A single character specifying a name that can be found in colData(inSCE) to directly use the cell annotation; or a character vector with as many elements as cells to indicates which sample each cell @@ -244,18 +246,18 @@

    Arguments

    each sample separately.

    -
    nmads
    +
    nmads

    Integer. Number of median absolute deviation. Parameter may be adjusted for more lenient or stringent outlier cutoff. Default 3.

    -
    type
    +
    type

    Character. Type/direction of outlier detection; whether the lower/higher outliers should be detected, or both. Options are "both", "lower", "higher".

    -
    overwrite
    +
    overwrite

    Boolean. If TRUE, and this function has previously generated an outlier decision on the same itemName, the outlier decision will be overwritten. Default TRUE.

    @@ -263,12 +265,9 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object with - '' added to the

    -

    -

    colData slot. Additionally, the +

    A SingleCellExperiment object with + ” added to the + colData slot. Additionally, the decontaminated counts will be added as an assay called 'decontXCounts'.

    @@ -277,28 +276,28 @@

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runDecontX(sce[,sample(ncol(sce),20)])
-#> Fri May  3 07:14:07 2024 ... Running 'DecontX'
+#> Thu Feb 13 10:27:13 2025 ... Running 'DecontX'
 #> --------------------------------------------------
 #> Starting DecontX
 #> --------------------------------------------------
-#> Fri May  3 07:14:07 2024 .. Analyzing all cells
-#> Fri May  3 07:14:07 2024 .... Generating UMAP and estimating cell types
-#> Fri May  3 07:14:09 2024 .... Estimating contamination
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 10 | converge: 0.01404
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 20 | converge: 0.004718
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 30 | converge: 0.002207
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 40 | converge: 0.001589
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 50 | converge: 0.001587
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 60 | converge: 0.001492
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 70 | converge: 0.001387
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 80 | converge: 0.001332
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 90 | converge: 0.001254
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 100 | converge: 0.00122
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 110 | converge: 0.00108
-#> Fri May  3 07:14:09 2024 ...... Completed iteration: 117 | converge: 0.0009928
-#> Fri May  3 07:14:09 2024 .. Calculating final decontaminated matrix
+#> Thu Feb 13 10:27:13 2025 .. Analyzing all cells
+#> Thu Feb 13 10:27:13 2025 .... Generating UMAP and estimating cell types
+#> Thu Feb 13 10:27:16 2025 .... Estimating contamination
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 10 | converge: 0.01404
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 20 | converge: 0.004718
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 30 | converge: 0.002207
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 40 | converge: 0.001589
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 50 | converge: 0.001587
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 60 | converge: 0.001492
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 70 | converge: 0.001387
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 80 | converge: 0.001332
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 90 | converge: 0.001254
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 100 | converge: 0.00122
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 110 | converge: 0.00108
+#> Thu Feb 13 10:27:16 2025 ...... Completed iteration: 117 | converge: 0.0009928
+#> Thu Feb 13 10:27:16 2025 .. Calculating final decontaminated matrix
 #> --------------------------------------------------
-#> Completed DecontX. Total time: 2.697716 secs
+#> Completed DecontX. Total time: 2.619526 secs
 #> --------------------------------------------------
 sce <- detectCellOutlier(sce, slotName = "colData", sample = sce$sample,
  nmads = 4, itemName = "decontX_contamination", type = "both")
@@ -316,15 +315,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/diffAbundanceFET.html b/docs/reference/diffAbundanceFET.html index 2b8260102..50d9cac8e 100644 --- a/docs/reference/diffAbundanceFET.html +++ b/docs/reference/diffAbundanceFET.html @@ -1,9 +1,9 @@ -Calculate Differential Abundance with FET — diffAbundanceFET • singleCellTKCalculate Differential Abundance with FET — diffAbundanceFET • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,44 +213,42 @@

    Calculate Differential Abundance with FET

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    cluster
    +
    cluster

    A single character, specifying the name to store the cluster label in colData.

    -
    variable
    +
    variable

    A single character, specifying the name to store the phenotype labels in colData.

    -
    control
    +
    control

    character. Specifying one or more categories that can be found in the vector specified by variable.

    -
    case
    +
    case

    character. Specifying one or more categories that can be found in the vector specified by variable.

    -
    analysisName
    +
    analysisName

    A single character. Will be used for naming the result table, which will be saved in metadata slot.

    Value

    - - -

    The original SingleCellExperiment

    - - -

    object with metadata(inSCE) updated with a list +

    The original SingleCellExperiment +object with metadata(inSCE) updated with a list diffAbundanceFET, containing a new data.frame for the analysis result, named by analysisName. The data.frame contains columns for number and fraction of cells that belong to different cases, as well as @@ -286,15 +284,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/discreteColorPalette.html b/docs/reference/discreteColorPalette.html index 46a480dd9..33f330034 100644 --- a/docs/reference/discreteColorPalette.html +++ b/docs/reference/discreteColorPalette.html @@ -1,12 +1,12 @@ -Generate given number of color codes — discreteColorPalette • singleCellTKGenerate given number of color codes — discreteColorPalette • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -224,31 +224,31 @@

    Generate given number of color codes

    Arguments

    -
    n
    + + +
    n

    An integer, the number of color codes to generate.

    -
    palette
    +
    palette

    A single character string. Select the method, available options are "ggplot", "celda" and "random". Default "random".

    -
    seed
    +
    seed

    An integer. Set the seed for random process that happens only in "random" generation. Default 12345.

    -
    ...
    +
    ...

    Other arguments that are passed to the internal function, according to the method selected.

    Value

    - - -

    A character vector of n hex color codes.

    +

    A character vector of n hex color codes.

    @@ -269,15 +269,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/distinctColors.html b/docs/reference/distinctColors.html index 9ed9fec39..ae57c7a0e 100644 --- a/docs/reference/distinctColors.html +++ b/docs/reference/distinctColors.html @@ -1,9 +1,9 @@ -Generate a distinct palette for coloring different clusters — distinctColors • singleCellTKGenerate a distinct palette for coloring different clusters — distinctColors • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -218,32 +218,32 @@

    Generate a distinct palette for coloring different clusters

    Arguments

    -
    n
    + + +
    n

    Integer; Number of colors to generate

    -
    hues
    +
    hues

    Character vector of R colors available from the colors() function. These will be used as the base colors for the clustering scheme. Different saturations and values (i.e. darkness) will be generated for each hue.

    -
    saturation.range
    +
    saturation.range

    Numeric vector of length 2 with values between 0 and 1. Default: c(0.25, 1)

    -
    value.range
    +
    value.range

    Numeric vector of length 2 with values between 0 and 1. Default: c(0.5, 1)

    Value

    - - -

    A vector of distinct colors that have been converted to HEX from +

    A vector of distinct colors that have been converted to HEX from HSV.

    @@ -266,15 +266,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/downSampleCells.html b/docs/reference/downSampleCells.html index e3bc1757b..87e4a87ec 100644 --- a/docs/reference/downSampleCells.html +++ b/docs/reference/downSampleCells.html @@ -1,12 +1,10 @@ -Estimate numbers of detected genes, significantly differentially expressed -genes, and median significant effect size — downSampleCells • singleCellTKEstimate numbers of detected genes, significantly differentially expressed genes, and median significant effect size — downSampleCells • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    Estimate numbers of detected genes, significantly differentially expressed -genes, and median significant effect size

    +

    Estimate numbers of detected genes, significantly differentially expressed genes, and median significant effect size

    Source: R/DownsampleMatrix.R
    @@ -229,62 +226,62 @@

    Estimate numbers of detected genes, significantly differentially expressed

    Arguments

    -
    originalData
    + + +
    originalData

    The SingleCellExperiment object storing all assay data from the shiny app.

    -
    useAssay
    +
    useAssay

    Character. The name of the assay to be used for subsampling.

    -
    minCountDetec
    +
    minCountDetec

    Numeric. The minimum number of reads found for a gene to be considered detected.

    -
    minCellsDetec
    +
    minCellsDetec

    Numeric. The minimum number of cells a gene must have at least 1 read in for it to be considered detected.

    -
    minCellnum
    +
    minCellnum

    Numeric. The minimum number of virtual cells to include in the smallest simulated dataset.

    -
    maxCellnum
    +
    maxCellnum

    Numeric. The maximum number of virtual cells to include in the largest simulated dataset

    -
    realLabels
    +
    realLabels

    Character. The name of the condition of interest. Must match a name from sample data. If only two factors present in the corresponding colData, will default to t-test. If multiple factors, will default to ANOVA.

    -
    depthResolution
    +
    depthResolution

    Numeric. How many different read depth should the script simulate? Will simulate a number of experimental designs ranging from 10 reads to maxReadDepth, with logarithmic spacing.

    -
    iterations
    +
    iterations

    Numeric. How many times should each experimental design be simulated?

    -
    totalReads
    +
    totalReads

    Numeric. How many aligned reads to put in each simulated dataset.

    Value

    - - -

    A 3-dimensional array, with dimensions = c(iterations, +

    A 3-dimensional array, with dimensions = c(iterations, depthResolution, 3). [,,1] contains the number of detected genes in each simulated dataset, [,,2] contains the number of significantly differentially expressed genes in each simulation, and [,,3] contains the mediansignificant @@ -313,15 +310,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/downSampleDepth.html b/docs/reference/downSampleDepth.html index 37c4b224e..4264c79a3 100644 --- a/docs/reference/downSampleDepth.html +++ b/docs/reference/downSampleDepth.html @@ -1,12 +1,10 @@ -Estimate numbers of detected genes, significantly differentially expressed -genes, and median significant effect size — downSampleDepth • singleCellTKEstimate numbers of detected genes, significantly differentially expressed genes, and median significant effect size — downSampleDepth • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    Estimate numbers of detected genes, significantly differentially expressed -genes, and median significant effect size

    +

    Estimate numbers of detected genes, significantly differentially expressed genes, and median significant effect size

    Source: R/DownsampleMatrix.R
    @@ -227,50 +224,50 @@

    Estimate numbers of detected genes, significantly differentially expressed

    Arguments

    -
    originalData
    + + +
    originalData

    SingleCellExperiment object storing all assay data from the shiny app.

    -
    useAssay
    +
    useAssay

    Character. The name of the assay to be used for subsampling.

    -
    minCount
    +
    minCount

    Numeric. The minimum number of reads found for a gene to be considered detected.

    -
    minCells
    +
    minCells

    Numeric. The minimum number of cells a gene must have at least 1 read in for it to be considered detected.

    -
    maxDepth
    +
    maxDepth

    Numeric. The highest number of total reads to be simulated.

    -
    realLabels
    +
    realLabels

    Character. The name of the condition of interest. Must match a name from sample data.

    -
    depthResolution
    +
    depthResolution

    Numeric. How many different read depth should the script simulate? Will simulate a number of experimental designs ranging from 10 reads to maxReadDepth, with logarithmic spacing.

    -
    iterations
    +
    iterations

    Numeric. How many times should each experimental design be simulated?

    Value

    - - -

    A 3-dimensional array, with dimensions = c(iterations, +

    A 3-dimensional array, with dimensions = c(iterations, depthResolution, 3). [,,1] contains the number of detected genes in each simulated dataset, [,,2] contains the number of significantly differentially expressed genes in each simulation, and [,,3] contains the mediansignificant @@ -308,15 +305,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/expData-ANY-character-method.html b/docs/reference/expData-ANY-character-method.html index 7fe3e6125..6eb6f7f79 100644 --- a/docs/reference/expData-ANY-character-method.html +++ b/docs/reference/expData-ANY-character-method.html @@ -1,12 +1,10 @@ -expData -Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item. — expData,ANY,character-method • singleCellTKexpData Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item. — expData,ANY,character-method • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    expData -Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item.

    +

    expData Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item.

    Source: R/sctkTagging.R
    @@ -213,25 +210,25 @@

    expData

    - 
    # S4 method for ANY,character
+    
    # S4 method for class 'ANY,character'
 expData(inSCE, assayName)

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    assayName
    +
    assayName

    Specify the name of the data item to retrieve.

    Value

    - - -

    Specified data item.

    +

    Specified data item.

    @@ -252,15 +249,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/expData-set-ANY-character-CharacterOrNullOrMissing-logical-method.html b/docs/reference/expData-set-ANY-character-CharacterOrNullOrMissing-logical-method.html index a8c05ec2c..29b3ef38f 100644 --- a/docs/reference/expData-set-ANY-character-CharacterOrNullOrMissing-logical-method.html +++ b/docs/reference/expData-set-ANY-character-CharacterOrNullOrMissing-logical-method.html @@ -1,12 +1,10 @@ -expData -Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item. — expData<-,ANY,character,CharacterOrNullOrMissing,logical-method • singleCellTKexpData Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item. — expData<-,ANY,character,CharacterOrNullOrMissing,logical-method • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    expData -Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item.

    +

    expData Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item.

    Source: R/sctkTagging.R
    @@ -213,37 +210,37 @@

    expData

    - 
    # S4 method for ANY,character,CharacterOrNullOrMissing,logical
+    
    # S4 method for class 'ANY,character,CharacterOrNullOrMissing,logical'
 expData(inSCE, assayName, tag = NULL, altExp = FALSE) <- value

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    assayName
    +
    assayName

    Specify the name of the input assay.

    -
    tag
    +
    tag

    Specify the tag to store against the input assay. Default is NULL, which will set the tag to "uncategorized".

    -
    altExp
    +
    altExp

    A logical value indicating if the input assay is a altExp or a subset assay.

    -
    value
    +
    value

    An input matrix-like value to store in the SCE object.

    Value

    - - -

    A SingleCellExperiment object containing the newly stored data.

    +

    A SingleCellExperiment object containing the newly stored data.

    @@ -265,15 +262,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/expData-set.html b/docs/reference/expData-set.html index 92abe5b48..1b2ed30fa 100644 --- a/docs/reference/expData-set.html +++ b/docs/reference/expData-set.html @@ -1,12 +1,10 @@ -expData -Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item. — expData<- • singleCellTKexpData Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item. — expData<- • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    expData -Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item.

    +

    expData Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item.

    Source: R/sctkTagging.R
    @@ -218,31 +215,31 @@

    expData

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    assayName
    +
    assayName

    Specify the name of the input assay.

    -
    tag
    +
    tag

    Specify the tag to store against the input assay. Default is NULL, which will set the tag to "uncategorized".

    -
    altExp
    +
    altExp

    A logical value indicating if the input assay is a altExp or a subset assay.

    -
    value
    +
    value

    An input matrix-like value to store in the SCE object.

    Value

    - - -

    A SingleCellExperiment object containing the newly stored data.

    +

    A SingleCellExperiment object containing the newly stored data.

    @@ -264,15 +261,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/expData.html b/docs/reference/expData.html index 61ce18e36..0b8a3f694 100644 --- a/docs/reference/expData.html +++ b/docs/reference/expData.html @@ -1,12 +1,10 @@ -expData -Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item. — expData • singleCellTKexpData Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item. — expData • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    expData -Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item.

    +

    expData Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item.

    Source: R/sctkTagging.R
    @@ -218,19 +215,19 @@

    expData

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    assayName
    +
    assayName

    Specify the name of the data item to retrieve.

    Value

    - - -

    Specified data item.

    +

    Specified data item.

    @@ -251,15 +248,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/expDataNames-ANY-method.html b/docs/reference/expDataNames-ANY-method.html index b9aff173c..2b65beaaa 100644 --- a/docs/reference/expDataNames-ANY-method.html +++ b/docs/reference/expDataNames-ANY-method.html @@ -1,12 +1,10 @@ -expDataNames -Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims. — expDataNames,ANY-method • singleCellTKexpDataNames Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims. — expDataNames,ANY-method • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    expDataNames -Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims.

    +

    expDataNames Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims.

    Source: R/sctkTagging.R
    @@ -213,21 +210,21 @@

    expDataNames

    - 
    # S4 method for ANY
+    
    # S4 method for class 'ANY'
 expDataNames(inSCE)

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    Value

    - - -

    A combined vector of assayNames, altExpNames and reducedDimNames.

    +

    A combined vector of assayNames, altExpNames and reducedDimNames.

    @@ -249,15 +246,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/expDataNames.html b/docs/reference/expDataNames.html index 698df79ad..d8e00d4bd 100644 --- a/docs/reference/expDataNames.html +++ b/docs/reference/expDataNames.html @@ -1,12 +1,10 @@ -expDataNames -Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims. — expDataNames • singleCellTKexpDataNames Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims. — expDataNames • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    expDataNames -Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims.

    +

    expDataNames Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims.

    Source: R/sctkTagging.R
    @@ -218,15 +215,15 @@

    expDataNames

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    Value

    - - -

    A combined vector of assayNames, altExpNames and reducedDimNames.

    +

    A combined vector of assayNames, altExpNames and reducedDimNames.

    @@ -248,15 +245,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/expDeleteDataTag.html b/docs/reference/expDeleteDataTag.html index d7d01d4cd..96b838190 100644 --- a/docs/reference/expDeleteDataTag.html +++ b/docs/reference/expDeleteDataTag.html @@ -1,12 +1,10 @@ -expDeleteDataTag -Remove tag against an input data from the stored tag information in the metadata of the input object. — expDeleteDataTag • singleCellTKexpDeleteDataTag Remove tag against an input data from the stored tag information in the metadata of the input object. — expDeleteDataTag • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    expDeleteDataTag -Remove tag against an input data from the stored tag information in the metadata of the input object.

    +

    expDeleteDataTag Remove tag against an input data from the stored tag information in the metadata of the input object.

    Source: R/sctkTagging.R
    @@ -218,19 +215,19 @@

    expDeleteDataTag

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    assay
    +
    assay

    Name of the assay or the data item against which a tag should be removed.

    Value

    - - -

    The input SingleCellExperiment object with tag information removed from the metadata slot.

    +

    The input SingleCellExperiment object with tag information removed from the metadata slot.

    @@ -252,15 +249,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/expSetDataTag.html b/docs/reference/expSetDataTag.html index 7d2944463..8b8e7faa3 100644 --- a/docs/reference/expSetDataTag.html +++ b/docs/reference/expSetDataTag.html @@ -1,12 +1,10 @@ -expSetDataTag -Set tag to an assay or a data item in the input SCE object. — expSetDataTag • singleCellTKexpSetDataTag Set tag to an assay or a data item in the input SCE object. — expSetDataTag • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    expSetDataTag -Set tag to an assay or a data item in the input SCE object.

    +

    expSetDataTag Set tag to an assay or a data item in the input SCE object.

    Source: R/sctkTagging.R
    @@ -218,23 +215,23 @@

    expSetDataTag

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    assayType
    +
    assayType

    Specify a character(1) value as a tag that should be set against a data item.

    -
    assays
    +
    assays

    Specify name(s) character() of data item(s) against which the tag should be set.

    Value

    - - -

    The input SingleCellExperiment object with tag information stored in the metadata slot.

    +

    The input SingleCellExperiment object with tag information stored in the metadata slot.

    @@ -255,15 +252,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/expTaggedData.html b/docs/reference/expTaggedData.html index eed21ed00..b1272db8e 100644 --- a/docs/reference/expTaggedData.html +++ b/docs/reference/expTaggedData.html @@ -1,15 +1,11 @@ -expTaggedData -Returns a list of names of data items from the -input SingleCellExperiment object based upon the input parameters. — expTaggedData • singleCellTKexpTaggedData Returns a list of names of data items from the input SingleCellExperiment object based upon the input parameters. — expTaggedData • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    expTaggedData -Returns a list of names of data items from the -input SingleCellExperiment object based upon the input parameters.

    +

    expTaggedData Returns a list of names of data items from the input SingleCellExperiment object based upon the input parameters.

    Source: R/sctkTagging.R

    expTaggedData -Returns a list of names of data items from the +Returns a list of names of data items from the input SingleCellExperiment object based upon the input parameters.

    @@ -229,37 +223,37 @@

    expTaggedData

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    tags
    -

    A character() value indicating if the data items should -be returned separated by the specified tags. Default is NULL -indicating that returned names of the data items are simply returned as a +

    tags
    +

    A character() value indicating if the data items should +be returned separated by the specified tags. Default is NULL +indicating that returned names of the data items are simply returned as a list with default tag as "uncategorized".

    -
    redDims
    -

    A logical value indicating if reducedDims +

    redDims
    +

    A logical value indicating if reducedDims should be returned as well separated with 'redDims' tag.

    -
    recommended
    -

    A character() vector indicating the tags that +

    +

    A character() vector indicating the tags that should be displayed as recommended. Default is NULL.

    -
    showTags
    -

    A logical value indicating if the tags should be +

    showTags
    +

    A logical value indicating if the tags should be shown. If FALSE, output is just a simple list, not separated by tags.

    Value

    - - -

    A list of names of data items specified by the other +

    A list of names of data items specified by the other parameters.

    @@ -282,15 +276,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/exportSCE.html b/docs/reference/exportSCE.html index 51d60940e..cb5dcbb4d 100644 --- a/docs/reference/exportSCE.html +++ b/docs/reference/exportSCE.html @@ -1,9 +1,9 @@ -Export data in SingleCellExperiment object — exportSCE • singleCellTKExport data in SingleCellExperiment object — exportSCE • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -219,44 +219,44 @@

    Export data in SingleCellExperiment object

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object that contains the data. QC metrics are stored in colData of the singleCellExperiment object.

    -
    samplename
    +
    samplename

    Sample name. This will be used as name of subdirectories and the prefix of flat file output. Default is 'sample'.

    -
    directory
    +
    directory

    Output directory. Default is './'.

    -
    type
    +
    type

    Type of data. The type of data stored in SingleCellExperiment object. It can be 'Droplets'(raw droplets matrix) or 'Cells' (cells matrix).

    -
    format
    +
    format

    The format of output. It currently supports flat files, rds files and python h5 files. It can output multiple formats. Default: c("SCE", "AnnData", "FlatFile", "HTAN").

    Value

    - - -

    Generates a file containing data from inSCE, in specified format.

    +

    Generates a file containing data from inSCE, in specified format.

    Examples

    data(scExample)
-if (FALSE) {
+if (FALSE) { # \dontrun{
 exportSCE(sce, format = "SCE")
-}
+} # }
    @@ -271,15 +271,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/exportSCEToSeurat.html b/docs/reference/exportSCEToSeurat.html index 7a8b87888..6c81dff1d 100644 --- a/docs/reference/exportSCEToSeurat.html +++ b/docs/reference/exportSCEToSeurat.html @@ -1,9 +1,9 @@ -Export data in Seurat object — exportSCEToSeurat • singleCellTKExport data in Seurat object — exportSCEToSeurat • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -221,41 +221,41 @@

    Export data in Seurat object

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object that contains the data. QC metrics are stored in colData of the singleCellExperiment object.

    -
    prefix
    +
    prefix

    Prefix to use for the name of the output file. Default "sample".

    -
    outputDir
    +
    outputDir

    Path to the directory where outputs will be written. Default is the current working directory.

    -
    overwrite
    +
    overwrite

    Boolean. Whether overwrite the output if it already exists in the outputDir. Default TRUE.

    -
    copyColData
    +
    copyColData

    Boolean. Whether copy 'colData' of SCE object to the 'meta.data' of Seurat object. Default TRUE.

    -
    copyReducedDim
    +
    copyReducedDim

    Boolean. Whether copy 'reducedDims' of the SCE object to the 'reductions' of Seurat object. Default TRUE.

    -
    copyDecontX
    +
    copyDecontX

    Boolean. Whether copy 'decontXcounts' assay of the SCE object to the 'assays' of Seurat object. Default TRUE.

    Value

    - - -

    Generates a Seurat object containing data from inSCE.

    +

    Generates a Seurat object containing data from inSCE.

    @@ -270,15 +270,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/exportSCEtoAnnData.html b/docs/reference/exportSCEtoAnnData.html index fbf91182c..6732a98c7 100644 --- a/docs/reference/exportSCEtoAnnData.html +++ b/docs/reference/exportSCEtoAnnData.html @@ -1,7 +1,5 @@ -Export a SingleCellExperiment R object as -Python annData object — exportSCEtoAnnData • singleCellTKExport a SingleCellExperiment R object as Python annData object — exportSCEtoAnnData • singleCellTK - +
    @@ -31,7 +29,7 @@
    - +
    -

    Export a SingleCellExperiment R object as -Python annData object

    +

    Export a SingleCellExperiment R object as Python annData object

    Source: R/exportSCEtoAnndata.R
    @@ -233,56 +230,56 @@

    Export a

    Arguments

    -
    sce
    + + +
    sce

    SingleCellExperiment R object to be exported.

    -
    useAssay
    +
    useAssay

    Character. The name of assay of interests that will be set as the primary matrix of the output AnnData. Default "counts".

    -
    outputDir
    +
    outputDir

    Path to the directory where .h5ad outputs will be written. Default is the current working directory.

    -
    prefix
    +
    prefix

    Prefix to use for the name of the output file. Default "sample".

    -
    overwrite
    +
    overwrite

    Boolean. Default TRUE.

    -
    compression
    +
    compression

    If output file compression is required, this variable accepts 'gzip', 'lzf' or "None" as inputs. Default "gzip".

    -
    compressionOpts
    +
    compressionOpts

    Integer. Sets the compression level

    -
    forceDense
    +
    forceDense

    Default False Write sparse data as a dense matrix. Refer anndata.write_h5ad documentation for details. Default NULL.

    Value

    - - -

    Generates a Python anndata object containing data from inSCE.

    +

    Generates a Python anndata object containing data from inSCE.

    Examples

    data(sce_chcl, package = "scds")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 exportSCEtoAnnData(sce=sce_chcl, compression="gzip")
-}
+} # }
    @@ -297,15 +294,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/exportSCEtoFlatFile.html b/docs/reference/exportSCEtoFlatFile.html index 05ba481df..30893542e 100644 --- a/docs/reference/exportSCEtoFlatFile.html +++ b/docs/reference/exportSCEtoFlatFile.html @@ -1,11 +1,11 @@ -Export a SingleCellExperiment object to flat text files — exportSCEtoFlatFile • singleCellTKExport a SingleCellExperiment object to flat text files — exportSCEtoFlatFile • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -223,43 +223,43 @@

    Export a

    Arguments

    -
    sce
    + + +
    sce

    SingleCellExperiment object to be exported.

    -
    outputDir
    +
    outputDir

    Name of the directory to store the exported file(s).

    -
    overwrite
    +
    overwrite

    Boolean. Whether to overwrite the output files. Default TRUE.

    -
    gzipped
    +
    gzipped

    Boolean. TRUE if the output files are to be gzip compressed. FALSE otherwise. Default TRUE.

    -
    prefix
    +
    prefix

    Prefix of file names.

    Value

    - - -

    Generates text files containing data from inSCE.

    +

    Generates text files containing data from inSCE.

    Examples

    data(sce_chcl, package = "scds")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 exportSCEtoFlatFile(sce_chcl, "sce_chcl")
-}
+} # }
    @@ -274,15 +274,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/featureIndex.html b/docs/reference/featureIndex.html index d02f57cfd..e2fc969c3 100644 --- a/docs/reference/featureIndex.html +++ b/docs/reference/featureIndex.html @@ -1,5 +1,5 @@ -Retrieve row index for a set of features — featureIndex • singleCellTKRetrieve row index for a set of features — featureIndex • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -229,17 +229,19 @@

    Retrieve row index for a set of features

    Arguments

    -
    features
    + + +
    features

    Character vector of feature names to find in the rows of inSCE.

    -
    inSCE
    +
    inSCE

    A data.frame, matrix, or SingleCellExperiment object to search.

    -
    by
    +
    by

    Character. Where to search for features in inSCE. If set to "rownames" then the features will be searched for among rownames(inSCE). If inSCE inherits from class @@ -248,37 +250,35 @@

    Arguments

    colnames(rowData(inSCE))).

    -
    exactMatch
    +
    exactMatch

    Boolean. Whether to only identify exact matches or to identify partial matches using grep.

    -
    removeNA
    +
    removeNA

    Boolean. If set to FALSE, features not found in inSCE will be given NA and the returned vector will be the same length as features. If set to TRUE, then the NA values will be removed from the returned vector. Default FALSE.

    -
    errorOnNoMatch
    +
    errorOnNoMatch

    Boolean. If TRUE, an error will be given if -no matches are found. If FALSE, an empty vector will be returned if -removeNA is set to TRUE or a vector of NA if +no matches are found. If FALSE, an empty vector will be returned if +removeNA is set to TRUE or a vector of NA if removeNA is set to FALSE. Default TRUE.

    -
    warningOnPartialMatch
    +
    warningOnPartialMatch

    Boolean. If TRUE, a warning will be -given if some of the entries in features were not found in +given if some of the entries in features were not found in inSCE. The warning will list the features not found. Default TRUE.

    Value

    - - -

    A vector of row indices for the matching features in inSCE.

    +

    A vector of row indices for the matching features in inSCE.

    See also

    @@ -311,15 +311,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generateHTANMeta.html b/docs/reference/generateHTANMeta.html index 85b971680..88945db76 100644 --- a/docs/reference/generateHTANMeta.html +++ b/docs/reference/generateHTANMeta.html @@ -1,9 +1,9 @@ -Generate HTAN manifest file for droplet and cell count data — generateHTANMeta • singleCellTKGenerate HTAN manifest file for droplet and cell count data — generateHTANMeta • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,37 +220,37 @@

    Generate HTAN manifest file for droplet and cell count data

    Arguments

    -
    dropletSCE
    + + +
    dropletSCE

    A SingleCellExperiment object containing droplet count matrix data

    -
    cellSCE
    +
    cellSCE

    A SingleCellExperiment object containing cell count matrix data

    -
    samplename
    +
    samplename

    The sample name of the SingleCellExperiment objects

    -
    htan_biospecimen_id
    +
    htan_biospecimen_id

    The HTAN biospecimen id of the sample in SingleCellExperiment object

    -
    dir
    +
    dir

    The output directory of the SCTK QC pipeline.

    -
    dataType
    +
    dataType

    Type of the input data. It can be one of "Droplet", "Cell" or "Both".

    Value

    - - -

    A SingleCellExperiment object which combines all +

    A SingleCellExperiment object which combines all objects in sceList. The colData is merged.

    @@ -266,15 +266,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generateMeta.html b/docs/reference/generateMeta.html index ece3635ff..6536d74b3 100644 --- a/docs/reference/generateMeta.html +++ b/docs/reference/generateMeta.html @@ -1,9 +1,9 @@ -Generate HTAN manifest file for droplet and cell count data — generateMeta • singleCellTKGenerate HTAN manifest file for droplet and cell count data — generateMeta • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,38 +220,38 @@

    Generate HTAN manifest file for droplet and cell count data

    Arguments

    -
    dropletSCE
    + + +
    dropletSCE

    A SingleCellExperiment object containing droplet count matrix data

    -
    cellSCE
    +
    cellSCE

    A SingleCellExperiment object containing cell count matrix data

    -
    samplename
    +
    samplename

    The sample name of the SingleCellExperiment objects

    -
    dir
    +
    dir

    The output directory of the SCTK QC pipeline.

    -
    HTAN
    -

    Whether generates manifest file including HTAN specific ID (HTAN Biospecimen ID, +

    HTAN
    +

    Whether generates manifest file including HTAN specific ID (HTAN Biospecimen ID, HTAN parent file ID and HTAN patient ID). Default is TRUE.

    -
    dataType
    +
    dataType

    Type of the input data. It can be one of "Droplet", "Cell" or "Both".

    Value

    - - -

    A SingleCellExperiment object which combines all +

    A SingleCellExperiment object which combines all objects in sceList. The colData is merged.

    @@ -267,15 +267,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/generateSimulatedData.html b/docs/reference/generateSimulatedData.html index b652021c2..b7756f360 100644 --- a/docs/reference/generateSimulatedData.html +++ b/docs/reference/generateSimulatedData.html @@ -1,12 +1,10 @@ -Generates a single simulated dataset, bootstrapping from the input counts -matrix. — generateSimulatedData • singleCellTKGenerates a single simulated dataset, bootstrapping from the input counts matrix. — generateSimulatedData • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    Generates a single simulated dataset, bootstrapping from the input counts -matrix.

    +

    Generates a single simulated dataset, bootstrapping from the input counts matrix.

    Source: R/DownsampleMatrix.R
    @@ -218,21 +215,23 @@

    Generates a single simulated dataset, bootstrapping from the input counts

    Arguments

    -
    totalReads
    + + +
    totalReads

    Numeric. The total number of reads in the simulated dataset, to be split between all simulated cells.

    -
    cells
    +
    cells

    Numeric. The number of virtual cells to simulate.

    -
    originalData
    +
    originalData

    Matrix. The original raw read count matrix. When used within the Shiny app, this will be assay(SCEsetObject, "counts").

    -
    realLabels
    +
    realLabels

    Factor. The condition labels for differential expression. If only two factors present, will default to t-test. If multiple factors, will default to ANOVA.

    @@ -240,9 +239,7 @@

    Arguments

    Value

    - - -

    A simulated counts matrix, the first row of which contains the 'true' +

    A simulated counts matrix, the first row of which contains the 'true' labels for each virtual cell.

    @@ -268,15 +265,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getBiomarker.html b/docs/reference/getBiomarker.html index 234867ee4..69eced5d5 100644 --- a/docs/reference/getBiomarker.html +++ b/docs/reference/getBiomarker.html @@ -1,12 +1,10 @@ -Given a list of genes and a SingleCellExperiment object, return -the binary or continuous expression of the genes. — getBiomarker • singleCellTKGiven a list of genes and a SingleCellExperiment object, return the binary or continuous expression of the genes. — getBiomarker • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    Given a list of genes and a SingleCellExperiment object, return -the binary or continuous expression of the genes.

    +

    Given a list of genes and a SingleCellExperiment object, return the binary or continuous expression of the genes.

    Source: R/getBiomarker.R
    @@ -225,37 +222,37 @@

    Given a list of genes and a SingleCellExperiment object, return

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    gene
    +
    gene

    gene list

    -
    binary
    +
    binary

    "Binary" for binary expression or "Continuous" for a gradient. Default: "Binary"

    -
    useAssay
    +
    useAssay

    Indicates which assay to use. The default is "counts".

    -
    featureLocation
    +
    featureLocation

    Indicates which column name of rowData to query gene.

    -
    featureDisplay
    +
    featureDisplay

    Indicates which column name of rowData to use to display feature for visualization.

    Value

    - - -

    getBiomarker(): A data.frame of expression values

    +

    getBiomarker(): A data.frame of expression values

    @@ -308,15 +305,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getDEGTopTable.html b/docs/reference/getDEGTopTable.html index 2769dd67a..d5ad5fe5e 100644 --- a/docs/reference/getDEGTopTable.html +++ b/docs/reference/getDEGTopTable.html @@ -1,12 +1,12 @@ -Get Top Table of a DEG analysis — getDEGTopTable • singleCellTKGet Top Table of a DEG analysis — getDEGTopTable • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -230,63 +230,63 @@

    Get Top Table of a DEG analysis

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object, with of the singleCellTK DEG method performed in advance.

    -
    useResult
    +
    useResult

    character. A string specifying the analysisName used when running a differential expression analysis function.

    -
    labelBy
    +
    labelBy

    A single character for a column of rowData(inSCE) as where to search for the labeling text. Leave NULL for rownames. Default metadata(inSCE)$featureDisplay (see setSCTKDisplayRow).

    -
    onlyPos
    +
    onlyPos

    logical. Whether to only fetch DEG with positive log2_FC value. Default FALSE.

    -
    log2fcThreshold
    +
    log2fcThreshold

    numeric. Only fetch DEGs with the absolute values of log2FC larger than this value. Default 0.25.

    -
    fdrThreshold
    +
    fdrThreshold

    numeric. Only fetch DEGs with FDR value smaller than this value. Default 0.05.

    -
    minGroup1MeanExp
    +
    minGroup1MeanExp

    numeric. Only fetch DEGs with mean expression in group1 greater then this value. Default NULL.

    -
    maxGroup2MeanExp
    +
    maxGroup2MeanExp

    numeric. Only fetch DEGs with mean expression in group2 less then this value. Default NULL.

    -
    minGroup1ExprPerc
    +
    minGroup1ExprPerc

    numeric. Only fetch DEGs expressed in greater then this fraction of cells in group1. Default NULL.

    -
    maxGroup2ExprPerc
    +
    maxGroup2ExprPerc

    numeric. Only fetch DEGs expressed in less then this fraction of cells in group2. Default NULL.

    Value

    - - -

    A data.frame object of the top DEGs, with variables of +

    A data.frame object of the top DEGs, with variables of Gene, Log2_FC, Pvalue, and FDR.

    @@ -299,7 +299,7 @@

    Examples

    classGroup1 = "alpha", classGroup2 = "beta", groupName1 = "w.alpha", groupName2 = "w.beta", analysisName = "w.aVSb") -#> Fri May 3 07:14:21 2024 ... Running DE with wilcox, Analysis name: w.aVSb +#> Thu Feb 13 10:27:26 2025 ... Running DE with wilcox, Analysis name: w.aVSb getDEGTopTable(sce.w, "w.aVSb") #> Gene Log2_FC Pvalue FDR group1MeanExp #> 2 GCG 9.1517909 2.368614e-19 4.737227e-18 18.2513675 @@ -431,15 +431,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getDiffAbundanceResults.html b/docs/reference/getDiffAbundanceResults.html index 3c996e1d7..a65f540ab 100644 --- a/docs/reference/getDiffAbundanceResults.html +++ b/docs/reference/getDiffAbundanceResults.html @@ -1,9 +1,9 @@ -Get/Set diffAbundanceFET result table — getDiffAbundanceResults • singleCellTKGet/Set diffAbundanceFET result table — getDiffAbundanceResults • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -210,36 +210,36 @@

    Get/Set diffAbundanceFET result table

    getDiffAbundanceResults(x, analysisName)
 
-# S4 method for SingleCellExperiment
+# S4 method for class 'SingleCellExperiment'
 getDiffAbundanceResults(x, analysisName)
 
 getDiffAbundanceResults(x, analysisName) <- value
 
-# S4 method for SingleCellExperiment
+# S4 method for class 'SingleCellExperiment'
 getDiffAbundanceResults(x, analysisName) <- value

    Arguments

    -
    x
    + + +
    x

    A SingleCellExperiment object.

    -
    analysisName
    -

    A single character string specifying an analysis +

    analysisName
    +

    A single character string specifying an analysis performed with diffAbundanceFET

    -
    value
    +
    value

    The output table of diffAbundanceFET

    Value

    - - -

    The differential abundance table for getter method, or update the SCE +

    The differential abundance table for getter method, or update the SCE object with new result for setter method.

    @@ -267,15 +267,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getEnrichRResult.html b/docs/reference/getEnrichRResult.html index 7912077c8..25e0a6267 100644 --- a/docs/reference/getEnrichRResult.html +++ b/docs/reference/getEnrichRResult.html @@ -1,9 +1,9 @@ -Get or Set EnrichR Result — getEnrichRResult<- • singleCellTKGet or Set EnrichR Result — getEnrichRResult<- • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -212,32 +212,32 @@

    Get or Set EnrichR Result

    getEnrichRResult(inSCE, analysisName) -# S4 method for SingleCellExperiment +# S4 method for class 'SingleCellExperiment' getEnrichRResult(inSCE, analysisName) -# S4 method for SingleCellExperiment +# S4 method for class 'SingleCellExperiment' getEnrichRResult(inSCE, analysisName) <- value

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    analysisName
    +
    analysisName

    A string that identifies each specific analysis

    -
    value
    +
    value

    The EnrichR result table

    Value

    - - -

    For getter method, a data.frame of the EnrichR result; +

    For getter method, a data.frame of the EnrichR result; For setter method, inSCE with EnrichR results updated.

    @@ -255,7 +255,7 @@

    Examples

    result <- getEnrichRResult(mouseBrainSubsetSCE, "analysis1") } #> Welcome to enrichR -#> Checking connection ... +#> Checking connections ... #> Enrichr ... #> Connection is Live! #> FlyEnrichr ... @@ -285,15 +285,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getFindMarkerTopTable.html b/docs/reference/getFindMarkerTopTable.html index 0592b2c8a..d9e6f139f 100644 --- a/docs/reference/getFindMarkerTopTable.html +++ b/docs/reference/getFindMarkerTopTable.html @@ -1,9 +1,9 @@ -Fetch the table of top markers that pass the filtering — getFindMarkerTopTable • singleCellTKFetch the table of top markers that pass the filtering — getFindMarkerTopTable • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -231,38 +231,40 @@

    Fetch the table of top markers that pass the filtering

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    log2fcThreshold
    +
    log2fcThreshold

    Only use DEGs with the absolute values of log2FC larger than this value. Default 1

    -
    fdrThreshold
    +
    fdrThreshold

    Only use DEGs with FDR value smaller than this value. Default 0.05

    -
    minClustExprPerc
    +
    minClustExprPerc

    A numeric scalar. The minimum cutoff of the percentage of cells in the cluster of interests that expressed the marker gene. Default 0.7.

    -
    maxCtrlExprPerc
    +
    maxCtrlExprPerc

    A numeric scalar. The maximum cutoff of the percentage of cells out of the cluster (control group) that expressed the marker gene. Default 0.4.

    -
    minMeanExpr
    +
    minMeanExpr

    A numeric scalar. The minimum cutoff of the mean expression value of the marker in the cluster of interests. Default 1.

    -
    topN
    +
    topN

    An integer. Only to fetch this number of top markers for each cluster in maximum, in terms of log2FC value. Use NULL to cancel the top N subscription. Default 10.

    @@ -270,9 +272,7 @@

    Arguments

    Value

    - - -

    An organized data.frame object, with the top marker gene +

    An organized data.frame object, with the top marker gene information.

    @@ -291,9 +291,9 @@

    Examples

    mouseBrainSubsetSCE <- runFindMarker(mouseBrainSubsetSCE, useAssay = "logcounts", cluster = "level1class") -#> Fri May 3 07:14:25 2024 ... Identifying markers for cluster 'microglia', using DE method 'wilcox' -#> Fri May 3 07:14:26 2024 ... Identifying markers for cluster 'oligodendrocytes', using DE method 'wilcox' -#> Fri May 3 07:14:27 2024 ... Organizing findMarker result +#> Thu Feb 13 10:27:36 2025 ... Identifying markers for cluster 'microglia', using DE method 'wilcox' +#> Thu Feb 13 10:27:37 2025 ... Identifying markers for cluster 'oligodendrocytes', using DE method 'wilcox' +#> Thu Feb 13 10:27:37 2025 ... Organizing findMarker result getFindMarkerTopTable(mouseBrainSubsetSCE) #> Gene Log2_FC Pvalue FDR level1class clusterExprPerc #> 1228 Apoe 4.439115 3.642815e-06 0.0001796628 microglia 1 @@ -315,15 +315,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getGenesetNamesFromCollection.html b/docs/reference/getGenesetNamesFromCollection.html index afdfaba88..8b5edac50 100644 --- a/docs/reference/getGenesetNamesFromCollection.html +++ b/docs/reference/getGenesetNamesFromCollection.html @@ -1,9 +1,9 @@ -List geneset names from geneSetCollection — getGenesetNamesFromCollection • singleCellTKList geneset names from geneSetCollection — getGenesetNamesFromCollection • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,19 +213,19 @@

    List geneset names from geneSetCollection

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    geneSetCollectionName
    +
    geneSetCollectionName

    The name of an imported geneSetCollection.

    Value

    - - -

    A character vector of available genesets from the collection.

    +

    A character vector of available genesets from the collection.

    @@ -240,15 +240,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getMSigDBTable.html b/docs/reference/getMSigDBTable.html index 20b5b2661..ef65caf99 100644 --- a/docs/reference/getMSigDBTable.html +++ b/docs/reference/getMSigDBTable.html @@ -1,11 +1,11 @@ -Shows MSigDB categories — getMSigDBTable • singleCellTKShows MSigDB categories — getMSigDBTable • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -217,9 +217,7 @@

    Shows MSigDB categories

    Value

    - - -

    data.frame, containing MSigDB categories

    +

    data.frame, containing MSigDB categories

    See also

    @@ -301,15 +299,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getPathwayResultNames.html b/docs/reference/getPathwayResultNames.html index 648911b82..a0f8ae027 100644 --- a/docs/reference/getPathwayResultNames.html +++ b/docs/reference/getPathwayResultNames.html @@ -1,9 +1,9 @@ -List pathway analysis result names — getPathwayResultNames • singleCellTKList pathway analysis result names — getPathwayResultNames • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,24 +213,24 @@

    List pathway analysis result names

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    stopIfNone
    +
    stopIfNone

    Whether to stop and raise an error if no results found. If FALSE, will return an empty character vector.

    -
    verbose
    +
    verbose

    Show warning if no result found. Default FALSE

    Value

    - - -

    A character vector of valid pathway analysis result names.

    +

    A character vector of valid pathway analysis result names.

    Details

    @@ -258,15 +258,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getSampleSummaryStatsTable.html b/docs/reference/getSampleSummaryStatsTable.html index 232003eeb..32f3ea1bd 100644 --- a/docs/reference/getSampleSummaryStatsTable.html +++ b/docs/reference/getSampleSummaryStatsTable.html @@ -1,10 +1,10 @@ -Stores and returns table of SCTK QC outputs to metadata. — getSampleSummaryStatsTable • singleCellTKStores and returns table of SCTK QC outputs to metadata. — getSampleSummaryStatsTable • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -214,42 +214,42 @@

    Stores and returns table of SCTK QC outputs to metadata.

    setSampleSummaryStatsTable(inSCE, statsName, ...) <- value -# S4 method for SingleCellExperiment +# S4 method for class 'SingleCellExperiment' getSampleSummaryStatsTable(inSCE, statsName, ...) -# S4 method for SingleCellExperiment +# S4 method for class 'SingleCellExperiment' setSampleSummaryStatsTable(inSCE, statsName, ...) <- value

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved assay data and/or colData data. Required.

    -
    statsName
    +
    statsName

    A character value indicating the slot that stores the stats table within the metadata of the SingleCellExperiment object. Required.

    -
    ...
    +
    ...

    Other arguments passed to the function.

    -
    value
    +
    value

    The summary table for QC statistics generated from SingleCellTK to be added to the SCE object.

    Value

    - - -

    For getSampleSummaryStatsTable, A matrix/array object. +

    For getSampleSummaryStatsTable, A matrix/array object. Contains a summary table for QC statistics generated from SingleCellTK. For -setSampleSummaryStatsTable<-, A SingleCellExperiment object where the +setSampleSummaryStatsTable<-, A SingleCellExperiment object where the summary table is updated in the metadata slot.

    @@ -279,15 +279,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getSceParams.html b/docs/reference/getSceParams.html index 0d39a704d..40d1f2eb7 100644 --- a/docs/reference/getSceParams.html +++ b/docs/reference/getSceParams.html @@ -1,9 +1,9 @@ -Extract QC parameters from the SingleCellExperiment object — getSceParams • singleCellTKExtract QC parameters from the SingleCellExperiment object — getSceParams • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -222,36 +222,36 @@

    Extract QC parameters from the SingleCellExperiment object

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    skip
    +
    skip

    Skip extracting the parameters of the provided QC functions.

    -
    ignore
    +
    ignore

    Skip extracting the content within QC functions.

    -
    directory
    +
    directory

    The output directory of the SCTK_runQC.R pipeline.

    -
    samplename
    +
    samplename

    The sample name of the SingleCellExperiment objects.

    -
    writeYAML
    +
    writeYAML

    Whether output yaml file to store parameters. Default if TRUE. If FALSE, return character object.

    Value

    - - -

    If writeYAML TRUE, a yaml object will be generated. If FALSE, character object.

    +

    If writeYAML TRUE, a yaml object will be generated. If FALSE, character object.

    @@ -266,15 +266,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getSeuratVariableFeatures.html b/docs/reference/getSeuratVariableFeatures.html index 5d2793226..35df1d9c5 100644 --- a/docs/reference/getSeuratVariableFeatures.html +++ b/docs/reference/getSeuratVariableFeatures.html @@ -1,9 +1,9 @@ -Get variable feature names after running runSeuratFindHVG function — getSeuratVariableFeatures • singleCellTKGet variable feature names after running runSeuratFindHVG function — getSeuratVariableFeatures • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,15 +213,15 @@

    Get variable feature names after running runSeuratFindHVG function

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    Value

    - - -

    A list of variable feature names.

    +

    A list of variable feature names.

    @@ -236,15 +236,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getSoupX.html b/docs/reference/getSoupX.html index 7cd2f1120..eced3a895 100644 --- a/docs/reference/getSoupX.html +++ b/docs/reference/getSoupX.html @@ -1,12 +1,12 @@ -Get or Set SoupX Result — getSoupX<- • singleCellTKGet or Set SoupX Result — getSoupX<- • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -218,43 +218,41 @@

    Get or Set SoupX Result

    getSoupX(inSCE, sampleID = NULL, background = FALSE) -# S4 method for SingleCellExperiment +# S4 method for class 'SingleCellExperiment' getSoupX(inSCE, sampleID = NULL, background = FALSE) -# S4 method for SingleCellExperiment +# S4 method for class 'SingleCellExperiment' getSoupX(inSCE, sampleID, background = FALSE) <- value

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object. For getter method, runSoupX must have been already applied.

    -
    sampleID
    +
    sampleID

    Character vector. For getter method, the samples that should be included in the returned list. Leave this NULL for all samples. Default NULL. For setter method, only one sample allowed.

    -
    background
    +
    background

    Logical. Whether background was applied when running runSoupX. Default FALSE.

    -
    value
    +
    value

    Dedicated list object of SoupX results.

    Value

    - - -

    For getter method, a list with SoupX results for specified samples. +

    For getter method, a list with SoupX results for specified samples. For setter method, inSCE with SoupX results updated.

    - -

    For getter method, a list with SoupX results for specified samples. For setter method, inSCE with SoupX results updated.

    @@ -265,11 +263,11 @@

    See also

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 sce <- importExampleData("pbmc3k")
 sce <- runSoupX(sce, sample = "sample")
 soupXResults <- getSoupX(sce)
-}
+} # }
    @@ -284,15 +282,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getTSCANResults.html b/docs/reference/getTSCANResults.html index d00d34cd4..435dcf4af 100644 --- a/docs/reference/getTSCANResults.html +++ b/docs/reference/getTSCANResults.html @@ -1,10 +1,10 @@ -getTSCANResults accessor function — getTSCANResults • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -212,50 +212,50 @@

    getTSCANResults accessor function

    getTSCANResults(x, analysisName = NULL, pathName = NULL)
 
-# S4 method for SingleCellExperiment
+# S4 method for class 'SingleCellExperiment'
 getTSCANResults(x, analysisName = NULL, pathName = NULL)
 
 getTSCANResults(x, analysisName, pathName = NULL) <- value
 
-# S4 method for SingleCellExperiment
+# S4 method for class 'SingleCellExperiment'
 getTSCANResults(x, analysisName, pathName = NULL) <- value
 
 listTSCANResults(x)
 
-# S4 method for SingleCellExperiment
+# S4 method for class 'SingleCellExperiment'
 listTSCANResults(x)
 
 listTSCANTerminalNodes(x)
 
-# S4 method for SingleCellExperiment
+# S4 method for class 'SingleCellExperiment'
 listTSCANTerminalNodes(x)

    Arguments

    -
    x
    + + +
    x

    Input SingleCellExperiment object.

    -
    analysisName
    +
    analysisName

    Algorithm name implemented, should be one of "Pseudotime", "DEG", or "ClusterDEAnalysis".

    -
    pathName
    +
    pathName

    Sub folder name within the analysisName. See details.

    -
    value
    +
    value

    Value to be stored within the pathName or analysisName

    Value

    - - -

    Get or set TSCAN results

    +

    Get or set TSCAN results

    Details

    @@ -276,15 +276,15 @@

    Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
 mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                 useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:14:30 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:14:31 2024 ...   Identified 2 clusters
-#> Fri May  3 07:14:31 2024 ... Running TSCAN to estimate pseudotime
+#> Thu Feb 13 10:27:40 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:27:41 2025 ...   Identified 2 clusters
+#> Thu Feb 13 10:27:41 2025 ... Running TSCAN to estimate pseudotime
 #> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
 #> Also defined by ‘spam’
 #> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
 #> Also defined by ‘spam’
-#> Fri May  3 07:14:32 2024 ...   Clusters involved in path index 2 are: 1, 2
-#> Fri May  3 07:14:32 2024 ...   Number of estimated paths is 1
+#> Thu Feb 13 10:27:41 2025 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:27:41 2025 ...   Number of estimated paths is 1
 results <- getTSCANResults(mouseBrainSubsetSCE, "Pseudotime")
    @@ -300,15 +300,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/getTopHVG.html b/docs/reference/getTopHVG.html index 2b03d30fc..da2ebbfbf 100644 --- a/docs/reference/getTopHVG.html +++ b/docs/reference/getTopHVG.html @@ -1,5 +1,5 @@ -Get or set top HVG after calculation — getTopHVG • singleCellTKGet or set top HVG after calculation — getTopHVG • singleCellTK - +
    @@ -32,7 +32,7 @@
    - +
    @@ -245,52 +245,54 @@

    Get or set top HVG after calculation

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    method
    +
    method

    Specify which method to use for variable gene extraction from Seurat "vst", "mean.var.plot", "dispersion" or -Scran "modelGeneVar" or Scanpy "seurat", "cell_ranger", +Scran "modelGeneVar" or Scanpy "seurat", "cell_ranger", "seurat_v3". Default "vst"

    -
    hvgNumber
    +
    hvgNumber

    Specify the number of top variable genes to extract.

    -
    useFeatureSubset
    +
    useFeatureSubset

    Get the feature names in the HVG list set by setTopHVG. method and hvgNumber will not be used if not this is not NULL. Default "hvf".

    -
    featureDisplay
    +
    featureDisplay

    A character string for the rowData variable name to indicate what type of feature ID should be displayed. If set by setSCTKDisplayRow, will by default use it. If NULL, will use rownames(inSCE).

    -
    featureSubsetName
    +
    featureSubsetName

    A character string for the rowData variable name to store a logical index of selected features. Default "hvg2000".

    -
    genes
    +
    genes

    A customized character vector of gene list to be set as a rowData variable. Will ignore method and hvgNumber if set. Default NULL.

    -
    genesBy
    +
    genesBy

    If setting customized genes, where should it be found in rowData? Leave NULL for matching rownames. Default NULL.

    -
    altExp
    +
    altExp

    TRUE for also creating a subset inSCE object with the selected HVGs and store this subset in the altExps slot, named by hvgListName. Default FALSE.

    @@ -298,7 +300,9 @@

    Arguments

    Value

    -
    getTopHVG
    + + +
    getTopHVG

    A character vector of the top hvgNumber variable feature names

    @@ -327,7 +331,7 @@

    Examples

    sce <- runSeuratFindHVG(sce, method = "vst", hvgNumber = 2000, createFeatureSubset = "hvf") #> Finding variable features for layer counts -#> Fri May 3 07:14:33 2024 ... Feature subset variable 'hvf' created. +#> Thu Feb 13 10:27:42 2025 ... Feature subset variable 'hvf' created. # Get the list of genes for a feature subset: hvgs <- getTopHVG(sce, useFeatureSubset = "hvf") @@ -335,7 +339,7 @@

    Examples

    # Create a new feature subset on the fly without rerunning the algorithm: sce <- setTopHVG(sce, method = "vst", hvgNumber = 100, featureSubsetName = "hvf100") -#> Fri May 3 07:14:33 2024 ... Feature subset variable 'hvf100' created. +#> Thu Feb 13 10:27:42 2025 ... Feature subset variable 'hvf100' created. hvgs <- getTopHVG(sce, useFeatureSubset = "hvf100") # Get a list of variable features without creating a new feature subset: @@ -356,15 +360,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importAlevin.html b/docs/reference/importAlevin.html index c6a7424a5..ef9de765d 100644 --- a/docs/reference/importAlevin.html +++ b/docs/reference/importAlevin.html @@ -1,9 +1,9 @@ -Construct SCE object from Salmon-Alevin output — importAlevin • singleCellTKConstruct SCE object from Salmon-Alevin output — importAlevin • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -219,41 +219,41 @@

    Construct SCE object from Salmon-Alevin output

    Arguments

    -
    alevinDir
    + + +
    alevinDir

    Character. The output directory of salmon-Alevin pipeline. It should contain subfolder named 'alevin', which contains the count data which is stored in 'quants_mat.gz'. Default NULL.

    -
    sampleName
    +
    sampleName

    Character. A user-defined sample name for the sample to be imported. The 'sampleName' will be appended to the begining of cell barcodes. Default is 'sample'.

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Default +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object containing the count +

    A SingleCellExperiment object containing the count matrix, the feature annotations, and the cell annotation (which includes QC metrics stored in 'featureDump.txt').

    @@ -270,15 +270,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importAnnData.html b/docs/reference/importAnnData.html index 6935daaf8..da9549ddc 100644 --- a/docs/reference/importAnnData.html +++ b/docs/reference/importAnnData.html @@ -1,11 +1,11 @@ -Create a SingleCellExperiment Object from Python AnnData .h5ad files — importAnnData • singleCellTKCreate a SingleCellExperiment Object from Python AnnData .h5ad files — importAnnData • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -223,7 +223,9 @@

    Create a SingleCellExperiment Object from Python AnnData .h5ad files

    Arguments

    -
    sampleDirs
    + + +
    sampleDirs

    Folder containing the .h5ad file. Can be one of -

    • Default current working directory.

    • Full path to the directory containing the .h5ad file. E.g sampleDirs = '/path/to/sample'

      • @@ -234,7 +236,7 @@

      Arguments

    -
    sampleNames
    +
    sampleNames

    The prefix/name of the .h5ad file without the .h5ad extension e.g. if 'sample.h5ad' is the filename, pass sampleNames = 'sample'. Can be one of -

    • Default sample.

      • @@ -245,28 +247,26 @@

      Arguments

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object. Default FALSE.

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Default +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object.

    +

    A SingleCellExperiment object.

    Details

    @@ -287,10 +287,10 @@

    Details

    Examples

    file.path <- system.file("extdata/annData_pbmc_3k", package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- importAnnData(sampleDirs = file.path,
                      sampleNames = 'pbmc3k_20by20')
-}
+} # }
    @@ -305,15 +305,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importBUStools.html b/docs/reference/importBUStools.html index c89cfd3ae..bdaf5faf5 100644 --- a/docs/reference/importBUStools.html +++ b/docs/reference/importBUStools.html @@ -1,12 +1,12 @@ -Construct SCE object from BUStools output — importBUStools • singleCellTKConstruct SCE object from BUStools output — importBUStools • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -229,34 +229,36 @@

    Construct SCE object from BUStools output

    Arguments

    -
    BUStoolsDirs
    + + +
    BUStoolsDirs

    A vector of paths to BUStools output files. Each sample should have its own path. For example: ./genecount. Must have the same length as samples.

    -
    samples
    +
    samples

    A vector of user-defined sample names for the samples to be imported. Must have the same length as BUStoolsDirs.

    -
    matrixFileNames
    +
    matrixFileNames

    Filenames for the Market Exchange Format (MEX) sparse matrix files (.mtx files). Must have length 1 or the same length as samples.

    -
    featuresFileNames
    +
    featuresFileNames

    Filenames for the feature annotation files. Must have length 1 or the same length as samples.

    -
    barcodesFileNames
    +
    barcodesFileNames

    Filenames for the cell barcode list file. Must have length 1 or the same length as samples.

    -
    gzipped
    +
    gzipped

    Boolean. TRUE if the BUStools output files (barcodes.txt, genes.txt, and genes.mtx) were gzip compressed. FALSE otherwise. This is FALSE in BUStools @@ -265,28 +267,26 @@

    Arguments

    samples.

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray-class object or not. Default FALSE.

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Default +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object containing the count +

    A SingleCellExperiment object containing the count matrix, the gene annotation, and the cell annotation.

    @@ -331,15 +331,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importCellRanger.html b/docs/reference/importCellRanger.html index d834e9456..f4b8ca1a7 100644 --- a/docs/reference/importCellRanger.html +++ b/docs/reference/importCellRanger.html @@ -1,12 +1,12 @@ -Construct SCE object from Cell Ranger output — importCellRanger • singleCellTKConstruct SCE object from Cell Ranger output — importCellRanger • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -254,14 +254,16 @@

    Construct SCE object from Cell Ranger output

    Arguments

    -
    cellRangerDirs
    + + +
    cellRangerDirs

    The root directories where Cell Ranger was run. These folders should contain sample specific folders. Default NULL, meaning the paths for each sample will be specified in samples argument.

    -
    sampleDirs
    +
    sampleDirs

    Default NULL. Can be one of

    • NULL. All samples within cellRangerDirs will be imported. The order of samples will be first determined by the order of cellRangerDirs and then by list.dirs. This is only @@ -277,7 +279,7 @@

      Arguments

      sampleDirs.

    -
    sampleNames
    +
    sampleNames

    A vector of user-defined sample names for the samples to be imported. Must have the same length as length(unlist(sampleDirs)) if @@ -287,7 +289,7 @@

    Arguments

    NULL, in which case the folder names will be used as sample names.

    -
    cellRangerOuts
    +
    cellRangerOuts

    Character vector. The intermediate paths to filtered or raw cell barcode, feature, and matrix files for each sample. Supercedes dayaType. If NULL, @@ -306,7 +308,7 @@

    Arguments

    "outs/filtered_gene_bc_matrix/", "outs/raw_gene_bc_matrix/".

    -
    dataType
    +
    dataType

    Character. The type of data to import. Can be one of "filtered" (which is equivalent to cellRangerOuts = "outs/filtered_feature_bc_matrix/" or @@ -317,7 +319,7 @@

    Arguments

    "filtered" which imports the counts for filtered cell barcodes only.

    -
    matrixFileNames
    +
    matrixFileNames

    Character vector. Filenames for the Market Exchange Format (MEX) sparse matrix files (matrix.mtx or matrix.mtx.gz files). Must have length 1 or the same @@ -327,7 +329,7 @@

    Arguments

    unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)).

    -
    featuresFileNames
    +
    featuresFileNames

    Character vector. Filenames for the feature annotation files. They are usually named features.tsv.gz or genes.tsv. Must have length 1 or the same @@ -337,7 +339,7 @@

    Arguments

    unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)).

    -
    barcodesFileNames
    +
    barcodesFileNames

    Character vector. Filename for the cell barcode list files. They are usually named barcodes.tsv.gz or barcodes.tsv. Must have length 1 or the same @@ -347,7 +349,7 @@

    Arguments

    unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)).

    -
    gzipped
    +
    gzipped

    TRUE if the Cell Ranger output files (barcodes.tsv, features.tsv, and matrix.mtx) were gzip compressed. FALSE otherwise. This is true after Cell Ranger @@ -360,24 +362,24 @@

    Arguments

    unlist(lapply(cellRangerDirs, list.dirs, recursive = FALSE)).

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Default +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Default TRUE.

    -
    dataTypeV2
    +
    dataTypeV2

    Character. The type of output to import for Cellranger version below 3.0.0. Whether to import the filtered or the raw data. Can be one of 'filtered' or 'raw'. Default 'filtered'. When @@ -385,7 +387,7 @@

    Arguments

    be ignored.

    -
    reference
    +
    reference

    Character vector. The reference genome names. Default NULL. If not NULL, it must gave the length and order as length(unlist(sampleDirs)) if sampleDirs is not NULL. @@ -394,7 +396,7 @@

    Arguments

    for Cellranger version below 3.0.0.

    -
    cellRangerOutsV2
    +
    cellRangerOutsV2

    Character vector. The intermediate paths to filtered or raw cell barcode, feature, and matrix files for each sample for Cellranger version below 3.0.0. If NULL, reference and @@ -405,9 +407,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object containing the combined count +

    A SingleCellExperiment object containing the combined count matrix, the feature annotations, and the cell annotation.

    @@ -472,15 +472,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importCellRangerV2Sample.html b/docs/reference/importCellRangerV2Sample.html index 914aacf2b..01cfa4c9e 100644 --- a/docs/reference/importCellRangerV2Sample.html +++ b/docs/reference/importCellRangerV2Sample.html @@ -1,11 +1,11 @@ -Construct SCE object from Cell Ranger V2 output for a single sample — importCellRangerV2Sample • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -223,37 +223,37 @@

    Construct SCE object from Cell Ranger V2 output for a single sample

    Arguments

    -
    dataDir
    + + +
    dataDir

    A path to the directory containing the data files. Default "./".

    -
    sampleName
    +
    sampleName

    A User-defined sample name. This will be prepended to all cell barcode IDs. Default "sample".

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Default +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object containing the count +

    A SingleCellExperiment object containing the count matrix, the feature annotations, and the cell annotation for the sample.

    @@ -278,15 +278,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importCellRangerV3Sample.html b/docs/reference/importCellRangerV3Sample.html index ebd98df26..8eb5ca59f 100644 --- a/docs/reference/importCellRangerV3Sample.html +++ b/docs/reference/importCellRangerV3Sample.html @@ -1,11 +1,11 @@ -Construct SCE object from Cell Ranger V3 output for a single sample — importCellRangerV3Sample • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -223,37 +223,37 @@

    Construct SCE object from Cell Ranger V3 output for a single sample

    Arguments

    -
    dataDir
    + + +
    dataDir

    A path to the directory containing the data files. Default "./".

    -
    sampleName
    +
    sampleName

    A User-defined sample name. This will be prepended to all cell barcode IDs. Default "sample".

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Default +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object containing the count +

    A SingleCellExperiment object containing the count matrix, the feature annotations, and the cell annotation for the sample.

    @@ -278,15 +278,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importDropEst.html b/docs/reference/importDropEst.html index 234f70bb6..1dfba4d85 100644 --- a/docs/reference/importDropEst.html +++ b/docs/reference/importDropEst.html @@ -1,12 +1,12 @@ -Create a SingleCellExperiment Object from DropEst output — importDropEst • singleCellTKCreate a SingleCellExperiment Object from DropEst output — importDropEst • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -227,45 +227,45 @@

    Create a SingleCellExperiment Object from DropEst output

    Arguments

    -
    sampleDirs
    + + +
    sampleDirs

    A path to the directory containing the data files. Default "./".

    -
    dataType
    +
    dataType

    can be "filtered" or "raw". Default "filtered".

    -
    rdsFileName
    +
    rdsFileName

    File name prefix of the DropEst RDS output. default is "cell.counts"

    -
    sampleNames
    +
    sampleNames

    A User-defined sample name. This will be prepended to all cell barcode IDs. Default "sample".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Default +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object containing the count matrix, +

    A SingleCellExperiment object containing the count matrix, the feature annotations from DropEst as ColData, and any metadata from DropEst

    @@ -300,15 +300,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importExampleData.html b/docs/reference/importExampleData.html index dd577daf9..253453e27 100644 --- a/docs/reference/importExampleData.html +++ b/docs/reference/importExampleData.html @@ -1,5 +1,5 @@ -Retrieve example datasets — importExampleData • singleCellTKRetrieve example datasets — importExampleData • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -226,11 +226,13 @@

    Retrieve example datasets

    Arguments

    -
    dataset
    + + +
    dataset

    Character. Name of the dataset to retrieve.

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" or "matrix". "Matrix" will store the data as a sparse matrix from package Matrix while @@ -238,21 +240,19 @@

    Arguments

    "Matrix".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Default +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Default TRUE.

    Value

    - - -

    The specified SingleCellExperiment object.

    +

    The specified SingleCellExperiment object.

    Details

    @@ -270,7 +270,7 @@

    Details

    "NestorowaHSCData"

    Retrieved with -NestorowaHSCData. Returns a dataset of 1920 mouse +NestorowaHSCData. Returns a dataset of 1920 mouse haematopoietic stem cells from Nestorowa et al. 2015

    "pbmc3k"
    @@ -323,15 +323,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importFromFiles.html b/docs/reference/importFromFiles.html index d656d5b43..08e15fd42 100644 --- a/docs/reference/importFromFiles.html +++ b/docs/reference/importFromFiles.html @@ -1,9 +1,9 @@ -Create a SingleCellExperiment object from files — importFromFiles • singleCellTKCreate a SingleCellExperiment object from files — importFromFiles • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -229,100 +229,100 @@

    Create a SingleCellExperiment object from files

    Arguments

    -
    assayFile
    -

    The path to a file in .mtx, .txt, .csv, .tab, or .tsv + + +

    assayFile
    +

    The path to a file in .mtx, .txt, .csv, .tab, or .tsv format.

    -
    annotFile
    +
    annotFile

    The path to a text file that contains columns of annotation -information for each cell in the assayFile. This file should have the +information for each cell in the assayFile. This file should have the same number of rows as there are columns in the assayFile. If multiple -samples are represented in the dataset, this should be denoted by a column +samples are represented in the dataset, this should be denoted by a column called 'sample' within the annotFile.

    -
    featureFile
    +
    featureFile

    The path to a text file that contains columns of annotation information for each gene in the count matrix. This file should have the same genes in the same order as assayFile. This is optional.

    -
    assayName
    +
    assayName

    The name of the assay that you are uploading. The default is "counts".

    -
    inputDataFrames
    +
    inputDataFrames

    If TRUE, assayFile, annotFile and -featureFile should be data.frames object (or its inheritance) +featureFile should be data.frames object (or its inheritance) instead of file paths. The default is FALSE.

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    -
    annotFileHeader
    -

    Whether there's a header (colnames) in the cell +

    annotFileHeader
    +

    Whether there's a header (colnames) in the cell annotation file. Default is FALSE.

    -
    annotFileRowName
    -

    Which column is used as the rownames for the cell -annotation file. This should match to the colnames of the assayFile. +

    annotFileRowName
    +

    Which column is used as the rownames for the cell +annotation file. This should match to the colnames of the assayFile. Default is 1 (first column).

    -
    annotFileSep
    -

    Separater used for the cell annotation file. Default is +

    annotFileSep
    +

    Separater used for the cell annotation file. Default is "\t".

    -
    featureHeader
    -

    Whether there's a header (colnames) in the feature +

    featureHeader
    +

    Whether there's a header (colnames) in the feature annotation file. Default is FALSE.

    -
    featureRowName
    -

    Which column is used as the rownames for the feature -annotation file. This should match to the rownames of the assayFile. +

    featureRowName
    +

    Which column is used as the rownames for the feature +annotation file. This should match to the rownames of the assayFile. Default is 1. (first column).

    -
    featureSep
    -

    Separater used for the feature annotation file. Default is +

    featureSep
    +

    Separater used for the feature annotation file. Default is "\t".

    -
    gzipped
    -

    Whether the input file is gzipped. Default is "auto" -and it will automatically detect whether the file is gzipped. Other options +

    gzipped
    +

    Whether the input file is gzipped. Default is "auto" +and it will automatically detect whether the file is gzipped. Other options are TRUE or FALSE.

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Default +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Default TRUE.

    Value

    - - -

    a SingleCellExperiment object

    +

    a SingleCellExperiment object

    Details

    -

    Creates a SingleCellExperiment object from a counts +

    Creates a SingleCellExperiment object from a counts file in various formats, and files of cell and feature annotation.

    @@ -338,15 +338,15 @@

    Details

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importGeneSetsFromCollection.html b/docs/reference/importGeneSetsFromCollection.html index df1df26fa..d2cc6c6ab 100644 --- a/docs/reference/importGeneSetsFromCollection.html +++ b/docs/reference/importGeneSetsFromCollection.html @@ -1,12 +1,12 @@ -Imports gene sets from a GeneSetCollection object — importGeneSetsFromCollection • singleCellTKImports gene sets from a GeneSetCollection object — importGeneSetsFromCollection • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -225,23 +225,25 @@

    Imports gene sets from a GeneSetCollection object

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    geneSetCollection
    +
    geneSetCollection

    A GeneSetCollection object. See GeneSetCollection for more details.

    -
    collectionName
    +
    collectionName

    Character. Name of collection to add gene sets to. If this collection already exists in inSCE, then these gene sets will be added to that collection. Any gene sets within the collection with the same name will be overwritten. Default GeneSetCollection.

    -
    by
    +
    by

    Character, character vector, or NULL. Describes the location within inSCE where the gene identifiers in geneSetCollection should be mapped. If set to "rownames" then the @@ -258,16 +260,14 @@

    Arguments

    Default "rownames".

    -
    noMatchError
    +
    noMatchError

    Boolean. Show an error if a collection does not have any matching features. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with gene set from collectionName output stored to the metadata slot.

    @@ -317,15 +317,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importGeneSetsFromGMT.html b/docs/reference/importGeneSetsFromGMT.html index f201345d2..03e234f8a 100644 --- a/docs/reference/importGeneSetsFromGMT.html +++ b/docs/reference/importGeneSetsFromGMT.html @@ -1,12 +1,12 @@ -Imports gene sets from a GMT file — importGeneSetsFromGMT • singleCellTKImports gene sets from a GMT file — importGeneSetsFromGMT • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -226,23 +226,25 @@

    Imports gene sets from a GMT file

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    file
    +
    file

    Character. Path to GMT file. See getGmt for more information on reading GMT files.

    -
    collectionName
    +
    collectionName

    Character. Name of collection to add gene sets to. If this collection already exists in inSCE, then these gene sets will be added to that collection. Any gene sets within the collection with the same name will be overwritten. Default GeneSetCollection.

    -
    by
    +
    by

    Character, character vector, or NULL. Describes the location within inSCE where the gene identifiers in geneSetList should be mapped. If set to "rownames" then the @@ -258,23 +260,20 @@

    Arguments

    Default "rownames".

    -
    sep
    +
    sep

    Character. Delimiter of the GMT file. Default "\t".

    -
    noMatchError
    +
    noMatchError

    Boolean. Show an error if a collection does not have any matching features. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object - with gene set from collectionName output stored to the

    -

    -

    metadata slot.

    +

    A SingleCellExperiment object + with gene set from collectionName output stored to the + metadata slot.

    Details

    @@ -323,15 +322,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importGeneSetsFromList.html b/docs/reference/importGeneSetsFromList.html index e37489519..dbbe31d18 100644 --- a/docs/reference/importGeneSetsFromList.html +++ b/docs/reference/importGeneSetsFromList.html @@ -1,12 +1,12 @@ -Imports gene sets from a list — importGeneSetsFromList • singleCellTKImports gene sets from a list — importGeneSetsFromList • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -225,25 +225,27 @@

    Imports gene sets from a list

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    geneSetList
    +
    geneSetList

    Named List. A list containing one or more gene sets. Each element of the list should be a character vector of gene identifiers. The names of the list will be become the gene set names in the GeneSetCollection object.

    -
    collectionName
    +
    collectionName

    Character. Name of collection to add gene sets to. If this collection already exists in inSCE, then these gene sets will be added to that collection. Any gene sets within the collection with the same name will be overwritten. Default GeneSetCollection.

    -
    by
    +
    by

    Character or character vector. Describes the location within inSCE where the gene identifiers in geneSetList should be mapped. If set to "rownames" then the @@ -257,16 +259,14 @@

    Arguments

    Default "rownames".

    -
    noMatchError
    +
    noMatchError

    Boolean. Show an error if a collection does not have any matching features. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with gene set from collectionName output stored to the metadata slot.

    @@ -324,15 +324,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importGeneSetsFromMSigDB.html b/docs/reference/importGeneSetsFromMSigDB.html index ec1b39ab3..0b5b401db 100644 --- a/docs/reference/importGeneSetsFromMSigDB.html +++ b/docs/reference/importGeneSetsFromMSigDB.html @@ -1,11 +1,11 @@ -Imports gene sets from MSigDB — importGeneSetsFromMSigDB • singleCellTKImports gene sets from MSigDB — importGeneSetsFromMSigDB • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -225,30 +225,32 @@

    Imports gene sets from MSigDB

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    categoryIDs
    +
    categoryIDs

    Character vector containing the MSigDB gene set ids. The column ID in the table returned by getMSigDBTable() shows -the list of possible gene set IDs that can be obtained. +the list of possible gene set IDs that can be obtained. Default is "H".

    -
    species
    +
    species

    Character. Species available can be found using the function msigdbr_show_species. Default "Homo sapiens".

    -
    mapping
    +
    mapping

    Character. One of "gene_symbol", "human_gene_symbol", or "entrez_gene". Gene identifiers to be used for MSigDB gene sets. IDs denoted by the by parameter must be either in gene symbol or Entrez gene id format to match IDs from MSigDB.

    -
    by
    +
    by

    Character. Describes the location within inSCE where the gene identifiers in the MSigDB gene sets should be mapped. If set to "rownames" then the @@ -259,20 +261,18 @@

    Arguments

    Default "rownames".

    -
    verbose
    +
    verbose

    Boolean. Whether to display progress. Default TRUE.

    -
    noMatchError
    +
    noMatchError

    Boolean. Show an error if a collection does not have any matching features. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with gene set from collectionName output stored to the metadata slot.

    @@ -305,9 +305,9 @@

    Examples

    species = "Homo sapiens", mapping = "gene_symbol", by = "feature_name") -#> Fri May 3 07:14:56 2024 .. Importing 'H' gene sets (n = 50) -#> Fri May 3 07:14:56 2024 .... Completed 50 gene sets for 1 -#> Fri May 3 07:14:56 2024 .. Matching gene sets to 'feature_name' +#> Thu Feb 13 10:28:05 2025 .. Importing 'H' gene sets (n = 50) +#> Thu Feb 13 10:28:05 2025 .... Completed 50 gene sets for 1 +#> Thu Feb 13 10:28:05 2025 .. Matching gene sets to 'feature_name'
    @@ -322,15 +322,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importMitoGeneSet.html b/docs/reference/importMitoGeneSet.html index 54c72b530..46c6d2e92 100644 --- a/docs/reference/importMitoGeneSet.html +++ b/docs/reference/importMitoGeneSet.html @@ -1,11 +1,11 @@ -Import mitochondrial gene sets — importMitoGeneSet • singleCellTKImport mitochondrial gene sets — importMitoGeneSet • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -224,20 +224,22 @@

    Import mitochondrial gene sets

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    reference
    +
    reference

    Character. Species available are "human" and "mouse".

    -
    id
    +
    id

    Types of gene id. Now it supports "symbol", "entrez", "ensembl" and "ensemblTranscriptID".

    -
    by
    +
    by

    Character. Describes the location within inSCE where the gene identifiers in the mitochondrial gene sets should be mapped. If set to "rownames" then the features will @@ -248,23 +250,21 @@

    Arguments

    Default "rownames".

    -
    collectionName
    +
    collectionName

    Character. Name of collection to add gene sets to. If this collection already exists in inSCE, then these gene sets will be added to that collection. Any gene sets within the collection with the same name will be overwritten. Default "mito".

    -
    noMatchError
    +
    noMatchError

    Boolean. Show an error if a collection does not have any matching features. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with gene set from collectionName output stored to the metadata slot.

    @@ -312,15 +312,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importMultipleSources.html b/docs/reference/importMultipleSources.html index ac490b6e8..1d4da8a23 100644 --- a/docs/reference/importMultipleSources.html +++ b/docs/reference/importMultipleSources.html @@ -1,9 +1,9 @@ -Imports samples from different sources and compiles them into a list of SCE objects — importMultipleSources • singleCellTKImports samples from different sources and compiles them into a list of SCE objects — importMultipleSources • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,20 +213,20 @@

    Imports samples from different sources and compiles them into a list of SCE

    Arguments

    -
    allImportEntries
    + + +
    allImportEntries

    object containing the sources and parameters of all the samples being imported (from the UI)

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    Value

    - - -

    A list of SingleCellExperiment object containing +

    A list of SingleCellExperiment object containing the droplet or cell data or both,depending on the dataType that users provided.

    @@ -242,15 +242,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importOptimus.html b/docs/reference/importOptimus.html index c24bca7e6..65ac047f6 100644 --- a/docs/reference/importOptimus.html +++ b/docs/reference/importOptimus.html @@ -1,11 +1,11 @@ -Construct SCE object from Optimus output — importOptimus • singleCellTKConstruct SCE object from Optimus output — importOptimus • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -229,7 +229,9 @@

    Construct SCE object from Optimus output

    Arguments

    -
    OptimusDirs
    + + +
    OptimusDirs

    A vector of root directories of Optimus output files. The paths should be something like this: /PATH/TO/bb4a2a5e-ff34-41b6-97d2-0c0c0c534530. @@ -237,12 +239,12 @@

    Arguments

    its own path. Must have the same length as samples.

    -
    samples
    +
    samples

    A vector of user-defined sample names for the sample to be imported. Must have the same length as OptimusDirs.

    -
    matrixLocation
    +
    matrixLocation

    Character. It is the intermediate path to the filtered count maxtrix file saved in sparse matrix format (.npz). Default @@ -250,32 +252,32 @@

    Arguments

    optimus_v1.4.0.

    -
    colIndexLocation
    +
    colIndexLocation

    Character. The intermediate path to the barcode index file. Default call-MergeCountFiles/sparse_counts_col_index.npy.

    -
    rowIndexLocation
    +
    rowIndexLocation

    Character. The intermediate path to the feature (gene) index file. Default call-MergeCountFiles/sparse_counts_row_index.npy.

    -
    cellMetricsLocation
    +
    cellMetricsLocation

    Character. It is the intermediate path to the cell metrics file (merged-cell-metrics.csv.gz). Default call-MergeCellMetrics/merged-cell-metrics.csv.gz which works for optimus_v1.4.0.

    -
    geneMetricsLocation
    +
    geneMetricsLocation

    Character. It is the intermediate path to the feature (gene) metrics file (merged-gene-metrics.csv.gz). Default call-MergeGeneMetrics/merged-gene-metrics.csv.gz which works for optimus_v1.4.0.

    -
    emptyDropsLocation
    +
    emptyDropsLocation

    Character. It is the intermediate path to emptyDrops metrics file (empty_drops_result.csv). @@ -283,28 +285,26 @@

    Arguments

    optimus_v1.4.0.

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Default +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object containing the count matrix, the gene annotation, and the cell annotation.

    @@ -313,10 +313,10 @@

    Value

    Examples

    file.path <- system.file("extdata/Optimus_20x1000",
   package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- importOptimus(OptimusDirs = file.path,
   samples = "Optimus_20x1000")
-}
+} # }
    @@ -331,15 +331,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importSEQC.html b/docs/reference/importSEQC.html index 4c170cc32..c9a57455e 100644 --- a/docs/reference/importSEQC.html +++ b/docs/reference/importSEQC.html @@ -1,11 +1,11 @@ -Construct SCE object from seqc output — importSEQC • singleCellTKConstruct SCE object from seqc output — importSEQC • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -228,83 +228,83 @@

    Construct SCE object from seqc output

    Arguments

    -
    seqcDirs
    + + +
    seqcDirs

    A vector of paths to seqc output files. Each sample -should have its own path. For example: "./pbmc_1k_50x50". Must have +should have its own path. For example: "./pbmc_1k_50x50". Must have the same length as samples.

    -
    samples
    +
    samples

    A vector of user-defined sample names for the samples to be imported. Must have the same length as seqcDirs.

    -
    prefix
    +
    prefix

    A vector containing the prefix of file names within each sample directory. It cannot be null and the vector should have the same length as samples.

    -
    gzipped
    +
    gzipped

    Boolean. TRUE if the seqc output files (sparse_counts_barcode.csv, sparse_counts_genes.csv, and -sparse_molecule_counts.mtx) were gzip compressed. FALSE otherwise. +sparse_molecule_counts.mtx) were gzip compressed. FALSE otherwise. Default seqc outputs are not gzipped. Default FALSE.

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE -object. Can be one of "Matrix" (as returned by readMM +object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    -
    cbNotFirstCol
    +
    cbNotFirstCol

    Boolean. TRUE if first column of -sparse_counts_barcode.csv is row index and it will be removed. FALSE +sparse_counts_barcode.csv is row index and it will be removed. FALSE the first column will be kept.

    -
    feNotFirstCol
    +
    feNotFirstCol

    Boolean. TRUE if first column of -sparse_counts_genes.csv is row index and it will be removed. FALSE +sparse_counts_genes.csv is row index and it will be removed. FALSE the first column will be kept.

    -
    combinedSample
    +
    combinedSample

    Boolean. If TRUE, importSEQC returns a SingleCellExperiment object containing the combined count matrix, - feature annotations and the cell annotations. If FALSE, + feature annotations and the cell annotations. If FALSE, importSEQC returns a list containing multiple SingleCellExperiment objects. Each SingleCellExperiment contains count matrix, feature annotations and cell annotations for each sample.

    -
    rowNamesDedup
    -

    Boolean. Whether to deduplicate rownames. Only applied -if combinedSample is TRUE or only one seqcDirs +

    rowNamesDedup
    +

    Boolean. Whether to deduplicate rownames. Only applied +if combinedSample is TRUE or only one seqcDirs specified. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object containing the combined count +

    A SingleCellExperiment object containing the combined count matrix, the feature annotations, and the cell annotation.

    Details

    -

    importSEQC imports output from seqc. The default +

    importSEQC imports output from seqc. The default sparse_counts_barcode.csv or sparse_counts_genes.csv from seqc output contains two columns. The first column is row index and the second column - is cell-barcode or gene symbol. importSEQC will remove first column. + is cell-barcode or gene symbol. importSEQC will remove first column. Alternatively, user can call cbNotFirstCol or feNotFirstCol as FALSE to keep the first column of these files. When combinedSample is TRUE, importSEQC @@ -338,15 +338,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/importSTARsolo.html b/docs/reference/importSTARsolo.html index 63b90c333..c7c69c037 100644 --- a/docs/reference/importSTARsolo.html +++ b/docs/reference/importSTARsolo.html @@ -1,11 +1,11 @@ -Construct SCE object from STARsolo outputs — importSTARsolo • singleCellTKConstruct SCE object from STARsolo outputs — importSTARsolo • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -228,7 +228,9 @@

    Construct SCE object from STARsolo outputs

    Arguments

    -
    STARsoloDirs
    + + +
    STARsoloDirs

    A vector of root directories of STARsolo output files. The paths should be something like this: /PATH/TO/prefixSolo.out. For example: ./Solo.out. @@ -236,12 +238,12 @@

    Arguments

    samples.

    -
    samples
    +
    samples

    A vector of user-defined sample names for the sample to be imported. Must have the same length as STARsoloDirs.

    -
    STARsoloOuts
    +
    STARsoloOuts

    Character. The intermediate folder to filtered or raw cell barcode, feature, and matrix files for each of samples. Default "Gene". @@ -249,25 +251,25 @@

    Arguments

    which data needs to be imported.

    -
    matrixFileNames
    +
    matrixFileNames

    Filenames for the Market Exchange Format (MEX) sparse matrix file (.mtx file). Must have length 1 or the same length as samples.

    -
    featuresFileNames
    +
    featuresFileNames

    Filenames for the feature annotation file. Must have length 1 or the same length as samples.

    -
    barcodesFileNames
    +
    barcodesFileNames

    Filenames for the cell barcode list file. Must have length 1 or the same length as samples.

    -
    gzipped
    +
    gzipped

    Boolean. TRUE if the STARsolo output files (barcodes.tsv, features.tsv, and matrix.mtx) were gzip compressed. FALSE otherwise. This is FALSE in STAR @@ -276,28 +278,26 @@

    Arguments

    length as samples.

    -
    class
    +
    class

    Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default FALSE.

    -
    rowNamesDedup
    +
    rowNamesDedup

    Boolean. Whether to deduplicate rownames. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object containing the count +

    A SingleCellExperiment object containing the count matrix, the gene annotation, and the cell annotation.

    @@ -345,15 +345,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index f43d1fbad..8a20f9d2e 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,9 @@ -Function reference • singleCellTKPackage index • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -420,30 +420,23 @@

    Normalization

    - + - + - + - + - + @@ -459,13 +452,11 @@

    Batch Effect Correction runMNNCorrect()

    -

    + - + @@ -473,8 +464,7 @@

    Batch Effect Correction runFastMNN()

    -

    + @@ -486,8 +476,7 @@

    Batch Effect Correction runSCANORAMA()

    -

    + @@ -495,8 +484,7 @@

    Batch Effect Correction runSeuratIntegration()

    -

    + @@ -504,8 +492,7 @@

    Batch Effect Correction plotBatchVariance()

    -

    + @@ -529,8 +516,7 @@

    Feature Selection

    - + @@ -562,27 +548,19 @@

    Dimensionality Reduction & Embed

    - + - + - + - + @@ -598,8 +576,7 @@

    Dimensionality Reduction & Embed

    - + @@ -619,9 +596,7 @@

    Clustering

    - + @@ -677,7 +652,7 @@

    Find Marker

    - + + @@ -753,8 +728,7 @@

    Trajectory Analysis

    - + @@ -786,14 +760,11 @@

    Seurat Curated Workflow runSeuratFindClusters()

    -

    + - + @@ -801,64 +772,47 @@

    Seurat Curated Workflow runSeuratHeatmap()

    -

    + - + - + - + - + - + - + - + - + - + - + @@ -870,14 +824,11 @@

    Scanpy Curated Workflow runScanpyFindClusters()

    -

    + - + @@ -885,32 +836,23 @@

    Scanpy Curated Workflow runScanpyNormalizeData()

    -

    + - + - + - + - + - + @@ -971,8 +912,7 @@

    Visualization

    - + @@ -988,7 +928,7 @@

    Visualization

    - + @@ -1128,9 +1068,7 @@

    Visualization

    - + @@ -1138,26 +1076,19 @@

    Visualization

    - + - + - + - + @@ -1165,8 +1096,7 @@

    Visualization

    - + @@ -1234,54 +1164,39 @@

    Report Generation

    - + - + - + - + - + - + - + - + - + - + @@ -1310,13 +1224,11 @@

    Datasets

    expData(<ANY>,<character>)

    -

    + - + - + - + - + - + - + - + - + - + @@ -1396,13 +1296,11 @@

    Other Data Processing convertSCEToSeurat()

    -

    + - + @@ -1426,13 +1324,11 @@

    Other Data Processing downSampleCells()

    -

    + - + @@ -1484,13 +1380,11 @@

    Other Data Processing generateSimulatedData()

    -

    + - + @@ -1514,13 +1408,11 @@

    Other Data Processing subDiffEx() subDiffExttest() subDiffExANOVA()

    -

    + - +
    pbmc4k -CTCCTAGTCTATGTGG-1 +TTTCCTCAGAGCTGGT-1 -2 +0 -2 +0 -100 +NaN -100 +NaN -100 +NaN -100 +NaN 0 @@ -507,13 +506,13 @@

    runDropletQC -0 +NaN

    		-2 +0 -2 +0 NA @@ -536,31 +535,31 @@

    runDropletQC -CTCTACGGTAAATGAC-1 +CGCGTTTGTCAAACTC-1

    		pbmc4k -CTCTACGGTAAATGAC-1 +CGCGTTTGTCAAACTC-1 -1 +0 -1 +0 -100 +NaN -100 +NaN -100 +NaN -100 +NaN 0 @@ -569,13 +568,13 @@

    runDropletQC -0 +NaN

    		-1 +0 -1 +0 NA @@ -598,31 +597,31 @@

    runDropletQC -TACTCGCCACAGATTC-1 +CTACGTCTCAGGCAAG-1

    		pbmc4k -TACTCGCCACAGATTC-1 +CTACGTCTCAGGCAAG-1 -1 +0 -1 +0 -100 +NaN -100 +NaN -100 +NaN -100 +NaN 0 @@ -631,13 +630,13 @@

    runDropletQC -0 +NaN

    		-1 +0 -1 +0 NA @@ -660,31 +659,31 @@

    runDropletQC -GCGCGATCACAGGAGT-1 +CGATCGGCACCATGTA-1

    		pbmc4k -GCGCGATCACAGGAGT-1 +CGATCGGCACCATGTA-1 -1 +0 -1 +0 -100 +NaN -100 +NaN -100 +NaN -100 +NaN 0 @@ -693,13 +692,13 @@

    runDropletQC -0 +NaN

    		-1 +0 -1 +0 NA @@ -722,31 +721,31 @@

    runDropletQC -GATTCAGGTAGTACCT-1 +AGTGTCACAAGTTAAG-1

    		pbmc4k -GATTCAGGTAGTACCT-1 +AGTGTCACAAGTTAAG-1 -0 +1 -0 +1 -NaN +100 -NaN +100 -NaN +100 -NaN +100 0 @@ -755,13 +754,13 @@

    runDropletQC -NaN +0

    		-0 +1 -0 +1 NA @@ -998,7 +997,7 @@

    Filtering the dataset
     #After filtering:
 dim(pbmc4k.droplet)
    -
    ## [1] 33694   293
    +
    ## [1] 33694   315

    We can compare the average total UMI counts per cell before and after cell filtration:

    @@ -1016,13 +1015,13 @@ 
    Filtering the dataset
    
  
    Session Information
-
    ## R version 4.3.3 (2024-02-29)
-## Platform: x86_64-apple-darwin20 (64-bit)
-## Running under: macOS Sonoma 14.4.1
+
    ## R version 4.4.2 (2024-10-31)
+## Platform: x86_64-apple-darwin20
+## Running under: macOS Sequoia 15.3
 ## 
 ## Matrix products: default
-## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
-## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
+## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
+## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
 ## 
 ## locale:
 ## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
@@ -1035,76 +1034,81 @@ 
    Filtering the dataset## [8] base     
 ## 
 ## other attached packages:
-##  [1] cowplot_1.1.3               BiocFileCache_2.10.2       
+##  [1] cowplot_1.1.3               BiocFileCache_2.14.0       
 ##  [3] dbplyr_2.5.0                dplyr_1.1.4                
-##  [5] singleCellTK_2.14.0         DelayedArray_0.28.0        
-##  [7] SparseArray_1.2.4           S4Arrays_1.2.1             
-##  [9] abind_1.4-5                 Matrix_1.6-5               
-## [11] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0
-## [13] Biobase_2.62.0              GenomicRanges_1.54.1       
-## [15] GenomeInfoDb_1.38.8         IRanges_2.36.0             
-## [17] S4Vectors_0.40.2            BiocGenerics_0.48.1        
-## [19] MatrixGenerics_1.14.0       matrixStats_1.3.0          
+##  [5] singleCellTK_2.16.1         DelayedArray_0.32.0        
+##  [7] SparseArray_1.6.1           S4Arrays_1.6.0             
+##  [9] abind_1.4-8                 Matrix_1.7-2               
+## [11] SingleCellExperiment_1.28.1 SummarizedExperiment_1.36.0
+## [13] Biobase_2.66.0              GenomicRanges_1.58.0       
+## [15] GenomeInfoDb_1.42.3         IRanges_2.40.1             
+## [17] S4Vectors_0.44.0            BiocGenerics_0.52.0        
+## [19] MatrixGenerics_1.18.1       matrixStats_1.5.0          
 ## 
 ## loaded via a namespace (and not attached):
-##   [1] rstudioapi_0.16.0         jsonlite_1.8.8           
-##   [3] magrittr_2.0.3            ggbeeswarm_0.7.2         
-##   [5] farver_2.1.1              rmarkdown_2.26           
-##   [7] fs_1.6.4                  zlibbioc_1.48.2          
-##   [9] ragg_1.3.0                vctrs_0.6.5              
-##  [11] memoise_2.0.1             DelayedMatrixStats_1.24.0
-##  [13] RCurl_1.98-1.14           htmltools_0.5.8.1        
-##  [15] curl_5.2.1                BiocNeighbors_1.20.2     
-##  [17] Rhdf5lib_1.24.2           rhdf5_2.46.1             
-##  [19] sass_0.4.9                bslib_0.7.0              
-##  [21] desc_1.4.3                plyr_1.8.9               
-##  [23] cachem_1.0.8              lifecycle_1.0.4          
-##  [25] pkgconfig_2.0.3           rsvd_1.0.5               
-##  [27] R6_2.5.1                  fastmap_1.1.1            
-##  [29] GenomeInfoDbData_1.2.11   digest_0.6.35            
-##  [31] colorspace_2.1-0          AnnotationDbi_1.64.1     
-##  [33] scater_1.30.1             dqrng_0.3.2              
-##  [35] irlba_2.3.5.1             textshaping_0.3.7        
-##  [37] RSQLite_2.3.6             beachmat_2.18.1          
-##  [39] labeling_0.4.3            filelock_1.0.3           
-##  [41] fansi_1.0.6               httr_1.4.7               
-##  [43] compiler_4.3.3            bit64_4.0.5              
-##  [45] withr_3.0.0               BiocParallel_1.36.0      
-##  [47] viridis_0.6.5             DBI_1.2.2                
-##  [49] highr_0.10                HDF5Array_1.30.1         
-##  [51] R.utils_2.12.3            tools_4.3.3              
-##  [53] vipor_0.4.7               beeswarm_0.4.0           
-##  [55] R.oo_1.26.0               glue_1.7.0               
-##  [57] rhdf5filters_1.14.1       grid_4.3.3               
-##  [59] reshape2_1.4.4            generics_0.1.3           
-##  [61] gtable_0.3.5              R.methodsS3_1.8.2        
-##  [63] xml2_1.3.6                BiocSingular_1.18.0      
-##  [65] ScaledMatrix_1.10.0       utf8_1.2.4               
-##  [67] XVector_0.42.0            ggrepel_0.9.5            
-##  [69] pillar_1.9.0              stringr_1.5.1            
-##  [71] limma_3.58.1              GSVAdata_1.38.0          
-##  [73] lattice_0.22-5            bit_4.0.5                
-##  [75] annotate_1.80.0           tidyselect_1.2.1         
-##  [77] locfit_1.5-9.9            Biostrings_2.70.3        
-##  [79] scuttle_1.12.0            knitr_1.46               
-##  [81] gridExtra_2.3             edgeR_4.0.16             
-##  [83] svglite_2.1.3             xfun_0.43                
-##  [85] statmod_1.5.0             DropletUtils_1.22.0      
-##  [87] eds_1.4.0                 stringi_1.8.3            
-##  [89] yaml_2.3.8                kableExtra_1.4.0         
-##  [91] evaluate_0.23             codetools_0.2-19         
-##  [93] tibble_3.2.1              graph_1.80.0             
-##  [95] cli_3.6.2                 xtable_1.8-4             
-##  [97] reticulate_1.36.1         systemfonts_1.0.6        
-##  [99] munsell_0.5.1             jquerylib_0.1.4          
-## [101] Rcpp_1.0.12               png_0.1-8                
-## [103] XML_3.99-0.16.1           parallel_4.3.3           
-## [105] pkgdown_2.0.7             ggplot2_3.5.1            
-## [107] blob_1.2.4                sparseMatrixStats_1.14.0 
-## [109] bitops_1.0-7              viridisLite_0.4.2        
-## [111] GSEABase_1.64.0           scales_1.3.0             
-## [113] purrr_1.0.2               crayon_1.5.2             
-## [115] rlang_1.1.3               KEGGREST_1.42.0
    
+##   [1] RColorBrewer_1.1-3        rstudioapi_0.17.1        
+##   [3] jsonlite_1.8.9            shape_1.4.6.1            
+##   [5] magrittr_2.0.3            ggbeeswarm_0.7.2         
+##   [7] farver_2.1.2              rmarkdown_2.29           
+##   [9] GlobalOptions_0.1.2       fs_1.6.5                 
+##  [11] zlibbioc_1.52.0           ragg_1.3.3               
+##  [13] vctrs_0.6.5               memoise_2.0.1            
+##  [15] DelayedMatrixStats_1.28.1 htmltools_0.5.8.1        
+##  [17] curl_6.2.0                BiocNeighbors_2.0.1      
+##  [19] Rhdf5lib_1.28.0           rhdf5_2.50.2             
+##  [21] sass_0.4.9                bslib_0.9.0              
+##  [23] htmlwidgets_1.6.4         desc_1.4.3               
+##  [25] plyr_1.8.9                cachem_1.1.0             
+##  [27] lifecycle_1.0.4           iterators_1.0.14         
+##  [29] pkgconfig_2.0.3           rsvd_1.0.5               
+##  [31] R6_2.6.0                  fastmap_1.2.0            
+##  [33] GenomeInfoDbData_1.2.13   clue_0.3-66              
+##  [35] digest_0.6.37             colorspace_2.1-1         
+##  [37] AnnotationDbi_1.68.0      scater_1.34.0            
+##  [39] dqrng_0.4.1               irlba_2.3.5.1            
+##  [41] textshaping_1.0.0         RSQLite_2.3.9            
+##  [43] beachmat_2.22.0           labeling_0.4.3           
+##  [45] filelock_1.0.3            httr_1.4.7               
+##  [47] compiler_4.4.2            bit64_4.6.0-1            
+##  [49] withr_3.0.2               doParallel_1.0.17        
+##  [51] BiocParallel_1.40.0       viridis_0.6.5            
+##  [53] DBI_1.2.3                 HDF5Array_1.34.0         
+##  [55] R.utils_2.12.3            rjson_0.2.23             
+##  [57] tools_4.4.2               vipor_0.4.7              
+##  [59] beeswarm_0.4.0            R.oo_1.27.0              
+##  [61] glue_1.8.0                rhdf5filters_1.18.0      
+##  [63] grid_4.4.2                cluster_2.1.8            
+##  [65] reshape2_1.4.4            generics_0.1.3           
+##  [67] gtable_0.3.6              R.methodsS3_1.8.2        
+##  [69] tidyr_1.3.1               xml2_1.3.6               
+##  [71] BiocSingular_1.22.0       ScaledMatrix_1.14.0      
+##  [73] XVector_0.46.0            ggrepel_0.9.6            
+##  [75] foreach_1.5.2             pillar_1.10.1            
+##  [77] stringr_1.5.1             limma_3.62.2             
+##  [79] circlize_0.4.16           GSVAdata_1.42.0          
+##  [81] lattice_0.22-6            bit_4.5.0.1              
+##  [83] annotate_1.84.0           tidyselect_1.2.1         
+##  [85] ComplexHeatmap_2.22.0     locfit_1.5-9.11          
+##  [87] Biostrings_2.74.1         scuttle_1.16.0           
+##  [89] knitr_1.49                gridExtra_2.3            
+##  [91] edgeR_4.4.2               svglite_2.1.3            
+##  [93] xfun_0.50                 statmod_1.5.0            
+##  [95] DropletUtils_1.26.0       eds_1.8.0                
+##  [97] stringi_1.8.4             UCSC.utils_1.2.0         
+##  [99] yaml_2.3.10               kableExtra_1.4.0         
+## [101] evaluate_1.0.3            codetools_0.2-20         
+## [103] tibble_3.2.1              graph_1.84.1             
+## [105] cli_3.6.3                 xtable_1.8-4             
+## [107] reticulate_1.40.0         systemfonts_1.2.1        
+## [109] munsell_0.5.1             jquerylib_0.1.4          
+## [111] Rcpp_1.0.14               png_0.1-8                
+## [113] XML_3.99-0.18             parallel_4.4.2           
+## [115] pkgdown_2.1.1             ggplot2_3.5.1            
+## [117] blob_1.2.4                sparseMatrixStats_1.18.0 
+## [119] viridisLite_0.4.2         GSEABase_1.68.0          
+## [121] scales_1.3.0              purrr_1.0.4              
+## [123] crayon_1.5.3              GetoptLong_1.0.5         
+## [125] rlang_1.1.5               KEGGREST_1.46.0
    @@ -1112,9 +1116,7 @@

    Filtering the dataset - - + @@ -1127,16 +1129,16 @@

    Filtering the dataset

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/cnsl_dropletqc_files/figure-html/Count_Violin_after_filtering-1.png b/docs/articles/cnsl_dropletqc_files/figure-html/Count_Violin_after_filtering-1.png index 5429b9304..ed8c21d12 100644 Binary files a/docs/articles/cnsl_dropletqc_files/figure-html/Count_Violin_after_filtering-1.png and b/docs/articles/cnsl_dropletqc_files/figure-html/Count_Violin_after_filtering-1.png differ diff --git a/docs/articles/cnsl_dropletqc_files/figure-html/run_kneeplot_barcoderank-1.png b/docs/articles/cnsl_dropletqc_files/figure-html/run_kneeplot_barcoderank-1.png index 65487cc1b..6ec7ecad4 100644 Binary files a/docs/articles/cnsl_dropletqc_files/figure-html/run_kneeplot_barcoderank-1.png and b/docs/articles/cnsl_dropletqc_files/figure-html/run_kneeplot_barcoderank-1.png differ diff --git a/docs/articles/cnsl_dropletqc_files/figure-html/scatter_emptydrops-1.png b/docs/articles/cnsl_dropletqc_files/figure-html/scatter_emptydrops-1.png index 56e24c551..fc668ee41 100644 Binary files a/docs/articles/cnsl_dropletqc_files/figure-html/scatter_emptydrops-1.png and b/docs/articles/cnsl_dropletqc_files/figure-html/scatter_emptydrops-1.png differ diff --git a/docs/articles/delete_data.html b/docs/articles/delete_data.html index f145a34b1..c26928dfb 100644 --- a/docs/articles/delete_data.html +++ b/docs/articles/delete_data.html @@ -6,21 +6,20 @@ Delete Data • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -328,9 +327,7 @@

    Workflow Guide - -

    +
    @@ -343,16 +340,16 @@

    Workflow Guide

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/differential_expression.html b/docs/articles/differential_expression.html index 572cf9955..cfe6cd8bb 100644 --- a/docs/articles/differential_expression.html +++ b/docs/articles/differential_expression.html @@ -6,21 +6,20 @@ Differential Expression • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -648,19 +647,19 @@

    Workflow GuideDEG <- getDEGTopTable(sce, "c1_2_VS_c5") head(DEG)

    ##         Gene  Log2_FC       Pvalue          FDR group1MeanExp group2MeanExp
-## 21054    LYZ 1.923606 6.697866e-37 8.770990e-34      2.450818    0.52721136
-## 1956  S100A9 1.725115 1.258673e-34 1.329239e-31      1.906373    0.18125751
-## 1958  S100A8 1.499733 2.665313e-43 4.362851e-40      1.543568    0.04383467
-## 28818   CST3 1.346308 5.206233e-36 6.087202e-33      1.542021    0.19571280
-## 18999   FTH1 1.335794 1.078589e-49 2.077108e-46      3.934564    2.59877029
-## 30934    FTL 1.295643 2.519141e-21 1.472708e-18      4.054030    2.75838685
+## 21054    LYZ 2.535345 1.348180e-48 1.050875e-45      3.136112    0.60076686
+## 1956  S100A9 2.399927 5.532280e-53 5.659868e-50      2.574507    0.17457975
+## 1958  S100A8 2.016443 7.806040e-56 8.812211e-53      2.104506    0.08806257
+## 1965  S100A4 1.986609 1.998237e-68 2.973558e-65      2.516309    0.52970004
+## 30430 TYROBP 1.838078 3.723853e-55 4.063717e-52      1.969446    0.13136797
+## 28818   CST3 1.825178 2.316276e-51 2.106396e-48      2.053687    0.22850832
 ##       group1ExprPerc group2ExprPerc
-## 21054      0.7086957     0.39080460
-## 1956       0.4895652     0.15229885
-## 1958       0.4408696     0.04022989
-## 28818      0.5060870     0.15804598
-## 18999      0.9947826     0.98275862
-## 30934      0.9921739     0.98563218
    +## 21054 0.7600979 0.42979943 +## 1956 0.5899633 0.14040115 +## 1958 0.5618115 0.08022923 +## 1965 0.8102815 0.36962751 +## 30430 0.5777234 0.11174785 +## 28818 0.6095471 0.18624642

    To visualize the result in a heatmap:

     plotDEGHeatmap(sce, useResult = "c1_2_VS_c5", log2fcThreshold = .5)
    @@ -729,9 +728,7 @@

    References - -

    + @@ -744,16 +741,16 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/differential_expression_files/figure-html/de_prep_plot-1.png b/docs/articles/differential_expression_files/figure-html/de_prep_plot-1.png index 99b0ceab8..aa41a3087 100644 Binary files a/docs/articles/differential_expression_files/figure-html/de_prep_plot-1.png and b/docs/articles/differential_expression_files/figure-html/de_prep_plot-1.png differ diff --git a/docs/articles/differential_expression_files/figure-html/plotDEHeatmap-1.png b/docs/articles/differential_expression_files/figure-html/plotDEHeatmap-1.png index 41c305114..2b595f0fd 100644 Binary files a/docs/articles/differential_expression_files/figure-html/plotDEHeatmap-1.png and b/docs/articles/differential_expression_files/figure-html/plotDEHeatmap-1.png differ diff --git a/docs/articles/differential_expression_files/figure-html/plotDEVolcano-1.png b/docs/articles/differential_expression_files/figure-html/plotDEVolcano-1.png index f4c26b222..141fe935b 100644 Binary files a/docs/articles/differential_expression_files/figure-html/plotDEVolcano-1.png and b/docs/articles/differential_expression_files/figure-html/plotDEVolcano-1.png differ diff --git a/docs/articles/dimensionality_reduction.html b/docs/articles/dimensionality_reduction.html index ced25d3aa..5c5200ae4 100644 --- a/docs/articles/dimensionality_reduction.html +++ b/docs/articles/dimensionality_reduction.html @@ -6,21 +6,20 @@ Dimensionality Reduction • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -548,9 +547,7 @@

    References - -

    +
    @@ -563,16 +560,16 @@

    References

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/articles/enrichR.html b/docs/articles/enrichR.html index 0c0fc2467..719728c82 100644 --- a/docs/articles/enrichR.html +++ b/docs/articles/enrichR.html @@ -6,21 +6,20 @@ Enrichment Analysis with enrichR • singleCellTK - + - - +
    @@ -43,7 +42,7 @@
  • - +
  • @@ -52,7 +51,7 @@
    • - +
    @@ -486,7 +485,7 @@

    Workflow Guide
    77507745 LINCS_L1000_Chem_Pert_down LJP006 MCF10A 3H-withaferin-a-3.33 3/68
    2867028665 PFOCR_Pathways PMC5640840 Zjv9991830150008 2/6
    77517746 LINCS_L1000_Chem_Pert_down LJP006 MCF10A 3H-radicicol-10 3/82
    3275832753 PFOCR_Pathways_2023 PMC5640840 F8 2/7
    55305525 LINCS_L1000_Chem_Pert_up LJP006 A375 24H-KIN001-043-1.11 3/91
    41564151 Genes_Associated_with_NIH_Grants R01GM072915 2/8

    scaterlogNormCounts()

    scaterlogNormCounts -Uses logNormCounts to log normalize input data

    scaterlogNormCounts Uses logNormCounts to log normalize input data

    scaterCPM()

    scaterCPM -Uses CPM from scater library to compute counts-per-million.

    scaterCPM Uses CPM from scater library to compute counts-per-million.

    runSeuratNormalizeData()

    runSeuratNormalizeData -Wrapper for NormalizeData() function from seurat library -Normalizes the sce object according to the input parameters

    runSeuratNormalizeData Wrapper for NormalizeData() function from seurat library Normalizes the sce object according to the input parameters

    runSeuratScaleData()

    runSeuratScaleData -Scales the input sce object according to the input parameters

    runSeuratScaleData Scales the input sce object according to the input parameters

    runSeuratSCTransform()

    runSeuratSCTransform -Runs the SCTransform function to transform/normalize the input -data

    runSeuratSCTransform Runs the SCTransform function to transform/normalize the input data

    computeZScore()

    Apply the mutual nearest neighbors (MNN) batch effect correction method to -SingleCellExperiment object

    Apply the mutual nearest neighbors (MNN) batch effect correction method to SingleCellExperiment object

    runComBatSeq()

    Apply ComBat-Seq batch effect correction method to SingleCellExperiment -object

    Apply ComBat-Seq batch effect correction method to SingleCellExperiment object

    runBBKNN()

    Apply a fast version of the mutual nearest neighbors (MNN) batch effect -correction method to SingleCellExperiment object

    Apply a fast version of the mutual nearest neighbors (MNN) batch effect correction method to SingleCellExperiment object

    runLimmaBC()

    Apply the mutual nearest neighbors (MNN) batch effect correction method to -SingleCellExperiment object

    Apply the mutual nearest neighbors (MNN) batch effect correction method to SingleCellExperiment object

    runSCMerge()

    runSeuratIntegration -A wrapper function to Seurat Batch-Correction/Integration workflow.

    runSeuratIntegration A wrapper function to Seurat Batch-Correction/Integration workflow.

    runZINBWaVE()

    Plot the percent of the variation that is explained by batch and condition -in the data

    Plot the percent of the variation that is explained by batch and condition in the data

    plotBatchCorrCompare()

    runSeuratFindHVG()

    runSeuratFindHVG -Find highly variable genes and store in the input sce object

    runSeuratFindHVG Find highly variable genes and store in the input sce object

    getTopHVG() setTopHVG()

    runSeuratICA()

    runSeuratICA -Computes ICA on the input sce object and stores the calculated independent -components within the sce object

    runSeuratICA Computes ICA on the input sce object and stores the calculated independent components within the sce object

    runSeuratPCA()

    runSeuratPCA -Computes PCA on the input sce object and stores the calculated principal -components within the sce object

    runSeuratPCA Computes PCA on the input sce object and stores the calculated principal components within the sce object

    runSeuratUMAP()

    runSeuratUMAP -Computes UMAP from the given sce object and stores the UMAP computations back -into the sce object

    runSeuratUMAP Computes UMAP from the given sce object and stores the UMAP computations back into the sce object

    runSeuratTSNE()

    runSeuratTSNE -Computes tSNE from the given sce object and stores the tSNE computations back -into the sce object

    runSeuratTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object

    plotPCA()

    plotDimRed()

    Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE -and UMAP

    Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE and UMAP

    plotSCEDimReduceColData()

    runSeuratFindClusters()

    runSeuratFindClusters -Computes the clusters from the input sce object and stores them back in sce -object

    runSeuratFindClusters Computes the clusters from the input sce object and stores them back in sce object

    runKMeans()

    plotFindMarkerHeatmap() plotMarkerDiffExp()

    Plot a heatmap to visualize the result of runFindMarker

    Plot a heatmap to visualize the result of runFindMarker

    Differential Abundance

    @@ -721,7 +696,7 @@

    Enrichment & Pathway Analysis runGSVA()

    -

    Run GSVA analysis on a SingleCellExperiment object

    Run GSVA analysis on a SingleCellExperiment object

    runVAM()

    plotTSCANClusterDEG()

    Plot features identified by runTSCANClusterDEAnalysis on -cell 2D embedding with MST overlaid

    Plot features identified by runTSCANClusterDEAnalysis on cell 2D embedding with MST overlaid

    plotTSCANClusterPseudo()

    runSeuratFindClusters -Computes the clusters from the input sce object and stores them back in sce -object

    runSeuratFindClusters Computes the clusters from the input sce object and stores them back in sce object

    runSeuratFindHVG()

    runSeuratFindHVG -Find highly variable genes and store in the input sce object

    runSeuratFindHVG Find highly variable genes and store in the input sce object

    runSeuratFindMarkers()

    runSeuratHeatmap -Computes the heatmap plot object from the pca slot in the input sce object

    runSeuratHeatmap Computes the heatmap plot object from the pca slot in the input sce object

    runSeuratICA()

    runSeuratICA -Computes ICA on the input sce object and stores the calculated independent -components within the sce object

    runSeuratICA Computes ICA on the input sce object and stores the calculated independent components within the sce object

    runSeuratIntegration()

    runSeuratIntegration -A wrapper function to Seurat Batch-Correction/Integration workflow.

    runSeuratIntegration A wrapper function to Seurat Batch-Correction/Integration workflow.

    runSeuratJackStraw()

    runSeuratJackStraw -Compute jackstraw plot and store the computations in the input sce object

    runSeuratJackStraw Compute jackstraw plot and store the computations in the input sce object

    runSeuratNormalizeData()

    runSeuratNormalizeData -Wrapper for NormalizeData() function from seurat library -Normalizes the sce object according to the input parameters

    runSeuratNormalizeData Wrapper for NormalizeData() function from seurat library Normalizes the sce object according to the input parameters

    runSeuratPCA()

    runSeuratPCA -Computes PCA on the input sce object and stores the calculated principal -components within the sce object

    runSeuratPCA Computes PCA on the input sce object and stores the calculated principal components within the sce object

    runSeuratSCTransform()

    runSeuratSCTransform -Runs the SCTransform function to transform/normalize the input -data

    runSeuratSCTransform Runs the SCTransform function to transform/normalize the input data

    runSeuratScaleData()

    runSeuratScaleData -Scales the input sce object according to the input parameters

    runSeuratScaleData Scales the input sce object according to the input parameters

    runSeuratTSNE()

    runSeuratTSNE -Computes tSNE from the given sce object and stores the tSNE computations back -into the sce object

    runSeuratTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object

    runSeuratUMAP()

    runSeuratUMAP -Computes UMAP from the given sce object and stores the UMAP computations back -into the sce object

    runSeuratUMAP Computes UMAP from the given sce object and stores the UMAP computations back into the sce object

    computeHeatmap()

    Computes heatmap for a set of features against dimensionality reduction -components

    Computes heatmap for a set of features against dimensionality reduction components

    getSeuratVariableFeatures()

    runScanpyFindClusters -Computes the clusters from the input sce object and stores them back in sce -object

    runScanpyFindClusters Computes the clusters from the input sce object and stores them back in sce object

    runScanpyFindHVG()

    runScanpyFindHVG -Find highly variable genes and store in the input sce object

    runScanpyFindHVG Find highly variable genes and store in the input sce object

    runScanpyFindMarkers()

    runScanpyNormalizeData -Wrapper for NormalizeData() function from scanpy library -Normalizes the sce object according to the input parameters

    runScanpyNormalizeData Wrapper for NormalizeData() function from scanpy library Normalizes the sce object according to the input parameters

    runScanpyPCA()

    runScanpyPCA -Computes PCA on the input sce object and stores the calculated principal -components within the sce object

    runScanpyPCA Computes PCA on the input sce object and stores the calculated principal components within the sce object

    runScanpyScaleData()

    runScanpyScaleData -Scales the input sce object according to the input parameters

    runScanpyScaleData Scales the input sce object according to the input parameters

    runScanpyTSNE()

    runScanpyTSNE -Computes tSNE from the given sce object and stores the tSNE computations back -into the sce object

    runScanpyTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object

    runScanpyUMAP()

    runScanpyUMAP -Computes UMAP from the given sce object and stores the UMAP computations back -into the sce object

    runScanpyUMAP Computes UMAP from the given sce object and stores the UMAP computations back into the sce object

    Visualization

    @@ -930,8 +872,7 @@

    Visualization

    plotBatchVariance()

    Plot the percent of the variation that is explained by batch and condition -in the data

    Plot the percent of the variation that is explained by batch and condition in the data

    plotBcdsResults()

    plotDimRed()

    Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE -and UMAP

    Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE and UMAP

    plotDoubletFinderResults()

    plotFindMarkerHeatmap() plotMarkerDiffExp()

    Plot a heatmap to visualize the result of runFindMarker

    Plot a heatmap to visualize the result of runFindMarker

    plotMASTThresholdGenes()

    plotSeuratElbow()

    plotSeuratElbow -Computes the plot object for elbow plot from the pca slot in the input sce -object

    plotSeuratElbow Computes the plot object for elbow plot from the pca slot in the input sce object

    plotSeuratGenes()

    plotSeuratHVG()

    plotSeuratHVG -Plot highly variable genes from input sce object (must have highly variable -genes computations stored)

    plotSeuratHVG Plot highly variable genes from input sce object (must have highly variable genes computations stored)

    plotSeuratHeatmap()

    plotSeuratHeatmap -Modifies the heatmap plot object so it contains specified number of heatmaps -in a single plot

    plotSeuratHeatmap Modifies the heatmap plot object so it contains specified number of heatmaps in a single plot

    plotSeuratJackStraw()

    plotSeuratJackStraw -Computes the plot object for jackstraw plot from the pca slot in the input -sce object

    plotSeuratJackStraw Computes the plot object for jackstraw plot from the pca slot in the input sce object

    plotSeuratReduction()

    plotSeuratReduction -Plots the selected dimensionality reduction method

    plotSeuratReduction Plots the selected dimensionality reduction method

    plotSoupXResults()

    plotTSCANClusterDEG()

    Plot features identified by runTSCANClusterDEAnalysis on -cell 2D embedding with MST overlaid

    Plot features identified by runTSCANClusterDEAnalysis on cell 2D embedding with MST overlaid

    plotTSCANClusterPseudo()

    reportSeurat()

    Generates an HTML report for the complete Seurat workflow and returns the - SCE object with the results computed and stored inside the object.

    Generates an HTML report for the complete Seurat workflow and returns the SCE object with the results computed and stored inside the object.

    reportSeuratClustering()

    Generates an HTML report for Seurat Clustering and returns the SCE object - with the results computed and stored inside the object.

    Generates an HTML report for Seurat Clustering and returns the SCE object with the results computed and stored inside the object.

    reportSeuratDimRed()

    Generates an HTML report for Seurat Dimensionality Reduction - and returns the SCE object with the results computed and stored - inside the object.

    Generates an HTML report for Seurat Dimensionality Reduction and returns the SCE object with the results computed and stored inside the object.

    reportSeuratFeatureSelection()

    Generates an HTML report for Seurat Feature Selection and returns the -SCE object with the results computed and stored inside the object.

    Generates an HTML report for Seurat Feature Selection and returns the SCE object with the results computed and stored inside the object.

    reportSeuratMarkerSelection()

    Generates an HTML report for Seurat Results (including Clustering & Marker - Selection) and returns the SCE object with the results computed and stored - inside the object.

    Generates an HTML report for Seurat Results (including Clustering & Marker Selection) and returns the SCE object with the results computed and stored inside the object.

    reportSeuratNormalization()

    Generates an HTML report for Seurat Normalization - and returns the SCE object with the results computed and stored - inside the object.

    Generates an HTML report for Seurat Normalization and returns the SCE object with the results computed and stored inside the object.

    reportSeuratResults()

    Generates an HTML report for Seurat Results (including Clustering & Marker - Selection) and returns the SCE object with the results computed and stored - inside the object.

    Generates an HTML report for Seurat Results (including Clustering & Marker Selection) and returns the SCE object with the results computed and stored inside the object.

    reportSeuratRun()

    Generates an HTML report for Seurat Run (including Normalization, - Feature Selection, Dimensionality Reduction & Clustering) and returns the - SCE object with the results computed and stored inside the object.

    Generates an HTML report for Seurat Run (including Normalization, Feature Selection, Dimensionality Reduction & Clustering) and returns the SCE object with the results computed and stored inside the object.

    reportSeuratScaling()

    Generates an HTML report for Seurat Scaling - and returns the SCE object with the results computed and stored - inside the object.

    Generates an HTML report for Seurat Scaling and returns the SCE object with the results computed and stored inside the object.

    Exporting Results

    @@ -1297,8 +1212,7 @@

    Exporting Results

    exportSCEtoAnnData()

    Export a SingleCellExperiment R object as -Python annData object

    Export a SingleCellExperiment R object as Python annData object

    exportSCEtoFlatFile()

    mouseBrainSubsetSCE

    Example Single Cell RNA-Seq data in SingleCellExperiment Object, GSE60361 -subset

    Example Single Cell RNA-Seq data in SingleCellExperiment Object, GSE60361 subset

    sceBatches

    Example Single Cell RNA-Seq data in SingleCellExperiment object, with -different batches annotated

    Example Single Cell RNA-Seq data in SingleCellExperiment object, with different batches annotated

    MitoGenes

    scExample

    Example Single Cell RNA-Seq data in SingleCellExperiment Object, -subset of 10x public dataset

    Example Single Cell RNA-Seq data in SingleCellExperiment Object, subset of 10x public dataset

    SEG

    expData -Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item.

    expData Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item.

    `expData<-`(<ANY>,<character>,<CharacterOrNullOrMissing>,<logical>)

    expData -Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item.

    expData Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item.

    `expData<-`()

    expData -Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item.

    expData Store data items using tags to identify the type of data item stored. To be used as a replacement for assay<- setter function but with additional parameter to set a tag to a data item.

    expData()

    expData -Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item.

    expData Get data item from an input SingleCellExperiment object. The data item can be an assay, altExp (subset) or a reducedDim, which is retrieved based on the name of the data item.

    expDataNames(<ANY>)

    expDataNames -Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims.

    expDataNames Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims.

    expDataNames()

    expDataNames -Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims.

    expDataNames Get names of all the data items in the input SingleCellExperiment object including assays, altExps and reducedDims.

    expDeleteDataTag()

    expDeleteDataTag -Remove tag against an input data from the stored tag information in the metadata of the input object.

    expDeleteDataTag Remove tag against an input data from the stored tag information in the metadata of the input object.

    expSetDataTag()

    expSetDataTag -Set tag to an assay or a data item in the input SCE object.

    expSetDataTag Set tag to an assay or a data item in the input SCE object.

    expTaggedData()

    expTaggedData -Returns a list of names of data items from the -input SingleCellExperiment object based upon the input parameters.

    expTaggedData Returns a list of names of data items from the input SingleCellExperiment object based upon the input parameters.

    calcEffectSizes()

    Finds the effect sizes for all genes in the original dataset, regardless of -significance.

    Finds the effect sizes for all genes in the original dataset, regardless of significance.

    combineSCE()

    convertSCEToSeurat -Converts sce object to seurat while retaining all assays and metadata

    convertSCEToSeurat Converts sce object to seurat while retaining all assays and metadata

    convertSeuratToSCE()

    convertSeuratToSCE -Converts the input seurat object to a sce object

    convertSeuratToSCE Converts the input seurat object to a sce object

    constructSCE()

    Estimate numbers of detected genes, significantly differentially expressed -genes, and median significant effect size

    Estimate numbers of detected genes, significantly differentially expressed genes, and median significant effect size

    downSampleDepth()

    Estimate numbers of detected genes, significantly differentially expressed -genes, and median significant effect size

    Estimate numbers of detected genes, significantly differentially expressed genes, and median significant effect size

    featureIndex()

    Generates a single simulated dataset, bootstrapping from the input counts -matrix.

    Generates a single simulated dataset, bootstrapping from the input counts matrix.

    getBiomarker()

    Given a list of genes and a SingleCellExperiment object, return -the binary or continuous expression of the genes.

    Given a list of genes and a SingleCellExperiment object, return the binary or continuous expression of the genes.

    getSceParams()

    Passes the output of generateSimulatedData() to differential expression -tests, picking either t-tests or ANOVA for data with only two conditions or -multiple conditions, respectively.

    Passes the output of generateSimulatedData() to differential expression tests, picking either t-tests or ANOVA for data with only two conditions or multiple conditions, respectively.

    summarizeSCE()

    Summarize an assay in a SingleCellExperiment

    Summarize an assay in a SingleCellExperiment

    Python Environment Setting

    @@ -1554,15 +1446,15 @@

    Python Environment Setting -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/iterateSimulations.html b/docs/reference/iterateSimulations.html index 3953dfad4..eb12c62e6 100644 --- a/docs/reference/iterateSimulations.html +++ b/docs/reference/iterateSimulations.html @@ -1,9 +1,9 @@ -Returns significance data from a snapshot. — iterateSimulations • singleCellTKReturns significance data from a snapshot. — iterateSimulations • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,39 +220,39 @@

    Returns significance data from a snapshot.

    Arguments

    -
    originalData
    + + +
    originalData

    The SingleCellExperiment object storing all assay data from the shiny app.

    -
    useAssay
    +
    useAssay

    Character. The name of the assay to be used for subsampling.

    -
    realLabels
    +
    realLabels

    Character. The name of the condition of interest. Must match a name from sample data.

    -
    totalReads
    +
    totalReads

    Numeric. The total number of reads in the simulated dataset, to be split between all simulated cells.

    -
    cells
    +
    cells

    Numeric. The number of virtual cells to simulate.

    -
    iterations
    +
    iterations

    Numeric. How many times should each experimental design be simulated.

    Value

    - - -

    A matrix of significance information from a snapshot

    +

    A matrix of significance information from a snapshot

    @@ -275,15 +275,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/listSampleSummaryStatsTables.html b/docs/reference/listSampleSummaryStatsTables.html index cedbb03f3..8750eb067 100644 --- a/docs/reference/listSampleSummaryStatsTables.html +++ b/docs/reference/listSampleSummaryStatsTables.html @@ -1,10 +1,10 @@ -Lists the table of SCTK QC outputs stored within the metadata. — listSampleSummaryStatsTables • singleCellTKLists the table of SCTK QC outputs stored within the metadata. — listSampleSummaryStatsTables • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -212,26 +212,26 @@

    Lists the table of SCTK QC outputs stored within the metadata.

    listSampleSummaryStatsTables(inSCE, ...)
 
-# S4 method for SingleCellExperiment
+# S4 method for class 'SingleCellExperiment'
 listSampleSummaryStatsTables(inSCE, ...)

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved table within the metadata data. Required.

    -
    ...
    +
    ...

    Other arguments passed to the function.

    Value

    - - -

    A character vector. Contains a list of summary tables +

    A character vector. Contains a list of summary tables within the SingleCellExperiment object.

    @@ -256,15 +256,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/mergeSCEColData.html b/docs/reference/mergeSCEColData.html index 6e011167b..be58035b0 100644 --- a/docs/reference/mergeSCEColData.html +++ b/docs/reference/mergeSCEColData.html @@ -1,11 +1,11 @@ -Merging colData from two singleCellExperiment objects — mergeSCEColData • singleCellTKMerging colData from two singleCellExperiment objects — mergeSCEColData • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -217,31 +217,31 @@

    Merging colData from two singleCellExperiment objects

    Arguments

    -
    inSCE1
    + + +
    inSCE1

    Input SingleCellExperiment object. The function will output this singleCellExperiment object with a combined colData from inSCE1 and inSCE2.

    -
    inSCE2
    +
    inSCE2

    Input SingleCellExperiment object. colData from this object will be merged with colData from inSCE1 and loaded into inSCE1.

    -
    id1
    +
    id1

    Character vector. Column in colData of inSCE1 that will be used to combine inSCE1 and inSCE2. Default "column_name"

    -
    id2
    +
    id2

    Character vector. Column in colData of inSCE2 that will be used to combine inSCE1 and inSCE2. Default "column_name"

    Value

    - - -

    SingleCellExperiment object containing combined colData from +

    SingleCellExperiment object containing combined colData from both singleCellExperiment for samples in inSCE1.

    @@ -270,15 +270,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/mouseBrainSubsetSCE.html b/docs/reference/mouseBrainSubsetSCE.html index 518997f0a..ddc880e86 100644 --- a/docs/reference/mouseBrainSubsetSCE.html +++ b/docs/reference/mouseBrainSubsetSCE.html @@ -1,7 +1,5 @@ -Example Single Cell RNA-Seq data in SingleCellExperiment Object, GSE60361 -subset — mouseBrainSubsetSCE • singleCellTKExample Single Cell RNA-Seq data in SingleCellExperiment Object, GSE60361 subset — mouseBrainSubsetSCE • singleCellTK - +
    @@ -31,7 +29,7 @@
    - +
    -

    Example Single Cell RNA-Seq data in SingleCellExperiment Object, GSE60361 -subset

    +

    Example Single Cell RNA-Seq data in SingleCellExperiment Object, GSE60361 subset

    Source: R/data.R
    @@ -232,9 +229,7 @@

    Source

    Value

    - - -

    A subset of 30 cells from a single cell RNA-Seq experiment

    +

    A subset of 30 cells from a single cell RNA-Seq experiment

    @@ -254,15 +249,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/msigdb_table.html b/docs/reference/msigdb_table.html index 30b22c63e..b055b181b 100644 --- a/docs/reference/msigdb_table.html +++ b/docs/reference/msigdb_table.html @@ -1,5 +1,5 @@ -MSigDB gene get Category table — msigdb_table • singleCellTKMSigDB gene get Category table — msigdb_table • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -225,9 +225,7 @@

    Format

    Value

    - - -

    A table of gene set categories

    +

    A table of gene set categories

    @@ -247,15 +245,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotBarcodeRankDropsResults-1.png b/docs/reference/plotBarcodeRankDropsResults-1.png index c2a197fa5..2da4a670c 100644 Binary files a/docs/reference/plotBarcodeRankDropsResults-1.png and b/docs/reference/plotBarcodeRankDropsResults-1.png differ diff --git a/docs/reference/plotBarcodeRankDropsResults.html b/docs/reference/plotBarcodeRankDropsResults.html index 13e52276c..84be86a14 100644 --- a/docs/reference/plotBarcodeRankDropsResults.html +++ b/docs/reference/plotBarcodeRankDropsResults.html @@ -1,11 +1,11 @@ -Plots for runBarcodeRankDrops outputs. — plotBarcodeRankDropsResults • singleCellTKPlots for runBarcodeRankDrops outputs. — plotBarcodeRankDropsResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -207,7 +207,7 @@

    Plots for runBarcodeRankDrops outputs.

    A wrapper function which visualizes outputs from the -runBarcodeRankDrops function stored in the metadata slot of +runBarcodeRankDrops function stored in the metadata slot of the SingleCellExperiment object.

    @@ -226,54 +226,54 @@

    Plots for runBarcodeRankDrops outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runBarcodeRankDrops. Required.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    defaultTheme
    -

    Removes grid in plot and sets axis title size to +

    defaultTheme
    +

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 18.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 15.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 18.

    -
    legendSize
    +
    legendSize

    size of legend. Default 15.

    Value

    - - -

    list of .ggplot objects

    +

    list of .ggplot objects

    Examples

    data(scExample, package = "singleCellTK")
 sce <- runBarcodeRankDrops(inSCE = sce)
-#> Fri May  3 07:15:02 2024 ... Running 'barcodeRanks'
+#> Thu Feb 13 10:28:11 2025 ... Running 'barcodeRanks'
 plotBarcodeRankDropsResults(inSCE = sce)
 #> $scatterBarcodeRank
 #> Warning: log-10 transformation introduced infinite values.
@@ -293,15 +293,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotBarcodeRankScatter-1.png b/docs/reference/plotBarcodeRankScatter-1.png index f39f181a4..e7f6e83e3 100644 Binary files a/docs/reference/plotBarcodeRankScatter-1.png and b/docs/reference/plotBarcodeRankScatter-1.png differ diff --git a/docs/reference/plotBarcodeRankScatter.html b/docs/reference/plotBarcodeRankScatter.html index aa6b33c4a..5ab56e745 100644 --- a/docs/reference/plotBarcodeRankScatter.html +++ b/docs/reference/plotBarcodeRankScatter.html @@ -1,11 +1,11 @@ -Plots for runBarcodeRankDrops outputs. — plotBarcodeRankScatter • singleCellTKPlots for runBarcodeRankDrops outputs. — plotBarcodeRankScatter • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -232,80 +232,80 @@

    Plots for runBarcodeRankDrops outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runBarcodeRankDrops. Required.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    defaultTheme
    -

    Removes grid in plot and sets axis title size to +

    defaultTheme
    +

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.1.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 18.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 12.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 15.

    -
    legendSize
    +
    legendSize

    size of legend. Default 10.

    -
    combinePlot
    -

    Must be either "all", "sample", or -"none". "all" will combine all plots into a single .ggplot -object, while "sample" will output a list of plots separated by +

    combinePlot
    +

    Must be either "all", "sample", or +"none". "all" will combine all plots into a single .ggplot +object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    sampleRelHeights
    -

    If there are multiple samples and combining by +

    sampleRelHeights
    +

    If there are multiple samples and combining by "all", the relative heights for each plot. Default 1.

    -
    sampleRelWidths
    -

    If there are multiple samples and combining by +

    sampleRelWidths
    +

    If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

    Value

    - - -

    a ggplot object of the scatter plot.

    +

    a ggplot object of the scatter plot.

    See also

    -

    plotBarcodeRankDropsResults, +

    plotBarcodeRankDropsResults, runBarcodeRankDrops

    @@ -313,7 +313,7 @@

    See also

    Examples

    data(scExample, package = "singleCellTK")
 sce <- runBarcodeRankDrops(inSCE = sce)
-#> Fri May  3 07:15:03 2024 ... Running 'barcodeRanks'
+#> Thu Feb 13 10:28:12 2025 ... Running 'barcodeRanks'
 plotBarcodeRankScatter(inSCE = sce)
 #> Warning: log-10 transformation introduced infinite values.
 
@@ -331,15 +331,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotBatchCorrCompare-1.png b/docs/reference/plotBatchCorrCompare-1.png index f77bd8031..64e6ade79 100644 Binary files a/docs/reference/plotBatchCorrCompare-1.png and b/docs/reference/plotBatchCorrCompare-1.png differ diff --git a/docs/reference/plotBatchCorrCompare.html b/docs/reference/plotBatchCorrCompare.html index 2d7228a70..1abe20eac 100644 --- a/docs/reference/plotBatchCorrCompare.html +++ b/docs/reference/plotBatchCorrCompare.html @@ -1,9 +1,9 @@ -Plot comparison of batch corrected result against original assay — plotBatchCorrCompare • singleCellTKPlot comparison of batch corrected result against original assay — plotBatchCorrCompare • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -222,40 +222,42 @@

    Plot comparison of batch corrected result against original assay

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    corrMat
    +
    corrMat

    A single character indicating the name of the corrected matrix.

    -
    batch
    +
    batch

    A single character. The name of batch annotation column in colData(inSCE).

    -
    condition
    +
    condition

    A single character. The name of an additional covariate annotation column in colData(inSCE).

    -
    origAssay
    +
    origAssay

    A single character indicating what the original assay used for batch correction is.

    -
    origLogged
    +
    origLogged

    Logical scalar indicating whether origAssay is log-normalized.

    -
    method
    +
    method

    A single character indicating the name of the batch correction method. Only used for the titles of plots.

    -
    matType
    +
    matType

    A single character indicating the type of the batch correction result matrix, choose from "assay", "altExp", "reducedDim".

    @@ -263,9 +265,7 @@

    Arguments

    Value

    - - -

    An object of class "gtable", combining four ggplots.

    +

    An object of class "gtable", combining four ggplots.

    Details

    @@ -288,8 +288,8 @@

    Examples

    logcounts(sceBatches) <- log1p(counts(sceBatches)) sceBatches <- runLimmaBC(sceBatches) plotBatchCorrCompare(sceBatches, "LIMMA", condition = "cell_type") -#> Fri May 3 07:15:04 2024 ... Computing Scater UMAP for sample '1'. -#> Fri May 3 07:15:07 2024 ... Computing Scater UMAP for sample '1'. +#> Thu Feb 13 10:28:13 2025 ... Computing Scater UMAP for sample '1'. +#> Thu Feb 13 10:28:17 2025 ... Computing Scater UMAP for sample '1'. #> Warning: Removed 54 rows containing missing values or values outside the scale range #> (`geom_point()`). @@ -307,15 +307,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotBatchVariance-1.png b/docs/reference/plotBatchVariance-1.png index fefe52375..f5ec4d054 100644 Binary files a/docs/reference/plotBatchVariance-1.png and b/docs/reference/plotBatchVariance-1.png differ diff --git a/docs/reference/plotBatchVariance.html b/docs/reference/plotBatchVariance.html index 79c8edf6f..8eb4ff608 100644 --- a/docs/reference/plotBatchVariance.html +++ b/docs/reference/plotBatchVariance.html @@ -1,14 +1,12 @@ -Plot the percent of the variation that is explained by batch and condition -in the data — plotBatchVariance • singleCellTKPlot the percent of the variation that is explained by batch and condition in the data — plotBatchVariance • singleCellTK - +
    @@ -30,7 +28,7 @@
    - +
    -

    Plot the percent of the variation that is explained by batch and condition -in the data

    +

    Plot the percent of the variation that is explained by batch and condition in the data

    Source: R/plotBatchVariance.R
    @@ -230,46 +227,46 @@

    Plot the percent of the variation that is explained by batch and condition

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    useAssay
    +
    useAssay

    A single character. The name of the assay that stores the value to plot. For useReddim and useAltExp also. Default NULL.

    -
    useReddim
    +
    useReddim

    A single character. The name of the dimension reduced matrix that stores the value to plot. Default NULL.

    -
    useAltExp
    +
    useAltExp

    A single character. The name of the alternative experiment that stores an assay of the value to plot. Default NULL.

    -
    batch
    +
    batch

    A single character. The name of batch annotation column in colData(inSCE). Default "batch".

    -
    condition
    +
    condition

    A single character. The name of an additional condition annotation column in colData(inSCE). Default NULL.

    -
    title
    +
    title

    A single character. The title text on the top. Default NULL.

    Value

    - - -

    A ggplot object of a boxplot of variation explained by batch, +

    A ggplot object of a boxplot of variation explained by batch, condition, and batch+condition.

    @@ -303,15 +300,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotBcdsResults-1.png b/docs/reference/plotBcdsResults-1.png index e5c1a2a16..6635df124 100644 Binary files a/docs/reference/plotBcdsResults-1.png and b/docs/reference/plotBcdsResults-1.png differ diff --git a/docs/reference/plotBcdsResults.html b/docs/reference/plotBcdsResults.html index fc801bbec..dfee937a6 100644 --- a/docs/reference/plotBcdsResults.html +++ b/docs/reference/plotBcdsResults.html @@ -1,11 +1,11 @@ -Plots for runBcds outputs. — plotBcdsResults • singleCellTKPlots for runBcds outputs. — plotBcdsResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -252,182 +252,182 @@

    Plots for runBcds outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runBcds. Required.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    shape
    +
    shape

    If provided, add shapes based on the value. Default NULL.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector -equal length to the number of the samples in inSCE, or can be +equal length to the number of the samples in inSCE, or can be retrieved from the colData slot. Default NULL.

    -
    combinePlot
    -

    Must be either "all", "sample", or -"none". "all" will combine all plots into a single .ggplot -object, while "sample" will output a list of plots separated by +

    combinePlot
    +

    Must be either "all", "sample", or +"none". "all" will combine all plots into a single .ggplot +object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    violin
    -

    Boolean. If TRUE, will plot the violin plot. Default +

    violin
    +

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    -

    Boolean. If TRUE, will plot boxplots for each violin +

    boxplot
    +

    Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    reducedDimName
    -

    Saved dimension reduction name in inSCE. +

    reducedDimName
    +

    Saved dimension reduction name in inSCE. Default "UMAP".

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    dim1
    -

    1st dimension to be used for plotting. Can either be a string -which specifies the name of the dimension to be plotted from reducedDims, or -a numeric value which specifies the index of the dimension to be plotted. +

    dim1
    +

    1st dimension to be used for plotting. Can either be a string +which specifies the name of the dimension to be plotted from reducedDims, or +a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    dim2
    -

    2nd dimension to be used for plotting. Similar to dim1. +

    dim2
    +

    2nd dimension to be used for plotting. Similar to dim1. Default is NULL.

    -
    bin
    -

    Numeric vector. If single value, will divide the numeric values +

    bin
    +

    Numeric vector. If single value, will divide the numeric values into bin groups. If more than one value, will bin numeric values using values as a cut point. Default NULL.

    -
    binLabel
    +
    binLabel

    Character vector. Labels for the bins created by bin. Default NULL.

    -
    defaultTheme
    -

    Removes grid in plot and sets axis title size to +

    defaultTheme
    +

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the -violin plot. Options are "mean" or "median". Default +violin plot. Options are "mean" or "median". Default NULL.

    -
    summaryTextSize
    +
    summaryTextSize

    The text size of the summary statistic displayed above the violin plot. Default 3.

    -
    transparency
    -

    Transparency of the dots, values will be 0-1. Default +

    transparency
    +

    Transparency of the dots, values will be 0-1. Default 1.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 12. -Can be overwritten by titleSize, axisSize, and +Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    legendSize
    +
    legendSize

    size of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default NULL.

    -
    relHeights
    -

    Relative heights of plots when combine is set. Default +

    relHeights
    +

    Relative heights of plots when combine is set. Default 1.

    -
    relWidths
    -

    Relative widths of plots when combine is set. Default +

    relWidths
    +

    Relative widths of plots when combine is set. Default c(1, 1, 1).

    -
    plotNCols
    -

    Number of columns when plots are combined in a grid. Default +

    plotNCols
    +

    Number of columns when plots are combined in a grid. Default NULL.

    -
    plotNRows
    -

    Number of rows when plots are combined in a grid. Default +

    plotNRows
    +

    Number of rows when plots are combined in a grid. Default NULL.

    -
    labelSamples
    -

    Will label sample name in title of plot if TRUE. Default +

    labelSamples
    +

    Will label sample name in title of plot if TRUE. Default TRUE.

    -
    samplePerColumn
    -

    If TRUE, when there are multiple samples and -combining by "all", the output .ggplot will have plots from each +

    samplePerColumn
    +

    If TRUE, when there are multiple samples and +combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

    -
    sampleRelHeights
    -

    If there are multiple samples and combining by +

    sampleRelHeights
    +

    If there are multiple samples and combining by "all", the relative heights for each plot. Default 1.

    -
    sampleRelWidths
    -

    If there are multiple samples and combining by +

    sampleRelWidths
    +

    If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

    Value

    - - -

    list of .ggplot objects

    +

    list of .ggplot objects

    See also

    @@ -439,9 +439,9 @@

    Examples

    data(scExample, package="singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runQuickUMAP(sce)
-#> Fri May  3 07:15:13 2024 ... Computing Scater UMAP for sample 'pbmc_4k'.
+#> Thu Feb 13 10:28:22 2025 ... Computing Scater UMAP for sample 'pbmc_4k'.
 sce <- runBcds(sce)
-#> Fri May  3 07:15:16 2024 ... Running 'bcds'
+#> Thu Feb 13 10:28:26 2025 ... Running 'bcds'
 plotBcdsResults(inSCE=sce, reducedDimName="UMAP")
    @@ -458,15 +458,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotClusterAbundance.html b/docs/reference/plotClusterAbundance.html index 20ab3f026..39557d2bf 100644 --- a/docs/reference/plotClusterAbundance.html +++ b/docs/reference/plotClusterAbundance.html @@ -1,9 +1,9 @@ -Plot the differential Abundance — plotClusterAbundance • singleCellTKPlot the differential Abundance — plotClusterAbundance • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,33 +213,33 @@

    Plot the differential Abundance

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    cluster
    +
    cluster

    A single character, specifying the name to store the cluster label in colData.

    -
    variable
    +
    variable

    A single character, specifying the name to store the phenotype labels in colData.

    -
    combinePlot
    -

    Must be either "all" or "none". "all" will combine all -plots into a single ggplot object. Default +

    combinePlot
    +

    Must be either "all" or "none". "all" will combine all +plots into a single ggplot object. Default "all".

    Value

    - - -

    When combinePlot = "none", a list with 4 -ggplot objects; when combinePlot = "all", a +

    When combinePlot = "none", a list with 4 +ggplot objects; when combinePlot = "all", a single ggplot object with for subplots.

    @@ -270,15 +270,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotCxdsResults-1.png b/docs/reference/plotCxdsResults-1.png index c549f05bd..d5b1a951a 100644 Binary files a/docs/reference/plotCxdsResults-1.png and b/docs/reference/plotCxdsResults-1.png differ diff --git a/docs/reference/plotCxdsResults.html b/docs/reference/plotCxdsResults.html index 5193a1385..f833dfbd7 100644 --- a/docs/reference/plotCxdsResults.html +++ b/docs/reference/plotCxdsResults.html @@ -1,11 +1,11 @@ -Plots for runCxds outputs. — plotCxdsResults • singleCellTKPlots for runCxds outputs. — plotCxdsResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -252,182 +252,182 @@

    Plots for runCxds outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runCxds. Required.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    shape
    +
    shape

    If provided, add shapes based on the value. Default NULL.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector -equal length to the number of the samples in inSCE, or can be +equal length to the number of the samples in inSCE, or can be retrieved from the colData slot. Default NULL.

    -
    combinePlot
    -

    Must be either "all", "sample", or -"none". "all" will combine all plots into a single .ggplot -object, while "sample" will output a list of plots separated by +

    combinePlot
    +

    Must be either "all", "sample", or +"none". "all" will combine all plots into a single .ggplot +object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    violin
    -

    Boolean. If TRUE, will plot the violin plot. Default +

    violin
    +

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    -

    Boolean. If TRUE, will plot boxplots for each violin +

    boxplot
    +

    Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    reducedDimName
    -

    Saved dimension reduction name in inSCE. +

    reducedDimName
    +

    Saved dimension reduction name in inSCE. Default "UMAP".

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    dim1
    -

    1st dimension to be used for plotting. Can either be a string -which specifies the name of the dimension to be plotted from reducedDims, or -a numeric value which specifies the index of the dimension to be plotted. +

    dim1
    +

    1st dimension to be used for plotting. Can either be a string +which specifies the name of the dimension to be plotted from reducedDims, or +a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    dim2
    -

    2nd dimension to be used for plotting. Similar to dim1. +

    dim2
    +

    2nd dimension to be used for plotting. Similar to dim1. Default is NULL.

    -
    bin
    -

    Numeric vector. If single value, will divide the numeric values +

    bin
    +

    Numeric vector. If single value, will divide the numeric values into bin groups. If more than one value, will bin numeric values using values as a cut point. Default NULL.

    -
    binLabel
    +
    binLabel

    Character vector. Labels for the bins created by bin. Default NULL.

    -
    defaultTheme
    -

    Removes grid in plot and sets axis title size to +

    defaultTheme
    +

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the -violin plot. Options are "mean" or "median". Default +violin plot. Options are "mean" or "median". Default NULL.

    -
    summaryTextSize
    +
    summaryTextSize

    The text size of the summary statistic displayed above the violin plot. Default 3.

    -
    transparency
    -

    Transparency of the dots, values will be 0-1. Default +

    transparency
    +

    Transparency of the dots, values will be 0-1. Default 1.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 12. -Can be overwritten by titleSize, axisSize, and +Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    legendSize
    +
    legendSize

    size of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default NULL.

    -
    relHeights
    -

    Relative heights of plots when combine is set. Default +

    relHeights
    +

    Relative heights of plots when combine is set. Default 1.

    -
    relWidths
    -

    Relative widths of plots when combine is set. Default +

    relWidths
    +

    Relative widths of plots when combine is set. Default c(1, 1, 1).

    -
    plotNCols
    -

    Number of columns when plots are combined in a grid. Default +

    plotNCols
    +

    Number of columns when plots are combined in a grid. Default NULL.

    -
    plotNRows
    -

    Number of rows when plots are combined in a grid. Default +

    plotNRows
    +

    Number of rows when plots are combined in a grid. Default NULL.

    -
    labelSamples
    -

    Will label sample name in title of plot if TRUE. Default +

    labelSamples
    +

    Will label sample name in title of plot if TRUE. Default TRUE.

    -
    samplePerColumn
    -

    If TRUE, when there are multiple samples and -combining by "all", the output .ggplot will have plots from each +

    samplePerColumn
    +

    If TRUE, when there are multiple samples and +combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

    -
    sampleRelHeights
    -

    If there are multiple samples and combining by +

    sampleRelHeights
    +

    If there are multiple samples and combining by "all", the relative heights for each plot. Default 1.

    -
    sampleRelWidths
    -

    If there are multiple samples and combining by +

    sampleRelWidths
    +

    If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

    Value

    - - -

    list of .ggplot objects

    +

    list of .ggplot objects

    See also

    @@ -439,9 +439,9 @@

    Examples

    data(scExample, package="singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runQuickUMAP(sce)
-#> Fri May  3 07:15:22 2024 ... Computing Scater UMAP for sample 'pbmc_4k'.
+#> Thu Feb 13 10:28:31 2025 ... Computing Scater UMAP for sample 'pbmc_4k'.
 sce <- runCxds(sce)
-#> Fri May  3 07:15:25 2024 ... Running 'cxds'
+#> Thu Feb 13 10:28:34 2025 ... Running 'cxds'
 plotCxdsResults(inSCE=sce, reducedDimName="UMAP")
    @@ -458,15 +458,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotDEGHeatmap-1.png b/docs/reference/plotDEGHeatmap-1.png index 0e5461896..216243ebb 100644 Binary files a/docs/reference/plotDEGHeatmap-1.png and b/docs/reference/plotDEGHeatmap-1.png differ diff --git a/docs/reference/plotDEGHeatmap.html b/docs/reference/plotDEGHeatmap.html index edf797645..179390d61 100644 --- a/docs/reference/plotDEGHeatmap.html +++ b/docs/reference/plotDEGHeatmap.html @@ -1,9 +1,9 @@ -Heatmap visualization of DEG result — plotDEGHeatmap • singleCellTKHeatmap visualization of DEG result — plotDEGHeatmap • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -236,110 +236,112 @@

    Heatmap visualization of DEG result

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    useResult
    +
    useResult

    character. A string specifying the analysisName used when running a differential expression analysis function.

    -
    onlyPos
    +
    onlyPos

    logical. Whether to only plot DEG with positive log2_FC value. Default FALSE.

    -
    log2fcThreshold
    +
    log2fcThreshold

    numeric. Only plot DEGs with the absolute values of log2FC larger than this value. Default 0.25.

    -
    fdrThreshold
    +
    fdrThreshold

    numeric. Only plot DEGs with FDR value smaller than this value. Default 0.05.

    -
    minGroup1MeanExp
    +
    minGroup1MeanExp

    numeric. Only plot DEGs with mean expression in group1 greater then this value. Default NULL.

    -
    maxGroup2MeanExp
    +
    maxGroup2MeanExp

    numeric. Only plot DEGs with mean expression in group2 less then this value. Default NULL.

    -
    minGroup1ExprPerc
    +
    minGroup1ExprPerc

    numeric. Only plot DEGs expressed in greater then this fraction of cells in group1. Default NULL.

    -
    maxGroup2ExprPerc
    +
    maxGroup2ExprPerc

    numeric. Only plot DEGs expressed in less then this fraction of cells in group2. Default NULL.

    -
    useAssay
    +
    useAssay

    character. A string specifying an assay of expression value to plot. By default the assay used for runMAST() will be used. Default NULL.

    -
    doLog
    +
    doLog

    Logical scalar. Whether to do log(assay + 1) transformation on the assay used for the analysis. Default FALSE.

    -
    featureAnnotations
    +
    featureAnnotations

    data.frame, with rownames containing all the features going to be plotted. Character columns should be factors. Default NULL.

    -
    cellAnnotations
    +
    cellAnnotations

    data.frame, with rownames containing all the cells going to be plotted. Character columns should be factors. Default NULL.

    -
    featureAnnotationColor
    +
    featureAnnotationColor

    A named list. Customized color settings for feature labeling. Should match the entries in the featureAnnotations or rowDataName. For each entry, there should be a list/vector of colors named with categories. Default NULL.

    -
    cellAnnotationColor
    +
    cellAnnotationColor

    A named list. Customized color settings for cell labeling. Should match the entries in the cellAnnotations or colDataName. For each entry, there should be a list/vector of colors named with categories. Default NULL.

    -
    rowDataName
    +
    rowDataName

    character. The column name(s) in rowData that need to be added to the annotation. Default NULL.

    -
    colDataName
    +
    colDataName

    character. The column name(s) in colData that need to be added to the annotation. Default NULL.

    -
    colSplitBy
    +
    colSplitBy

    character. Do semi-heatmap based on the grouping of this(these) annotation(s). Should exist in either colDataName or names(cellAnnotations). Default "condition".

    -
    rowSplitBy
    +
    rowSplitBy

    character. Do semi-heatmap based on the grouping of this(these) annotation(s). Should exist in either rowDataName or names(featureAnnotations). Default "regulation".

    -
    rowLabel
    +
    rowLabel

    FALSE for not displaying; a variable in rowData to display feature identifiers stored there; if have run setSCTKDisplayRow, display the specified feature name; @@ -348,20 +350,18 @@

    Arguments

    than 60. Default looks for setSCTKDisplayRow information.

    -
    title
    +
    title

    character. Main title of the heatmap. Default "DE Analysis: <useResult>".

    -
    ...
    +
    ...

    Other arguments passed to plotSCEHeatmap

    Value

    - - -

    A ggplot object

    +

    A ggplot object

    Details

    @@ -388,7 +388,7 @@

    Examples

    classGroup1 = "alpha", classGroup2 = "beta", groupName1 = "w.alpha", groupName2 = "w.beta", analysisName = "w.aVSb") -#> Fri May 3 07:15:27 2024 ... Running DE with wilcox, Analysis name: w.aVSb +#> Thu Feb 13 10:28:35 2025 ... Running DE with wilcox, Analysis name: w.aVSb plotDEGHeatmap(sce.w, "w.aVSb")
    @@ -405,15 +405,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotDEGRegression-1.png b/docs/reference/plotDEGRegression-1.png index 90836bc0b..73e99bd8a 100644 Binary files a/docs/reference/plotDEGRegression-1.png and b/docs/reference/plotDEGRegression-1.png differ diff --git a/docs/reference/plotDEGRegression.html b/docs/reference/plotDEGRegression.html index eaced7390..17264351b 100644 --- a/docs/reference/plotDEGRegression.html +++ b/docs/reference/plotDEGRegression.html @@ -1,9 +1,9 @@ -Create linear regression plot to show the expression the of top DEGs — plotDEGRegression • singleCellTKCreate linear regression plot to show the expression the of top DEGs — plotDEGRegression • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -223,55 +223,55 @@

    Create linear regression plot to show the expression the of top DEGs

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    useResult
    +
    useResult

    character. A string specifying the analysisName used when running a differential expression analysis function.

    -
    threshP
    +
    threshP

    logical. Whether to plot threshold values from adaptive thresholding, instead of using the assay used by when performing DE analysis. Default FALSE.

    -
    labelBy
    +
    labelBy

    A single character for a column of rowData(inSCE) as where to search for the labeling text. Default NULL.

    -
    nrow
    +
    nrow

    Integer. Number of rows in the plot grid. Default 6.

    -
    ncol
    +
    ncol

    Integer. Number of columns in the plot grid. Default 6.

    -
    defaultTheme
    +
    defaultTheme

    Logical scalar. Whether to use default SCTK theme in ggplot. Default TRUE.

    -
    isLogged
    +
    isLogged

    Logical scalar. Whether the assay used for the analysis is logged. If not, will do a log(assay + 1) transformation. Default TRUE.

    -
    check_sanity
    +
    check_sanity

    Logical scalar. Whether to perform MAST's sanity check to see if the counts are logged. Default TRUE

    Value

    - - -

    A ggplot object of linear regression

    +

    A ggplot object of linear regression

    Details

    @@ -288,7 +288,7 @@

    Examples

    classGroup1 = "alpha", classGroup2 = "beta", groupName1 = "w.alpha", groupName2 = "w.beta", analysisName = "w.aVSb") -#> Fri May 3 07:15:30 2024 ... Running DE with wilcox, Analysis name: w.aVSb +#> Thu Feb 13 10:28:38 2025 ... Running DE with wilcox, Analysis name: w.aVSb plotDEGRegression(sce.w, "w.aVSb")
    @@ -305,15 +305,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotDEGViolin-1.png b/docs/reference/plotDEGViolin-1.png index ebd343e55..fe992b273 100644 Binary files a/docs/reference/plotDEGViolin-1.png and b/docs/reference/plotDEGViolin-1.png differ diff --git a/docs/reference/plotDEGViolin.html b/docs/reference/plotDEGViolin.html index cff518077..d4fb1aa53 100644 --- a/docs/reference/plotDEGViolin.html +++ b/docs/reference/plotDEGViolin.html @@ -1,9 +1,9 @@ -Generate violin plot to show the expression of top DEGs — plotDEGViolin • singleCellTKGenerate violin plot to show the expression of top DEGs — plotDEGViolin • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -223,55 +223,55 @@

    Generate violin plot to show the expression of top DEGs

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    useResult
    +
    useResult

    character. A string specifying the analysisName used when running a differential expression analysis function.

    -
    threshP
    +
    threshP

    logical. Whether to plot threshold values from adaptive thresholding, instead of using the assay used by runMAST(). Default FALSE.

    -
    labelBy
    +
    labelBy

    A single character for a column of rowData(inSCE) as where to search for the labeling text. Default NULL.

    -
    nrow
    +
    nrow

    Integer. Number of rows in the plot grid. Default 6.

    -
    ncol
    +
    ncol

    Integer. Number of columns in the plot grid. Default 6.

    -
    defaultTheme
    +
    defaultTheme

    Logical scalar. Whether to use default SCTK theme in ggplot. Default TRUE.

    -
    isLogged
    +
    isLogged

    Logical scalar. Whether the assay used for the analysis is logged. If not, will do a log(assay + 1) transformation. Default TRUE.

    -
    check_sanity
    +
    check_sanity

    Logical scalar. Whether to perform MAST's sanity check to see if the counts are logged. Default TRUE

    Value

    - - -

    A ggplot object of violin plot

    +

    A ggplot object of violin plot

    Details

    @@ -288,7 +288,7 @@

    Examples

    classGroup1 = "alpha", classGroup2 = "beta", groupName1 = "w.alpha", groupName2 = "w.beta", analysisName = "w.aVSb") -#> Fri May 3 07:15:34 2024 ... Running DE with wilcox, Analysis name: w.aVSb +#> Thu Feb 13 10:28:41 2025 ... Running DE with wilcox, Analysis name: w.aVSb plotDEGViolin(sce.w, "w.aVSb")
    @@ -305,15 +305,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotDEGVolcano-1.png b/docs/reference/plotDEGVolcano-1.png index 8bd6e64ed..2b1ef623e 100644 Binary files a/docs/reference/plotDEGVolcano-1.png and b/docs/reference/plotDEGVolcano-1.png differ diff --git a/docs/reference/plotDEGVolcano.html b/docs/reference/plotDEGVolcano.html index 3a2c82af1..bcad437c1 100644 --- a/docs/reference/plotDEGVolcano.html +++ b/docs/reference/plotDEGVolcano.html @@ -1,9 +1,9 @@ -Generate volcano plot for DEGs — plotDEGVolcano • singleCellTKGenerate volcano plot for DEGs — plotDEGVolcano • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,31 +220,33 @@

    Generate volcano plot for DEGs

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    useResult
    +
    useResult

    character. A string specifying the analysisName used when running a differential expression analysis function.

    -
    labelTopN
    +
    labelTopN

    Integer, label this number of top DEGs that pass the filters. FALSE for not labeling. Default 10.

    -
    log2fcThreshold
    +
    log2fcThreshold

    numeric. Label genes with the absolute values of log2FC greater than this value as regulated. Default 0.25.

    -
    fdrThreshold
    +
    fdrThreshold

    numeric. Label genes with FDR value less than this value as regulated. Default 0.05.

    -
    featureDisplay
    +
    featureDisplay

    A character string to indicate a variable in rowData(inSCE) for feature labeling. NULL for using rownames. Default metadata(inSCE)$featureDisplay (see @@ -253,9 +255,7 @@

    Arguments

    Value

    - - -

    A ggplot object of volcano plot

    +

    A ggplot object of volcano plot

    Details

    @@ -276,7 +276,7 @@

    Examples

    classGroup1 = "alpha", classGroup2 = "beta", groupName1 = "w.alpha", groupName2 = "w.beta", analysisName = "w.aVSb") -#> Fri May 3 07:15:39 2024 ... Running DE with wilcox, Analysis name: w.aVSb +#> Thu Feb 13 10:28:45 2025 ... Running DE with wilcox, Analysis name: w.aVSb plotDEGVolcano(sce.w, "w.aVSb")
    @@ -293,15 +293,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotDecontXResults-1.png b/docs/reference/plotDecontXResults-1.png index c49f12ee9..0c4bd6d73 100644 Binary files a/docs/reference/plotDecontXResults-1.png and b/docs/reference/plotDecontXResults-1.png differ diff --git a/docs/reference/plotDecontXResults.html b/docs/reference/plotDecontXResults.html index 828a03c67..912ad4cb9 100644 --- a/docs/reference/plotDecontXResults.html +++ b/docs/reference/plotDecontXResults.html @@ -1,11 +1,11 @@ -Plots for runDecontX outputs. — plotDecontXResults • singleCellTKPlots for runDecontX outputs. — plotDecontXResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -255,185 +255,185 @@

    Plots for runDecontX outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runDecontX. Required.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to. Default NULL.

    -
    bgResult
    +
    bgResult

    Boolean. If TRUE, will plot decontX results generated with raw/droplet matrix Default FALSE.

    -
    shape
    +
    shape

    If provided, add shapes based on the value.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    violin
    +
    violin

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    +
    boxplot

    Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    reducedDimName
    +
    reducedDimName

    Saved dimension reduction name in the SingleCellExperiment object. Required. Default = "UMAP"

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    dim1
    +
    dim1

    1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    dim2
    +
    dim2

    2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    bin
    +
    bin

    Numeric vector. If single value, will divide the numeric values into the `bin` groups. If more than one value, will bin numeric values using values as a cut point.

    -
    binLabel
    +
    binLabel

    Character vector. Labels for the bins created by the `bin` parameter. Default NULL.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.

    -
    summaryTextSize
    +
    summaryTextSize

    The text size of the summary statistic displayed above the violin plot. Default 3.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    legendSize
    +
    legendSize

    size of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default NULL.

    -
    relHeights
    +
    relHeights

    Relative heights of plots when combine is set.

    -
    relWidths
    +
    relWidths

    Relative widths of plots when combine is set.

    -
    plotNCols
    +
    plotNCols

    Number of columns when plots are combined in a grid.

    -
    plotNRows
    +
    plotNRows

    Number of rows when plots are combined in a grid.

    -
    labelSamples
    +
    labelSamples

    Will label sample name in title of plot if TRUE. Default TRUE.

    -
    labelClusters
    +
    labelClusters

    Logical. Whether the cluster labels are plotted. Default FALSE.

    -
    clusterLabelSize
    +
    clusterLabelSize

    Numeric. Determines the size of cluster label when `labelClusters` is set to TRUE. Default 3.5.

    -
    samplePerColumn
    +
    samplePerColumn

    If TRUE, when there are multiple samples and combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

    -
    sampleRelHeights
    +
    sampleRelHeights

    If there are multiple samples and combining by "all", the relative heights for each plot.

    -
    sampleRelWidths
    +
    sampleRelWidths

    If there are multiple samples and combining by "all", the relative widths for each plot.

    Value

    - - -

    list of .ggplot objects

    +

    list of .ggplot objects

    @@ -441,27 +441,27 @@

    Examples

    data(scExample, package="singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runDecontX(sce)
-#> Fri May  3 07:15:40 2024 ... Running 'DecontX'
+#> Thu Feb 13 10:28:46 2025 ... Running 'DecontX'
 #> --------------------------------------------------
 #> Starting DecontX
 #> --------------------------------------------------
-#> Fri May  3 07:15:40 2024 .. Analyzing all cells
-#> Fri May  3 07:15:40 2024 .... Generating UMAP and estimating cell types
-#> Fri May  3 07:15:44 2024 .... Estimating contamination
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 10 | converge: 0.0278
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 20 | converge: 0.01058
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 30 | converge: 0.00584
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 40 | converge: 0.004697
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 50 | converge: 0.003356
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 60 | converge: 0.002634
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 70 | converge: 0.001941
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 80 | converge: 0.001413
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 90 | converge: 0.001284
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 100 | converge: 0.00111
-#> Fri May  3 07:15:44 2024 ...... Completed iteration: 104 | converge: 0.0009827
-#> Fri May  3 07:15:44 2024 .. Calculating final decontaminated matrix
+#> Thu Feb 13 10:28:46 2025 .. Analyzing all cells
+#> Thu Feb 13 10:28:46 2025 .... Generating UMAP and estimating cell types
+#> Thu Feb 13 10:28:50 2025 .... Estimating contamination
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 10 | converge: 0.0278
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 20 | converge: 0.01058
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 30 | converge: 0.00584
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 40 | converge: 0.004697
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 50 | converge: 0.003356
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 60 | converge: 0.002634
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 70 | converge: 0.001941
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 80 | converge: 0.001413
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 90 | converge: 0.001284
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 100 | converge: 0.00111
+#> Thu Feb 13 10:28:50 2025 ...... Completed iteration: 104 | converge: 0.0009827
+#> Thu Feb 13 10:28:50 2025 .. Calculating final decontaminated matrix
 #> --------------------------------------------------
-#> Completed DecontX. Total time: 4.065205 secs
+#> Completed DecontX. Total time: 3.789843 secs
 #> --------------------------------------------------
 plotDecontXResults(inSCE=sce, reducedDimName="decontX_UMAP")
 
@@ -479,15 +479,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotDimRed-1.png b/docs/reference/plotDimRed-1.png index 1d887b104..1d7a27e55 100644 Binary files a/docs/reference/plotDimRed-1.png and b/docs/reference/plotDimRed-1.png differ diff --git a/docs/reference/plotDimRed.html b/docs/reference/plotDimRed.html index c192ed285..39dfd4b20 100644 --- a/docs/reference/plotDimRed.html +++ b/docs/reference/plotDimRed.html @@ -1,12 +1,10 @@ -Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE -and UMAP — plotDimRed • singleCellTKPlot dimensionality reduction from computed metrics including PCA, ICA, tSNE and UMAP — plotDimRed • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE -and UMAP

    +

    Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE and UMAP

    Source: R/plotDimRed.R
    @@ -226,43 +223,43 @@

    Plot dimensionality reduction from computed metrics including PCA, ICA, tSNE

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SCE object

    -
    useReduction
    +
    useReduction

    Reduction to plot. Default is "PCA".

    -
    showLegend
    +
    showLegend

    If legends should be plotted or not

    -
    xDim
    +
    xDim

    Numeric value indicating the dimension to use for X-axis. Default is 1 (refers to PC1).

    -
    yDim
    +
    yDim

    Numeric value indicating the dimension to use for Y-axis. Default is 2 (refers to PC2).

    -
    xAxisLabel
    +
    xAxisLabel

    Specify the label for x-axis. Default is NULL which will specify the label as 'x'.

    -
    yAxisLabel
    +
    yAxisLabel

    Specify the label for y-axis. Default is NULL which will specify the label as 'y'.

    Value

    - - -

    plot object

    +

    plot object

    @@ -284,15 +281,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotDoubletFinderResults-1.png b/docs/reference/plotDoubletFinderResults-1.png index bb7def64c..cc0923420 100644 Binary files a/docs/reference/plotDoubletFinderResults-1.png and b/docs/reference/plotDoubletFinderResults-1.png differ diff --git a/docs/reference/plotDoubletFinderResults.html b/docs/reference/plotDoubletFinderResults.html index 6cefcb83f..e61c04381 100644 --- a/docs/reference/plotDoubletFinderResults.html +++ b/docs/reference/plotDoubletFinderResults.html @@ -1,11 +1,11 @@ -Plots for runDoubletFinder outputs. — plotDoubletFinderResults • singleCellTKPlots for runDoubletFinder outputs. — plotDoubletFinderResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -252,182 +252,182 @@

    Plots for runDoubletFinder outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runDoubletFinder. Required.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    shape
    +
    shape

    If provided, add shapes based on the value. Default NULL.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector -equal length to the number of the samples in inSCE, or can be +equal length to the number of the samples in inSCE, or can be retrieved from the colData slot. Default NULL.

    -
    combinePlot
    -

    Must be either "all", "sample", or -"none". "all" will combine all plots into a single .ggplot -object, while "sample" will output a list of plots separated by +

    combinePlot
    +

    Must be either "all", "sample", or +"none". "all" will combine all plots into a single .ggplot +object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    violin
    -

    Boolean. If TRUE, will plot the violin plot. Default +

    violin
    +

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    -

    Boolean. If TRUE, will plot boxplots for each violin +

    boxplot
    +

    Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    reducedDimName
    -

    Saved dimension reduction name in inSCE. +

    reducedDimName
    +

    Saved dimension reduction name in inSCE. Default "UMAP".

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    dim1
    -

    1st dimension to be used for plotting. Can either be a string -which specifies the name of the dimension to be plotted from reducedDims, or -a numeric value which specifies the index of the dimension to be plotted. +

    dim1
    +

    1st dimension to be used for plotting. Can either be a string +which specifies the name of the dimension to be plotted from reducedDims, or +a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    dim2
    -

    2nd dimension to be used for plotting. Similar to dim1. +

    dim2
    +

    2nd dimension to be used for plotting. Similar to dim1. Default is NULL.

    -
    bin
    -

    Numeric vector. If single value, will divide the numeric values +

    bin
    +

    Numeric vector. If single value, will divide the numeric values into bin groups. If more than one value, will bin numeric values using values as a cut point. Default NULL.

    -
    binLabel
    +
    binLabel

    Character vector. Labels for the bins created by bin. Default NULL.

    -
    defaultTheme
    -

    Removes grid in plot and sets axis title size to +

    defaultTheme
    +

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the -violin plot. Options are "mean" or "median". Default +violin plot. Options are "mean" or "median". Default NULL.

    -
    summaryTextSize
    +
    summaryTextSize

    The text size of the summary statistic displayed above the violin plot. Default 3.

    -
    transparency
    -

    Transparency of the dots, values will be 0-1. Default +

    transparency
    +

    Transparency of the dots, values will be 0-1. Default 1.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 12. -Can be overwritten by titleSize, axisSize, and +Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    legendSize
    +
    legendSize

    size of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default NULL.

    -
    relHeights
    -

    Relative heights of plots when combine is set. Default +

    relHeights
    +

    Relative heights of plots when combine is set. Default 1.

    -
    relWidths
    -

    Relative widths of plots when combine is set. Default +

    relWidths
    +

    Relative widths of plots when combine is set. Default c(1, 1, 1).

    -
    plotNCols
    -

    Number of columns when plots are combined in a grid. Default +

    plotNCols
    +

    Number of columns when plots are combined in a grid. Default NULL.

    -
    plotNRows
    -

    Number of rows when plots are combined in a grid. Default +

    plotNRows
    +

    Number of rows when plots are combined in a grid. Default NULL.

    -
    labelSamples
    -

    Will label sample name in title of plot if TRUE. Default +

    labelSamples
    +

    Will label sample name in title of plot if TRUE. Default TRUE.

    -
    samplePerColumn
    -

    If TRUE, when there are multiple samples and -combining by "all", the output .ggplot will have plots from each +

    samplePerColumn
    +

    If TRUE, when there are multiple samples and +combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

    -
    sampleRelHeights
    -

    If there are multiple samples and combining by +

    sampleRelHeights
    +

    If there are multiple samples and combining by "all", the relative heights for each plot. Default 1.

    -
    sampleRelWidths
    -

    If there are multiple samples and combining by +

    sampleRelWidths
    +

    If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

    Value

    - - -

    list of .ggplot objects

    +

    list of .ggplot objects

    See also

    @@ -439,9 +439,9 @@

    Examples

    data(scExample, package="singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runQuickUMAP(sce)
-#> Fri May  3 07:15:48 2024 ... Computing Scater UMAP for sample 'pbmc_4k'.
+#> Thu Feb 13 10:28:52 2025 ... Computing Scater UMAP for sample 'pbmc_4k'.
 sce <- runDoubletFinder(sce)
-#> Fri May  3 07:15:51 2024 ... Running 'doubletFinder'
+#> Thu Feb 13 10:28:57 2025 ... Running 'doubletFinder'
 #> Normalizing layer: counts
 #> Finding variable features for layer counts
 #> Centering and scaling data matrix
@@ -464,15 +464,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotEmptyDropsResults-1.png b/docs/reference/plotEmptyDropsResults-1.png index 2665c04f1..57ef6c56e 100644 Binary files a/docs/reference/plotEmptyDropsResults-1.png and b/docs/reference/plotEmptyDropsResults-1.png differ diff --git a/docs/reference/plotEmptyDropsResults.html b/docs/reference/plotEmptyDropsResults.html index 6925da25a..76b3010be 100644 --- a/docs/reference/plotEmptyDropsResults.html +++ b/docs/reference/plotEmptyDropsResults.html @@ -1,11 +1,11 @@ -Plots for runEmptyDrops outputs. — plotEmptyDropsResults • singleCellTKPlots for runEmptyDrops outputs. — plotEmptyDropsResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -207,7 +207,7 @@

    Plots for runEmptyDrops outputs.

    A wrapper function which visualizes outputs from the -runEmptyDrops function stored in the colData slot of the +runEmptyDrops function stored in the colData slot of the SingleCellExperiment object.

    @@ -234,90 +234,90 @@

    Plots for runEmptyDrops outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runEmptyDrops. Required.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or object, -"none". "all" will combine all plots into a single .ggplot -while "sample" will output a list of plots separated by sample. +"none". "all" will combine all plots into a single .ggplot +while "sample" will output a list of plots separated by sample. Default "all".

    -
    fdrCutoff
    +
    fdrCutoff

    Numeric. Thresholds barcodes based on the FDR values from -runEmptyDrops as "Empty Droplet" or "Putative Cell". Default +runEmptyDrops as "Empty Droplet" or "Putative Cell". Default 0.01.

    -
    defaultTheme
    -

    Removes grid in plot and sets axis title size to +

    defaultTheme
    +

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 18.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 18.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 15.

    -
    legendSize
    +
    legendSize

    size of legend. Default 15.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default 16.

    -
    relHeights
    -

    Relative heights of plots when combine is set. Default +

    relHeights
    +

    Relative heights of plots when combine is set. Default 1.

    -
    relWidths
    -

    Relative widths of plots when combine is set. Default +

    relWidths
    +

    Relative widths of plots when combine is set. Default 1.

    -
    samplePerColumn
    -

    If TRUE, when there are multiple samples and -combining by "all", the output .ggplot will have plots from each +

    samplePerColumn
    +

    If TRUE, when there are multiple samples and +combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

    -
    sampleRelHeights
    -

    If there are multiple samples and combining by +

    sampleRelHeights
    +

    If there are multiple samples and combining by "all", the relative heights for each plot. Default 1.

    -
    sampleRelWidths
    -

    If there are multiple samples and combining by +

    sampleRelWidths
    +

    If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

    Value

    - - -

    list of .ggplot objects

    +

    list of .ggplot objects

    See also

    @@ -328,7 +328,7 @@

    See also

    Examples

    data(scExample, package = "singleCellTK")
 sce <- runEmptyDrops(inSCE = sce)
-#> Fri May  3 07:16:16 2024 ... Running 'emptyDrops'
+#> Thu Feb 13 10:29:20 2025 ... Running 'emptyDrops'
 plotEmptyDropsResults(inSCE = sce)
 #> $scatterEmptyDrops
 
@@ -347,15 +347,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotEmptyDropsScatter-1.png b/docs/reference/plotEmptyDropsScatter-1.png index b6aed4da1..bc4de5740 100644 Binary files a/docs/reference/plotEmptyDropsScatter-1.png and b/docs/reference/plotEmptyDropsScatter-1.png differ diff --git a/docs/reference/plotEmptyDropsScatter.html b/docs/reference/plotEmptyDropsScatter.html index 6acea1c49..56a0b9547 100644 --- a/docs/reference/plotEmptyDropsScatter.html +++ b/docs/reference/plotEmptyDropsScatter.html @@ -1,11 +1,11 @@ -Plots for runEmptyDrops outputs. — plotEmptyDropsScatter • singleCellTKPlots for runEmptyDrops outputs. — plotEmptyDropsScatter • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -207,7 +207,7 @@

    Plots for runEmptyDrops outputs.

    A plotting function which visualizes outputs from the -runEmptyDrops function stored in the colData slot of the +runEmptyDrops function stored in the colData slot of the SingleCellExperiment object via scatter plots.

    @@ -238,106 +238,106 @@

    Plots for runEmptyDrops outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runEmptyDrops. Required.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    fdrCutoff
    +
    fdrCutoff

    Numeric. Thresholds barcodes based on the FDR values from -runEmptyDrops as "Empty Droplet" or "Putative Cell". Default +runEmptyDrops as "Empty Droplet" or "Putative Cell". Default 0.01.

    -
    defaultTheme
    -

    Removes grid in plot and sets axis title size to +

    defaultTheme
    +

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.1.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 18.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 12.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 15.

    -
    legendTitle
    +
    legendTitle

    Title of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default 12.

    -
    legendSize
    +
    legendSize

    size of legend. Default 10.

    -
    combinePlot
    -

    Must be either "all", "sample", or -"none". "all" will combine all plots into a single .ggplot -object, while "sample" will output a list of plots separated by +

    combinePlot
    +

    Must be either "all", "sample", or +"none". "all" will combine all plots into a single .ggplot +object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    relHeights
    -

    Relative heights of plots when combine is set. Default +

    relHeights
    +

    Relative heights of plots when combine is set. Default 1.

    -
    relWidths
    -

    Relative widths of plots when combine is set. Default +

    relWidths
    +

    Relative widths of plots when combine is set. Default 1.

    -
    samplePerColumn
    -

    If TRUE, when there are multiple samples and -combining by "all", the output .ggplot will have plots from each +

    samplePerColumn
    +

    If TRUE, when there are multiple samples and +combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

    -
    sampleRelHeights
    -

    If there are multiple samples and combining by +

    sampleRelHeights
    +

    If there are multiple samples and combining by "all", the relative heights for each plot. Default 1.

    -
    sampleRelWidths
    -

    If there are multiple samples and combining by +

    sampleRelWidths
    +

    If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

    Value

    - - -

    a ggplot object of the scatter plot.

    +

    a ggplot object of the scatter plot.

    See also

    @@ -348,7 +348,7 @@

    See also

    Examples

    data(scExample, package = "singleCellTK")
 sce <- runEmptyDrops(inSCE = sce)
-#> Fri May  3 07:16:21 2024 ... Running 'emptyDrops'
+#> Thu Feb 13 10:29:25 2025 ... Running 'emptyDrops'
 plotEmptyDropsScatter(inSCE = sce)
    @@ -365,15 +365,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotFindMarkerHeatmap-1.png b/docs/reference/plotFindMarkerHeatmap-1.png index f4131731a..8abc90bff 100644 Binary files a/docs/reference/plotFindMarkerHeatmap-1.png and b/docs/reference/plotFindMarkerHeatmap-1.png differ diff --git a/docs/reference/plotFindMarkerHeatmap.html b/docs/reference/plotFindMarkerHeatmap.html index ca106e7c0..925875e48 100644 --- a/docs/reference/plotFindMarkerHeatmap.html +++ b/docs/reference/plotFindMarkerHeatmap.html @@ -1,5 +1,5 @@ -Plot a heatmap to visualize the result of runFindMarker — plotFindMarkerHeatmap • singleCellTK - +
    @@ -36,7 +36,7 @@
    - +
    @@ -282,98 +282,100 @@

    Plot a heatmap to visualize the result of

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    orderBy
    +
    orderBy

    The ordering method of the clusters on the splitted heatmap. Can be chosen from "size" or "name", specified with vector of ordered unique cluster labels, or set as NULL for unsplitted heatmap. Default "size".

    -
    log2fcThreshold
    +
    log2fcThreshold

    Only use DEGs with the absolute values of log2FC larger than this value. Default 1

    -
    fdrThreshold
    +
    fdrThreshold

    Only use DEGs with FDR value smaller than this value. Default 0.05

    -
    minClustExprPerc
    +
    minClustExprPerc

    A numeric scalar. The minimum cutoff of the percentage of cells in the cluster of interests that expressed the marker gene. Default 0.7.

    -
    maxCtrlExprPerc
    +
    maxCtrlExprPerc

    A numeric scalar. The maximum cutoff of the percentage of cells out of the cluster (control group) that expressed the marker gene. Default 0.4.

    -
    minMeanExpr
    +
    minMeanExpr

    A numeric scalar. The minimum cutoff of the mean expression value of the marker in the cluster of interests. Default 1.

    -
    topN
    +
    topN

    An integer. Only to plot this number of top markers for each cluster in maximum, in terms of log2FC value. Use NULL to cancel the top N subscription. Default 10.

    -
    decreasing
    +
    decreasing

    Order the cluster decreasingly. Default TRUE.

    -
    rowLabel
    +
    rowLabel

    TRUE for displaying rownames of inSCE, a rowData variable to use other feature identifiers, or a vector for customized row labels. Use FALSE for not displaying. Default TRUE.

    -
    rowDataName
    +
    rowDataName

    character. The column name(s) in rowData that need to be added to the annotation. Default NULL.

    -
    colDataName
    +
    colDataName

    character. The column name(s) in colData that need to be added to the annotation. Default NULL.

    -
    featureAnnotations
    +
    featureAnnotations

    data.frame, with rownames containing all the features going to be plotted. Character columns should be factors. Default NULL.

    -
    cellAnnotations
    +
    cellAnnotations

    data.frame, with rownames containing all the cells going to be plotted. Character columns should be factors. Default NULL.

    -
    featureAnnotationColor
    +
    featureAnnotationColor

    A named list. Customized color settings for feature labeling. Should match the entries in the featureAnnotations or rowDataName. For each entry, there should be a list/vector of colors named with categories. Default NULL.

    -
    cellAnnotationColor
    +
    cellAnnotationColor

    A named list. Customized color settings for cell labeling. Should match the entries in the cellAnnotations or colDataName. For each entry, there should be a list/vector of colors named with categories. Default NULL.

    -
    colSplitBy
    +
    colSplitBy

    character vector. Do semi-heatmap based on the grouping of this(these) annotation(s). Should exist in either colDataName or names(cellAnnotations). Default is the value of cluster in @@ -381,35 +383,33 @@

    Arguments

    NULL otherwise.

    -
    rowSplitBy
    +
    rowSplitBy

    character vector. Do semi-heatmap based on the grouping of this(these) annotation(s). Should exist in either rowDataName or names(featureAnnotations). Default "marker", which indicates an auto generated annotation for this plot.

    -
    rowDend
    +
    rowDend

    Whether to display row dendrogram. Default FALSE.

    -
    colDend
    +
    colDend

    Whether to display column dendrogram. Default FALSE.

    -
    title
    +
    title

    Text of the title, at the top of the heatmap. Default "Top Marker Heatmap".

    -
    ...
    +
    ...

    Other arguments passed to plotSCEHeatmap.

    Value

    - - -

    A Heatmap object

    +

    A Heatmap object

    See also

    @@ -426,9 +426,9 @@

    Examples

    logcounts(sceBatches) <- log1p(counts(sceBatches)) sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'") sce.w <- runFindMarker(sce.w, method = "wilcox", cluster = "cell_type") -#> Fri May 3 07:16:26 2024 ... Identifying markers for cluster 'beta', using DE method 'wilcox' -#> Fri May 3 07:16:26 2024 ... Identifying markers for cluster 'alpha', using DE method 'wilcox' -#> Fri May 3 07:16:26 2024 ... Organizing findMarker result +#> Thu Feb 13 10:29:29 2025 ... Identifying markers for cluster 'beta', using DE method 'wilcox' +#> Thu Feb 13 10:29:29 2025 ... Identifying markers for cluster 'alpha', using DE method 'wilcox' +#> Thu Feb 13 10:29:30 2025 ... Organizing findMarker result plotFindMarkerHeatmap(sce.w)
    @@ -445,15 +445,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotMASTThresholdGenes-1.png b/docs/reference/plotMASTThresholdGenes-1.png index f3e2caf62..29048efa6 100644 Binary files a/docs/reference/plotMASTThresholdGenes-1.png and b/docs/reference/plotMASTThresholdGenes-1.png differ diff --git a/docs/reference/plotMASTThresholdGenes.html b/docs/reference/plotMASTThresholdGenes.html index 2e8b3ae62..e0631d434 100644 --- a/docs/reference/plotMASTThresholdGenes.html +++ b/docs/reference/plotMASTThresholdGenes.html @@ -1,11 +1,11 @@ -MAST Identify adaptive thresholds — plotMASTThresholdGenes • singleCellTKMAST Identify adaptive thresholds — plotMASTThresholdGenes • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -223,39 +223,37 @@

    MAST Identify adaptive thresholds

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment object

    -
    useAssay
    +
    useAssay

    character, default "logcounts"

    -
    doPlot
    +
    doPlot

    Logical scalar. Whether to directly plot in the plotting area. If FALSE, will return a graphical object which can be visualized with grid.draw(). Default TRUE.

    -
    isLogged
    +
    isLogged

    Logical scalar. Whether the assay used for the analysis is logged. If not, will do a log(assay + 1) transformation. Default TRUE.

    -
    check_sanity
    +
    check_sanity

    Logical scalar. Whether to perform MAST's sanity check to see if the counts are logged. Default TRUE

    Value

    - - -

    Plot the thresholding onto the plotting region if plot == TRUE

    - - -

    or a graphical object if plot == FALSE.

    +

    Plot the thresholding onto the plotting region if plot == TRUE +or a graphical object if plot == FALSE.

    @@ -281,15 +279,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotPCA-1.png b/docs/reference/plotPCA-1.png index 1d4f8011e..52458847d 100644 Binary files a/docs/reference/plotPCA-1.png and b/docs/reference/plotPCA-1.png differ diff --git a/docs/reference/plotPCA.html b/docs/reference/plotPCA.html index 19dd97021..35aaa415a 100644 --- a/docs/reference/plotPCA.html +++ b/docs/reference/plotPCA.html @@ -1,9 +1,9 @@ -Plot PCA run data from its components. — plotPCA • singleCellTKPlot PCA run data from its components. — plotPCA • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -222,46 +222,46 @@

    Plot PCA run data from its components.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    colorBy
    +
    colorBy

    The variable to color clusters by

    -
    shape
    +
    shape

    Shape of the points

    -
    pcX
    +
    pcX

    User choice for the first principal component

    -
    pcY
    +
    pcY

    User choice for the second principal component

    -
    reducedDimName
    +
    reducedDimName

    a name to store the results of the dimension reduction coordinates obtained from this method. This is stored in the SingleCellExperiment object in the reducedDims slot. Required.

    -
    runPCA
    +
    runPCA

    Run PCA if the reducedDimName does not exist. the Default is FALSE.

    -
    useAssay
    +
    useAssay

    Indicate which assay to use. The default is "logcounts".

    Value

    - - -

    A PCA plot

    +

    A PCA plot

    @@ -284,15 +284,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotPathway-1.png b/docs/reference/plotPathway-1.png index cee10c5d9..22699a114 100644 Binary files a/docs/reference/plotPathway-1.png and b/docs/reference/plotPathway-1.png differ diff --git a/docs/reference/plotPathway.html b/docs/reference/plotPathway.html index 4b6649f19..737b0dc2a 100644 --- a/docs/reference/plotPathway.html +++ b/docs/reference/plotPathway.html @@ -1,9 +1,9 @@ -Generate violin plots for pathway analysis results — plotPathway • singleCellTKGenerate violin plots for pathway analysis results — plotPathway • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -230,86 +230,86 @@

    Generate violin plots for pathway analysis results

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object. With runGSVA() or runVAM() applied in advance.

    -
    resultName
    +
    resultName

    A single character of the name of a score matrix, which should be found in getPathwayResultNames(inSCE).

    -
    geneset
    +
    geneset

    A single character specifying the geneset of interest. Should be found in the geneSetCollection used for performing the analysis.

    -
    groupBy
    +
    groupBy

    Either a single character specifying a column of colData(inSCE) or a vector of equal length as the number of cells. Default NULL.

    -
    boxplot
    +
    boxplot

    Boolean, Whether to add a boxplot. Default FALSE.

    -
    violin
    +
    violin

    Boolean, Whether to add a violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean, If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median", and NULL for not adding. Default "median".

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 10.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 10.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    gridLine
    +
    gridLine

    Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.

    -
    title
    +
    title

    Title of plot. Default using geneset.

    -
    titleSize
    +
    titleSize

    Size of the title of the plot. Default 15.

    Value

    - - -

    A ggplot object for the violin plot

    +

    A ggplot object for the violin plot

    Details

    @@ -329,7 +329,7 @@

    Examples

    by = "rownames") sce <- runVAM(inSCE = sce, geneSetCollectionName = "GeneSetCollection", useAssay = "logcounts") -#> Fri May 3 07:16:33 2024 ... Running VAM +#> Thu Feb 13 10:29:36 2025 ... Running VAM #> gene.weights not specified, defaulting all weights to 1 #> Computing VAM distances for 2 gene sets, 195 cells and 200 genes. #> Min set size: 10, median size: 10 @@ -349,15 +349,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotRunPerCellQCResults-1.png b/docs/reference/plotRunPerCellQCResults-1.png index 6c2f6ed8c..2a3267f44 100644 Binary files a/docs/reference/plotRunPerCellQCResults-1.png and b/docs/reference/plotRunPerCellQCResults-1.png differ diff --git a/docs/reference/plotRunPerCellQCResults.html b/docs/reference/plotRunPerCellQCResults.html index db048362b..7aece310c 100644 --- a/docs/reference/plotRunPerCellQCResults.html +++ b/docs/reference/plotRunPerCellQCResults.html @@ -1,11 +1,11 @@ -Plots for runPerCellQC outputs. — plotRunPerCellQCResults • singleCellTKPlots for runPerCellQC outputs. — plotRunPerCellQCResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -242,133 +242,133 @@

    Plots for runPerCellQC outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runPerCellQC. Required.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. Users may input a vector -equal length to the number of the samples in inSCE, or can be +equal length to the number of the samples in inSCE, or can be retrieved from the colData slot. Default NULL.

    -
    combinePlot
    -

    Must be either "all", "sample", or -"none". "all" will combine all plots into a single ggplot -object, while "sample" will output a list of plots separated by +

    combinePlot
    +

    Must be either "all", "sample", or +"none". "all" will combine all plots into a single ggplot +object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    violin
    -

    Boolean. If TRUE, will plot the violin plot. Default +

    violin
    +

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    -

    Boolean. If TRUE, will plot boxplots for each violin +

    boxplot
    +

    Boolean. If TRUE, will plot boxplots for each violin plot. Default FALSE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the -violin plot. Options are "mean" or "median". Default +violin plot. Options are "mean" or "median". Default "median".

    -
    summaryTextSize
    +
    summaryTextSize

    The text size of the summary statistic displayed above the violin plot. Default 3.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 15. -Can be overwritten by titleSize, axisSize, and +Can be overwritten by titleSize, axisSize, and axisLabelSize.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    defaultTheme
    -

    Removes grid in plot and sets axis title size to +

    defaultTheme
    +

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default NULL.

    -
    relHeights
    -

    Relative heights of plots when combine is set. Default +

    relHeights
    +

    Relative heights of plots when combine is set. Default 1.

    -
    relWidths
    -

    Relative widths of plots when combine is set. Default +

    relWidths
    +

    Relative widths of plots when combine is set. Default 1.

    -
    labelSamples
    -

    Will label sample name in title of plot if TRUE. +

    labelSamples
    +

    Will label sample name in title of plot if TRUE. Default TRUE.

    -
    plotNCols
    -

    Number of columns when plots are combined in a grid. Default +

    plotNCols
    +

    Number of columns when plots are combined in a grid. Default NULL.

    -
    plotNRows
    -

    Number of rows when plots are combined in a grid. Default +

    plotNRows
    +

    Number of rows when plots are combined in a grid. Default NULL.

    -
    samplePerColumn
    -

    If TRUE, when there are multiple samples and -combining by "all", the output .ggplot will have plots from each +

    samplePerColumn
    +

    If TRUE, when there are multiple samples and +combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

    -
    sampleRelHeights
    -

    If there are multiple samples and combining by +

    sampleRelHeights
    +

    If there are multiple samples and combining by "all", the relative heights for each plot. Default 1.

    -
    sampleRelWidths
    -

    If there are multiple samples and combining by +

    sampleRelWidths
    +

    If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

    Value

    - - -

    list of .ggplot objects

    +

    list of .ggplot objects

    See also

    @@ -380,8 +380,8 @@

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runPerCellQC(sce)
-#> Fri May  3 07:16:34 2024 ... Running 'perCellQCMetrics'
-#> Fri May  3 07:16:34 2024 ...... Attempting to find mitochondrial genes by identifying features in 'rownames' that match mitochondrial genes from reference 'human' and ID type 'ensembl'.
+#> Thu Feb 13 10:29:37 2025 ... Running 'perCellQCMetrics'
+#> Thu Feb 13 10:29:37 2025 ...... Attempting to find mitochondrial genes by identifying features in 'rownames' that match mitochondrial genes from reference 'human' and ID type 'ensembl'.
 plotRunPerCellQCResults(inSCE = sce)
    @@ -398,15 +398,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEBarAssayData-1.png b/docs/reference/plotSCEBarAssayData-1.png index 51b743bbd..f777cd862 100644 Binary files a/docs/reference/plotSCEBarAssayData-1.png and b/docs/reference/plotSCEBarAssayData-1.png differ diff --git a/docs/reference/plotSCEBarAssayData.html b/docs/reference/plotSCEBarAssayData.html index 4715631a8..0df14ab03 100644 --- a/docs/reference/plotSCEBarAssayData.html +++ b/docs/reference/plotSCEBarAssayData.html @@ -1,10 +1,10 @@ -Bar plot of assay data. — plotSCEBarAssayData • singleCellTKBar plot of assay data. — plotSCEBarAssayData • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -235,87 +235,89 @@

    Bar plot of assay data.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    feature
    +
    feature

    Name of feature stored in assay of SingleCellExperiment object.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    useAssay
    +
    useAssay

    Indicate which assay to use. Default "counts".

    -
    featureLocation
    +
    featureLocation

    Indicates which column name of rowData to query gene.

    -
    featureDisplay
    +
    featureDisplay

    Indicates which column name of rowData to use to display feature for visualization.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 10.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 10.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.1.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    gridLine
    +
    gridLine

    Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    combinePlot
    +
    combinePlot

    Boolean. If multiple plots are generated (multiple samples, etc.), will combined plots using `cowplot::plot_grid`. Default TRUE.

    @@ -323,9 +325,7 @@

    Arguments

    Value

    - - -

    a ggplot of the barplot of assay data.

    +

    a ggplot of the barplot of assay data.

    @@ -350,15 +350,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEBarColData-1.png b/docs/reference/plotSCEBarColData-1.png index 4269c47cb..cc5adb194 100644 Binary files a/docs/reference/plotSCEBarColData-1.png and b/docs/reference/plotSCEBarColData-1.png differ diff --git a/docs/reference/plotSCEBarColData.html b/docs/reference/plotSCEBarColData.html index f0f58e971..59d7a378f 100644 --- a/docs/reference/plotSCEBarColData.html +++ b/docs/reference/plotSCEBarColData.html @@ -1,10 +1,10 @@ -Bar plot of colData. — plotSCEBarColData • singleCellTKBar plot of colData. — plotSCEBarColData • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -233,78 +233,80 @@

    Bar plot of colData.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    coldata
    +
    coldata

    colData value that will be plotted.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 10.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 10.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.1.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    gridLine
    +
    gridLine

    Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    combinePlot
    +
    combinePlot

    Boolean. If multiple plots are generated (multiple samples, etc.), will combined plots using `cowplot::plot_grid`. Default TRUE.

    @@ -312,9 +314,7 @@

    Arguments

    Value

    - - -

    a ggplot of the barplot of coldata.

    +

    a ggplot of the barplot of coldata.

    @@ -339,15 +339,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEBatchFeatureMean-1.png b/docs/reference/plotSCEBatchFeatureMean-1.png index 21d29a0ca..d064869e4 100644 Binary files a/docs/reference/plotSCEBatchFeatureMean-1.png and b/docs/reference/plotSCEBatchFeatureMean-1.png differ diff --git a/docs/reference/plotSCEBatchFeatureMean.html b/docs/reference/plotSCEBatchFeatureMean.html index ae7c2b6fc..657524cdd 100644 --- a/docs/reference/plotSCEBatchFeatureMean.html +++ b/docs/reference/plotSCEBatchFeatureMean.html @@ -1,9 +1,9 @@ -Plot mean feature value in each batch of a SingleCellExperiment object — plotSCEBatchFeatureMean • singleCellTKPlot mean feature value in each batch of a SingleCellExperiment object — plotSCEBatchFeatureMean • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -222,48 +222,48 @@

    Plot mean feature value in each batch of a SingleCellExperiment object

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    useAssay
    +
    useAssay

    A single character. The name of the assay that stores the value to plot. For useReddim and useAltExp also. Default NULL.

    -
    useReddim
    +
    useReddim

    A single character. The name of the dimension reduced matrix that stores the value to plot. Default NULL.

    -
    useAltExp
    +
    useAltExp

    A single character. The name of the alternative experiment that stores an assay of the value to plot. Default NULL.

    -
    batch
    +
    batch

    A single character. The name of batch annotation column in colData(inSCE). Default "batch".

    -
    xlab
    +
    xlab

    label for x-axis. Default "batch".

    -
    ylab
    +
    ylab

    label for y-axis. Default "Feature Mean".

    -
    ...
    +
    ...

    Additional arguments passed to .ggViolin.

    Value

    - - -

    ggplot

    +

    ggplot

    @@ -285,15 +285,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEDensity-1.png b/docs/reference/plotSCEDensity-1.png index 87f295315..d8a749fb9 100644 Binary files a/docs/reference/plotSCEDensity-1.png and b/docs/reference/plotSCEDensity-1.png differ diff --git a/docs/reference/plotSCEDensity.html b/docs/reference/plotSCEDensity.html index 81bdceb16..38af4ada5 100644 --- a/docs/reference/plotSCEDensity.html +++ b/docs/reference/plotSCEDensity.html @@ -1,10 +1,10 @@ -Density plot of any data stored in the SingleCellExperiment object. — plotSCEDensity • singleCellTKDensity plot of any data stored in the SingleCellExperiment object. — plotSCEDensity • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -233,91 +233,91 @@

    Density plot of any data stored in the SingleCellExperiment object.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    slotName
    +
    slotName

    Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata", "reducedDims". Required.

    -
    itemName
    +
    itemName

    Desired vector within the slot used for plotting. Required.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    feature
    +
    feature

    Desired name of feature stored in assay of SingleCellExperiment object. Only used when "assays" slotName is selected. Default NULL.

    -
    dimension
    +
    dimension

    Desired dimension stored in the specified reducedDims. Either an integer which indicates the column or a character vector specifies column name. By default, the 1st dimension/column will be used. Only used when "reducedDims" slotName is selected. Default NULL.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 10.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 10.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    cutoff
    +
    cutoff

    Numeric value. The plot will be annotated with a vertical line if set. Default NULL.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".

    -
    plotLabels
    +
    plotLabels

    labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

    Value

    - - -

    a ggplot object of the density plot.

    +

    a ggplot object of the density plot.

    @@ -342,15 +342,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEDensityAssayData-1.png b/docs/reference/plotSCEDensityAssayData-1.png index 0aafce601..fad0ce5ee 100644 Binary files a/docs/reference/plotSCEDensityAssayData-1.png and b/docs/reference/plotSCEDensityAssayData-1.png differ diff --git a/docs/reference/plotSCEDensityAssayData.html b/docs/reference/plotSCEDensityAssayData.html index 7ef0e4170..12aa76264 100644 --- a/docs/reference/plotSCEDensityAssayData.html +++ b/docs/reference/plotSCEDensityAssayData.html @@ -1,10 +1,10 @@ -Density plot of assay data. — plotSCEDensityAssayData • singleCellTKDensity plot of assay data. — plotSCEDensityAssayData • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -233,88 +233,88 @@

    Density plot of assay data.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    feature
    +
    feature

    Name of feature stored in assay of SingleCellExperiment object.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    useAssay
    +
    useAssay

    Indicate which assay to use. Default "counts".

    -
    featureLocation
    +
    featureLocation

    Indicates which column name of rowData to query gene.

    -
    featureDisplay
    +
    featureDisplay

    Indicates which column name of rowData to use to display feature for visualization.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 10.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 10.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    cutoff
    +
    cutoff

    Numeric value. The plot will be annotated with a vertical line if set. Default NULL.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".

    -
    plotLabels
    +
    plotLabels

    labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

    Value

    - - -

    a ggplot of the density plot of assay data.

    +

    a ggplot of the density plot of assay data.

    @@ -341,15 +341,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEDensityColData-1.png b/docs/reference/plotSCEDensityColData-1.png index 65ec62ff9..b7000f282 100644 Binary files a/docs/reference/plotSCEDensityColData-1.png and b/docs/reference/plotSCEDensityColData-1.png differ diff --git a/docs/reference/plotSCEDensityColData.html b/docs/reference/plotSCEDensityColData.html index 54839a629..4ef5b54e9 100644 --- a/docs/reference/plotSCEDensityColData.html +++ b/docs/reference/plotSCEDensityColData.html @@ -1,10 +1,10 @@ -Density plot of colData. — plotSCEDensityColData • singleCellTKDensity plot of colData. — plotSCEDensityColData • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -231,80 +231,80 @@

    Density plot of colData.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    coldata
    +
    coldata

    colData value that will be plotted.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    cutoff
    +
    cutoff

    Numeric value. The plot will be annotated with a vertical line if set. Default NULL.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".

    -
    plotLabels
    +
    plotLabels

    labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

    Value

    - - -

    a ggplot of the density plot of colData.

    +

    a ggplot of the density plot of colData.

    @@ -331,15 +331,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEDimReduceColData-1.png b/docs/reference/plotSCEDimReduceColData-1.png index 201459356..240291208 100644 Binary files a/docs/reference/plotSCEDimReduceColData-1.png and b/docs/reference/plotSCEDimReduceColData-1.png differ diff --git a/docs/reference/plotSCEDimReduceColData-2.png b/docs/reference/plotSCEDimReduceColData-2.png index f9010c63f..c29c770e4 100644 Binary files a/docs/reference/plotSCEDimReduceColData-2.png and b/docs/reference/plotSCEDimReduceColData-2.png differ diff --git a/docs/reference/plotSCEDimReduceColData.html b/docs/reference/plotSCEDimReduceColData.html index ba8db9116..9f14a9001 100644 --- a/docs/reference/plotSCEDimReduceColData.html +++ b/docs/reference/plotSCEDimReduceColData.html @@ -1,10 +1,10 @@ -Dimension reduction plot tool for colData — plotSCEDimReduceColData • singleCellTKDimension reduction plot tool for colData — plotSCEDimReduceColData • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -248,165 +248,165 @@

    Dimension reduction plot tool for colData

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    colorBy
    +
    colorBy

    Color by a condition(any column of the annotation data). Required.

    -
    reducedDimName
    +
    reducedDimName

    Saved dimension reduction matrix name in the SingleCellExperiment object. Required.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    groupBy
    +
    groupBy

    Group by a condition(any column of the annotation data). Default NULL.

    -
    conditionClass
    +
    conditionClass

    Class of the annotation data used in colorBy. Options are NULL, "factor" or "numeric". If NULL, class will default to the original class. Default NULL.

    -
    shape
    +
    shape

    Add shapes to each condition.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    dim1
    +
    dim1

    1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    dim2
    +
    dim2

    2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    bin
    +
    bin

    Numeric vector. If single value, will divide the numeric values into the `bin` groups. If more than one value, will bin numeric values using values as a cut point.

    -
    binLabel
    +
    binLabel

    Character vector. Labels for the bins created by the `bin` parameter. Default NULL.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.1.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    colorScale
    +
    colorScale

    Vector. Needs to be same length as the number of unique levels of colorBy. Will be used only if conditionClass = "factor" or "character". Default NULL.

    -
    colorLow
    +
    colorLow

    Character. A color available from `colors()`. The color will be used to signify the lowest values on the scale. Default 'white'.

    -
    colorMid
    +
    colorMid

    Character. A color available from `colors()`. The color will be used to signify the midpoint on the scale. Default 'gray'.

    -
    colorHigh
    +
    colorHigh

    Character. A color available from `colors()`. The color will be used to signify the highest values on the scale. Default 'blue'.

    -
    defaultTheme
    +
    defaultTheme

    adds grid to plot when TRUE. Default TRUE.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    labelClusters
    +
    labelClusters

    Logical. Whether the cluster labels are plotted.

    -
    clusterLabelSize
    +
    clusterLabelSize

    Numeric. Determines the size of cluster label when `labelClusters` is set to TRUE. Default 3.5.

    -
    legendTitle
    +
    legendTitle

    title of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default 12.

    -
    legendSize
    +
    legendSize

    size of legend. Default NULL. Default FALSE.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".

    -
    plotLabels
    +
    plotLabels

    labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

    Value

    - - -

    a ggplot of the reduced dimension plot of coldata.

    +

    a ggplot of the reduced dimension plot of coldata.

    @@ -441,15 +441,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEDimReduceFeatures-1.png b/docs/reference/plotSCEDimReduceFeatures-1.png index e79a742d3..337443212 100644 Binary files a/docs/reference/plotSCEDimReduceFeatures-1.png and b/docs/reference/plotSCEDimReduceFeatures-1.png differ diff --git a/docs/reference/plotSCEDimReduceFeatures.html b/docs/reference/plotSCEDimReduceFeatures.html index be96a5019..46130d4ad 100644 --- a/docs/reference/plotSCEDimReduceFeatures.html +++ b/docs/reference/plotSCEDimReduceFeatures.html @@ -1,10 +1,10 @@ -Dimension reduction plot tool for assay data — plotSCEDimReduceFeatures • singleCellTKDimension reduction plot tool for assay data — plotSCEDimReduceFeatures • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -246,150 +246,150 @@

    Dimension reduction plot tool for assay data

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    feature
    +
    feature

    Name of feature stored in assay of SingleCellExperiment object.

    -
    reducedDimName
    +
    reducedDimName

    saved dimension reduction name in the SingleCellExperiment object. Required.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    featureLocation
    +
    featureLocation

    Indicates which column name of rowData to query gene.

    -
    featureDisplay
    +
    featureDisplay

    Indicates which column name of rowData to use to display feature for visualization.

    -
    shape
    +
    shape

    add shapes to each condition. Default NULL.

    -
    useAssay
    +
    useAssay

    Indicate which assay to use. The default is "logcounts"

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 10.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 10.

    -
    dim1
    +
    dim1

    1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    dim2
    +
    dim2

    2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    bin
    +
    bin

    Numeric vector. If single value, will divide the numeric values into the `bin` groups. If more than one value, will bin numeric values using values as a cut point.

    -
    binLabel
    +
    binLabel

    Character vector. Labels for the bins created by the `bin` parameter. Default NULL.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.1.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    colorLow
    +
    colorLow

    Character. A color available from `colors()`. The color will be used to signify the lowest values on the scale. Default 'white'.

    -
    colorMid
    +
    colorMid

    Character. A color available from `colors()`. The color will be used to signify the midpoint on the scale. Default 'gray'.

    -
    colorHigh
    +
    colorHigh

    Character. A color available from `colors()`. The color will be used to signify the highest values on the scale. Default 'blue'.

    -
    defaultTheme
    +
    defaultTheme

    adds grid to plot when TRUE. Default TRUE.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    legendTitle
    +
    legendTitle

    title of legend. Default NULL.

    -
    legendSize
    +
    legendSize

    size of legend. Default 10.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default 12.

    -
    groupBy
    +
    groupBy

    Facet wrap the scatterplot based on value. Default NULL.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".

    -
    plotLabels
    +
    plotLabels

    labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

    Value

    - - -

    a ggplot of the reduced dimension plot of feature data.

    +

    a ggplot of the reduced dimension plot of feature data.

    @@ -415,15 +415,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEHeatmap-1.png b/docs/reference/plotSCEHeatmap-1.png index c4b1f788c..487869465 100644 Binary files a/docs/reference/plotSCEHeatmap-1.png and b/docs/reference/plotSCEHeatmap-1.png differ diff --git a/docs/reference/plotSCEHeatmap.html b/docs/reference/plotSCEHeatmap.html index 914c8bf56..dea20e8b4 100644 --- a/docs/reference/plotSCEHeatmap.html +++ b/docs/reference/plotSCEHeatmap.html @@ -1,9 +1,9 @@ -Plot heatmap of using data stored in SingleCellExperiment Object — plotSCEHeatmap • singleCellTKPlot heatmap of using data stored in SingleCellExperiment Object — plotSCEHeatmap • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -219,6 +219,8 @@

    Plot heatmap of using data stored in SingleCellExperiment Object

    trim = c(-2, 2), featureIndexBy = "rownames", cellIndexBy = "rownames", + cluster_columns = FALSE, + cluster_rows = FALSE, rowDataName = NULL, colDataName = NULL, aggregateRow = NULL, @@ -228,6 +230,8 @@

    Plot heatmap of using data stored in SingleCellExperiment Object

    featureAnnotationColor = NULL, cellAnnotationColor = NULL, palette = c("ggplot", "celda", "random"), + heatmapPalette = c("sequential", "diverging"), + addCellSummary = NULL, rowSplitBy = NULL, colSplitBy = NULL, rowLabel = FALSE, @@ -249,203 +253,224 @@

    Plot heatmap of using data stored in SingleCellExperiment Object

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    useAssay
    +
    useAssay

    character. A string indicating the assay name that provides the expression level to plot. Only for plotSCEHeatmap.

    -
    useReducedDim
    +
    useReducedDim

    character. A string indicating the reducedDim name that provides the expression level to plot. Only for plotSCEDimReduceHeatmap.

    -
    doLog
    +
    doLog

    Logical scalar. Whether to do log(assay + 1) transformation on the assay indicated by useAssay. Default FALSE.

    -
    featureIndex
    +
    featureIndex

    A vector that can subset the input SCE object by rows (features). Alternatively, it can be a vector identifying features in another feature list indicated by featureIndexBy. Default NULL.

    -
    cellIndex
    +
    cellIndex

    A vector that can subset the input SCE object by columns (cells). Alternatively, it can be a vector identifying cells in another cell list indicated by featureIndexBy. Default NULL.

    -
    scale
    -

    Whether to perform z-score scaling on each row. Default -TRUE.

    +
    scale
    +

    Whether to perform z-score or min-max scaling on each row.Choose from "zscore", "min-max" or default +TRUE or FALSE

    -
    trim
    +
    trim

    A 2-element numeric vector. Values outside of this range will be trimmed to their nearst bound. Default c(-2, 2)

    -
    featureIndexBy
    +
    featureIndexBy

    A single character specifying a column name of rowData(inSCE), or a vector of the same length as nrow(inSCE), where we search for the non-rowname feature indices. Not applicable for plotSCEDimReduceHeatmap. Default "rownames".

    -
    cellIndexBy
    +
    cellIndexBy

    A single character specifying a column name of colData(inSCE), or a vector of the same length as ncol(inSCE), where we search for the non-rowname cell indices. Default "rownames".

    -
    rowDataName
    +
    cluster_columns
    +

    A logical scalar that turns on/off +clustering of columns. Default FALSE. Clustering columns should be turned off when using reduced dim +for plotting as it will be sorted by PCs

    + + +
    cluster_rows
    +

    A logical scalar that turns on/off clustering of rows. +Default FALSE.

    + + +
    rowDataName

    character. The column name(s) in rowData that need to be added to the annotation. Not applicable for plotSCEDimReduceHeatmap. Default NULL.

    -
    colDataName
    +
    colDataName

    character. The column name(s) in colData that need to be added to the annotation. Default NULL.

    -
    aggregateRow
    +
    aggregateRow

    Feature variable for aggregating the heatmap by row. Can be a vector or a rowData column name for feature variable. Multiple variables are allowed. Default NULL.

    -
    aggregateCol
    +
    aggregateCol

    Cell variable for aggregating the heatmap by column. Can be a vector or a colData column name for cell variable. Multiple variables are allowed. Default NULL.

    -
    featureAnnotations
    +
    featureAnnotations

    data.frame, with rownames containing all the features going to be plotted. Character columns should be factors. Default NULL.

    -
    cellAnnotations
    +
    cellAnnotations

    data.frame, with rownames containing all the cells going to be plotted. Character columns should be factors. Default NULL.

    -
    featureAnnotationColor
    +
    featureAnnotationColor

    A named list. Customized color settings for feature labeling. Should match the entries in the featureAnnotations or rowDataName. For each entry, there should be a list/vector of colors named with categories. Default NULL.

    -
    cellAnnotationColor
    +
    cellAnnotationColor

    A named list. Customized color settings for cell labeling. Should match the entries in the cellAnnotations or colDataName. For each entry, there should be a list/vector of colors named with categories. Default NULL.

    -
    palette
    +
    palette

    Choose from "ggplot", "celda" or "random" to generate unique category colors.

    -
    rowSplitBy
    +
    heatmapPalette
    +

    Choose from "sequential", "diverging" or supply custom palette with colorScheme +to generate unique category colors. Default is "sequential"

    + + +
    addCellSummary
    +

    Add summary barplots to column annotation. Supply the name of the column in colData as a character. This option will add summary for categorical variables +as stacked barplots.

    + + +
    rowSplitBy

    character. Do semi-heatmap based on the grouping of this(these) annotation(s). Should exist in either rowDataName or names(featureAnnotations). Default NULL.

    -
    colSplitBy
    +
    colSplitBy

    character. Do semi-heatmap based on the grouping of this(these) annotation(s). Should exist in either colDataName or names(cellAnnotations). Default NULL.

    -
    rowLabel
    +
    rowLabel

    Use a logical for whether to display all the feature names, a single character to display a column of rowData(inSCE) annotation, a vector of the same length as full/subset nrow(inSCE) to display customized info. Default FALSE.

    -
    colLabel
    +
    colLabel

    Use a logical for whether to display all the cell names, a single character to display a column of colData(inSCE) annotation, a vector of the same length as full/subset ncol(inSCE) to display customized info. Default FALSE.

    -
    rowLabelSize
    +
    rowLabelSize

    A number for the font size of feature names. Default 8

    -
    colLabelSize
    +
    colLabelSize

    A number for the font size of cell names. Default 8

    -
    rowDend
    +
    rowDend

    Whether to display row dendrogram. Default TRUE.

    -
    colDend
    +
    colDend

    Whether to display column dendrogram. Default TRUE.

    -
    title
    +
    title

    The main title of the whole plot. Default NULL.

    -
    rowTitle
    +
    rowTitle

    The subtitle for the rows. Default "Genes".

    -
    colTitle
    +
    colTitle

    The subtitle for the columns. Default "Cells".

    -
    rowGap
    +
    rowGap

    A numeric value or a unit object. For the gap size between rows of the splitted heatmap. Default grid::unit(0, 'mm').

    -
    colGap
    +
    colGap

    A numeric value or a unit object. For the gap size between columns of the splitted heatmap. Default grid::unit(0, 'mm').

    -
    border
    +
    border

    A logical scalar. Whether to show the border of the heatmap or splitted heatmaps. Default TRUE.

    -
    colorScheme
    +
    colorScheme

    function. A function that generates color code by giving a value. Can be generated by colorRamp2. Default NULL.

    -
    ...
    +
    ...

    Other arguments passed to Heatmap.

    Value

    - - -

    A ggplot object.

    +

    A ggplot object.

    Author

    @@ -471,15 +496,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEScatter-1.png b/docs/reference/plotSCEScatter-1.png index 2e5c56a17..b548261b6 100644 Binary files a/docs/reference/plotSCEScatter-1.png and b/docs/reference/plotSCEScatter-1.png differ diff --git a/docs/reference/plotSCEScatter.html b/docs/reference/plotSCEScatter.html index e8751d732..db81588a8 100644 --- a/docs/reference/plotSCEScatter.html +++ b/docs/reference/plotSCEScatter.html @@ -1,10 +1,10 @@ -Dimension reduction plot tool for all types of data — plotSCEScatter • singleCellTKDimension reduction plot tool for all types of data — plotSCEScatter • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -247,156 +247,156 @@

    Dimension reduction plot tool for all types of data

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    annotation
    +
    annotation

    Desired vector within the slot used for plotting. Default NULL.

    -
    reducedDimName
    +
    reducedDimName

    saved dimension reduction name in the SingleCellExperiment object.

    -
    slot
    +
    slot

    Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata", "reducedDims". Default NULL.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    feature
    +
    feature

    name of feature stored in assay of SingleCellExperiment object. Will be used only if "assays" slot is chosen. Default NULL.

    -
    groupBy
    +
    groupBy

    Group by a condition(any column of the annotation data). Default NULL.

    -
    shape
    +
    shape

    add shapes to each condition.

    -
    conditionClass
    +
    conditionClass

    class of the annotation data used in colorBy. Options are NULL, "factor" or "numeric". If NULL, class will default to the original class. Default NULL.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 10.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 10.

    -
    dim1
    +
    dim1

    1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    dim2
    +
    dim2

    2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    bin
    +
    bin

    Numeric vector. If single value, will divide the numeric values into the `bin` groups. If more than one value, will bin numeric values using values as a cut point.

    -
    binLabel
    +
    binLabel

    Character vector. Labels for the bins created by the `bin` parameter. Default NULL.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.1.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    colorLow
    +
    colorLow

    Character. A color available from `colors()`. The color will be used to signify the lowest values on the scale. Default 'white'.

    -
    colorMid
    +
    colorMid

    Character. A color available from `colors()`. The color will be used to signify the midpoint on the scale. Default 'gray'.

    -
    colorHigh
    +
    colorHigh

    Character. A color available from `colors()`. The color will be used to signify the highest values on the scale. Default 'blue'.

    -
    defaultTheme
    +
    defaultTheme

    adds grid to plot when TRUE. Default TRUE.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    labelClusters
    +
    labelClusters

    Logical. Whether the cluster labels are plotted.

    -
    legendTitle
    +
    legendTitle

    title of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default 12.

    -
    legendSize
    +
    legendSize

    size of legend. Default 10.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".

    -
    plotLabels
    +
    plotLabels

    labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

    Value

    - - -

    a ggplot of the reduced dimensions.

    +

    a ggplot of the reduced dimensions.

    @@ -422,15 +422,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEViolin-1.png b/docs/reference/plotSCEViolin-1.png index fed69d918..d09f1149e 100644 Binary files a/docs/reference/plotSCEViolin-1.png and b/docs/reference/plotSCEViolin-1.png differ diff --git a/docs/reference/plotSCEViolin.html b/docs/reference/plotSCEViolin.html index 913585432..f8fd8b5a5 100644 --- a/docs/reference/plotSCEViolin.html +++ b/docs/reference/plotSCEViolin.html @@ -1,10 +1,10 @@ -Violin plot of any data stored in the SingleCellExperiment object. — plotSCEViolin • singleCellTKViolin plot of any data stored in the SingleCellExperiment object. — plotSCEViolin • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -248,164 +248,164 @@

    Violin plot of any data stored in the SingleCellExperiment object.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    slotName
    +
    slotName

    Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata", "reducedDims". Required.

    -
    itemName
    +
    itemName

    Desired vector within the slot used for plotting. Required.

    -
    feature
    +
    feature

    Desired name of feature stored in assay of SingleCellExperiment object. Only used when "assays" slotName is selected. Default NULL.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    dimension
    -

    Desired dimension stored in the specified reducedDims. -Either an integer which indicates the column or a character vector specifies -column name. By default, the 1st dimension/column will be used. +

    dimension
    +

    Desired dimension(s) stored in the specified reducedDims. +Either an integer which indicates the column(s) or a character vector specifies +column name(s). By default, the 1st dimension/column will be used. Only used when "reducedDims" slotName is selected. Default NULL.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

    -
    violin
    +
    violin

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    +
    boxplot

    Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    plotOrder
    +
    plotOrder

    Character vector. If set, reorders the violin plots in the order of the character vector when `groupBy` is set. Default NULL.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 10.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 10.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.1.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    gridLine
    +
    gridLine

    Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    hcutoff
    +
    hcutoff

    Adds a horizontal line with the y-intercept at given value. Default NULL.

    -
    hcolor
    +
    hcolor

    Character. A color available from `colors()`. Controls the color of the horizontal cutoff line, if drawn. Default 'black'.

    -
    hsize
    +
    hsize

    Size of horizontal line, if drawn. Default 0.5.

    -
    hlinetype
    +
    hlinetype

    Type of horizontal line, if drawn. can be specified with either an integer or a name (0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash). Default 1.

    -
    vcutoff
    +
    vcutoff

    Adds a vertical line with the x-intercept at given value. Default NULL.

    -
    vcolor
    +
    vcolor

    Character. A color available from `colors()`. Controls the color of the vertical cutoff line, if drawn. Default 'black'.

    -
    vsize
    +
    vsize

    Size of vertical line, if drawn. Default 0.5.

    -
    vlinetype
    +
    vlinetype

    Type of vertical line, if drawn. can be specified with either an integer or a name (0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash). Default 1.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".

    -
    plotLabels
    +
    plotLabels

    labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

    Value

    - - -

    a ggplot of the violin plot.

    +

    a ggplot of the violin plot.

    @@ -430,15 +430,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEViolinAssayData-1.png b/docs/reference/plotSCEViolinAssayData-1.png index 0d0170261..6bd04ef21 100644 Binary files a/docs/reference/plotSCEViolinAssayData-1.png and b/docs/reference/plotSCEViolinAssayData-1.png differ diff --git a/docs/reference/plotSCEViolinAssayData.html b/docs/reference/plotSCEViolinAssayData.html index fb59dfb2f..0429f3d5e 100644 --- a/docs/reference/plotSCEViolinAssayData.html +++ b/docs/reference/plotSCEViolinAssayData.html @@ -1,10 +1,10 @@ -Violin plot of assay data. — plotSCEViolinAssayData • singleCellTKViolin plot of assay data. — plotSCEViolinAssayData • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -248,161 +248,161 @@

    Violin plot of assay data.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    feature
    +
    feature

    Name of feature stored in assay of SingleCellExperiment object.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    useAssay
    +
    useAssay

    Indicate which assay to use. Default "counts".

    -
    featureLocation
    +
    featureLocation

    Indicates which column name of rowData to query gene.

    -
    featureDisplay
    +
    featureDisplay

    Indicates which column name of rowData to use to display feature for visualization.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

    -
    violin
    +
    violin

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    +
    boxplot

    Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    plotOrder
    +
    plotOrder

    Character vector. If set, reorders the violin plots in the order of the character vector when `groupBy` is set. Default NULL.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default 10.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default 10.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.1.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    gridLine
    +
    gridLine

    Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    hcutoff
    +
    hcutoff

    Adds a horizontal line with the y-intercept at given value. Default NULL.

    -
    hcolor
    +
    hcolor

    Character. A color available from `colors()`. Controls the color of the horizontal cutoff line, if drawn. Default 'black'.

    -
    hsize
    +
    hsize

    Size of horizontal line, if drawn. Default 0.5.

    -
    hlinetype
    +
    hlinetype

    Type of horizontal line, if drawn. can be specified with either an integer or a name (0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash). Default 1.

    -
    vcutoff
    +
    vcutoff

    Adds a vertical line with the x-intercept at given value. Default NULL.

    -
    vcolor
    +
    vcolor

    Character. A color available from `colors()`. Controls the color of the vertical cutoff line, if drawn. Default 'black'.

    -
    vsize
    +
    vsize

    Size of vertical line, if drawn. Default 0.5.

    -
    vlinetype
    +
    vlinetype

    Type of vertical line, if drawn. can be specified with either an integer or a name (0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash). Default 1.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".

    -
    plotLabels
    +
    plotLabels

    labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

    Value

    - - -

    a ggplot of the violin plot of assay data.

    +

    a ggplot of the violin plot of assay data.

    @@ -427,15 +427,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSCEViolinColData-1.png b/docs/reference/plotSCEViolinColData-1.png index 0d6261f05..4124a91bf 100644 Binary files a/docs/reference/plotSCEViolinColData-1.png and b/docs/reference/plotSCEViolinColData-1.png differ diff --git a/docs/reference/plotSCEViolinColData.html b/docs/reference/plotSCEViolinColData.html index 7cd8df9f8..7bd1465dd 100644 --- a/docs/reference/plotSCEViolinColData.html +++ b/docs/reference/plotSCEViolinColData.html @@ -1,10 +1,10 @@ -Violin plot of colData. — plotSCEViolinColData • singleCellTKViolin plot of colData. — plotSCEViolinColData • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -247,157 +247,157 @@

    Violin plot of colData.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    coldata
    +
    coldata

    colData value that will be plotted.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

    -
    violin
    +
    violin

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    +
    boxplot

    Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    plotOrder
    +
    plotOrder

    Character vector. If set, reorders the violin plots in the order of the character vector when `groupBy` is set. Default NULL.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.1.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    gridLine
    +
    gridLine

    Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.

    -
    summaryTextSize
    +
    summaryTextSize

    The text size of the summary statistic displayed above the violin plot. Default 3.

    -
    title
    +
    title

    Title of plot. Default NULL.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default 15.

    -
    hcutoff
    +
    hcutoff

    Adds a horizontal line with the y-intercept at given value. Default NULL.

    -
    hcolor
    +
    hcolor

    Character. A color available from `colors()`. Controls the color of the horizontal cutoff line, if drawn. Default 'black'.

    -
    hsize
    +
    hsize

    Size of horizontal line, if drawn. Default 0.5.

    -
    hlinetype
    +
    hlinetype

    Type of horizontal line, if drawn. can be specified with either an integer or a name (0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash). Default 1.

    -
    vcutoff
    +
    vcutoff

    Adds a vertical line with the x-intercept at given value. Default NULL.

    -
    vcolor
    +
    vcolor

    Character. A color available from `colors()`. Controls the color of the vertical cutoff line, if drawn. Default 'black'.

    -
    vsize
    +
    vsize

    Size of vertical line, if drawn. Default 0.5.

    -
    vlinetype
    +
    vlinetype

    Type of vertical line, if drawn. can be specified with either an integer or a name (0 = blank, 1 = solid, 2 = dashed, 3 = dotted, 4 = dotdash, 5 = longdash, 6 = twodash). Default 1.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".

    -
    plotLabels
    +
    plotLabels

    labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

    Value

    - - -

    a ggplot of the violin plot of coldata.

    +

    a ggplot of the violin plot of coldata.

    @@ -422,15 +422,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScDblFinderResults-1.png b/docs/reference/plotScDblFinderResults-1.png index 7a575eaf3..e43396c2e 100644 Binary files a/docs/reference/plotScDblFinderResults-1.png and b/docs/reference/plotScDblFinderResults-1.png differ diff --git a/docs/reference/plotScDblFinderResults.html b/docs/reference/plotScDblFinderResults.html index 4f5bd4a51..f7252f723 100644 --- a/docs/reference/plotScDblFinderResults.html +++ b/docs/reference/plotScDblFinderResults.html @@ -1,11 +1,11 @@ -Plots for runScDblFinder outputs. — plotScDblFinderResults • singleCellTKPlots for runScDblFinder outputs. — plotScDblFinderResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -252,181 +252,181 @@

    Plots for runScDblFinder outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runScDblFinder. Required.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    shape
    +
    shape

    If provided, add shapes based on the value. Default NULL.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector -equal length to the number of the samples in inSCE, or can be +equal length to the number of the samples in inSCE, or can be retrieved from the colData slot. Default NULL.

    -
    combinePlot
    -

    Must be either "all", "sample", or -"none". "all" will combine all plots into a single .ggplot -object, while "sample" will output a list of plots separated by +

    combinePlot
    +

    Must be either "all", "sample", or +"none". "all" will combine all plots into a single .ggplot +object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    violin
    -

    Boolean. If TRUE, will plot the violin plot. Default +

    violin
    +

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    -

    Boolean. If TRUE, will plot boxplots for each violin +

    boxplot
    +

    Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    reducedDimName
    -

    Saved dimension reduction name in inSCE. +

    reducedDimName
    +

    Saved dimension reduction name in inSCE. Default "UMAP".

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    dim1
    -

    1st dimension to be used for plotting. Can either be a string -which specifies the name of the dimension to be plotted from reducedDims, or -a numeric value which specifies the index of the dimension to be plotted. +

    dim1
    +

    1st dimension to be used for plotting. Can either be a string +which specifies the name of the dimension to be plotted from reducedDims, or +a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    dim2
    -

    2nd dimension to be used for plotting. Similar to dim1. +

    dim2
    +

    2nd dimension to be used for plotting. Similar to dim1. Default is NULL.

    -
    bin
    -

    Numeric vector. If single value, will divide the numeric values +

    bin
    +

    Numeric vector. If single value, will divide the numeric values into bin groups. If more than one value, will bin numeric values using values as a cut point. Default NULL.

    -
    binLabel
    +
    binLabel

    Character vector. Labels for the bins created by bin. Default NULL.

    -
    defaultTheme
    -

    Removes grid in plot and sets axis title size to +

    defaultTheme
    +

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the -violin plot. Options are "mean" or "median". Default +violin plot. Options are "mean" or "median". Default NULL.

    -
    summaryTextSize
    +
    summaryTextSize

    The text size of the summary statistic displayed above the violin plot. Default 3.

    -
    transparency
    -

    Transparency of the dots, values will be 0-1. Default +

    transparency
    +

    Transparency of the dots, values will be 0-1. Default 1.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 12. -Can be overwritten by titleSize, axisSize, and +Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    legendSize
    +
    legendSize

    size of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default NULL.

    -
    relHeights
    +
    relHeights

    Relative heights of plots when combine is set. Default 1.

    -
    relWidths
    -

    Relative widths of plots when combine is set. Default +

    relWidths
    +

    Relative widths of plots when combine is set. Default c(1, 1, 1).

    -
    plotNCols
    -

    Number of columns when plots are combined in a grid. Default +

    plotNCols
    +

    Number of columns when plots are combined in a grid. Default NULL.

    -
    plotNRows
    -

    Number of rows when plots are combined in a grid. Default +

    plotNRows
    +

    Number of rows when plots are combined in a grid. Default NULL.

    -
    labelSamples
    -

    Will label sample name in title of plot if TRUE. Default +

    labelSamples
    +

    Will label sample name in title of plot if TRUE. Default TRUE.

    -
    samplePerColumn
    +
    samplePerColumn

    If TRUE, when there are multiple samples and combining -by "all", the output .ggplot will have plots from each sample on a +by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

    -
    sampleRelHeights
    -

    If there are multiple samples and combining by +

    sampleRelHeights
    +

    If there are multiple samples and combining by "all", the relative heights for each plot. Default 1.

    -
    sampleRelWidths
    -

    If there are multiple samples and combining by +

    sampleRelWidths
    +

    If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

    Value

    - - -

    list of .ggplot objects

    +

    list of .ggplot objects

    See also

    @@ -438,9 +438,9 @@

    Examples

    data(scExample, package="singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runQuickUMAP(sce)
-#> Fri May  3 07:16:45 2024 ... Computing Scater UMAP for sample 'pbmc_4k'.
+#> Thu Feb 13 10:30:01 2025 ... Computing Scater UMAP for sample 'pbmc_4k'.
 sce <- runScDblFinder(sce)
-#> Fri May  3 07:16:49 2024 ... Running 'scDblFinder'
+#> Thu Feb 13 10:30:06 2025 ... Running 'scDblFinder'
 plotScDblFinderResults(inSCE = sce, reducedDimName = "UMAP")
    @@ -457,15 +457,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyDotPlot.html b/docs/reference/plotScanpyDotPlot.html index 185a72552..2ebe75780 100644 --- a/docs/reference/plotScanpyDotPlot.html +++ b/docs/reference/plotScanpyDotPlot.html @@ -1,9 +1,9 @@ -plotScanpyDotPlot — plotScanpyDotPlot • singleCellTKplotScanpyDotPlot — plotScanpyDotPlot • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -223,61 +223,61 @@

    plotScanpyDotPlot

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Assay to use for plotting. By default it will use counts assay.

    -
    features
    +
    features

    Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes). The var_names could be a dictionary or a list.

    -
    groupBy
    +
    groupBy

    The key of the observation grouping to consider.

    -
    standardScale
    -

    Whether or not to standardize the given dimension -between 0 and 1, meaning for each variable or group, subtract the minimum and +

    standardScale
    +

    Whether or not to standardize the given dimension +between 0 and 1, meaning for each variable or group, subtract the minimum and divide each by its maximum. Default NULL means that it doesn't perform any scaling.

    -
    title
    +
    title

    Provide title for the figure.

    -
    vmin
    -

    The value representing the lower limit of the color scale. -Values smaller than vmin are plotted with the same color as vmin. +

    vmin
    +

    The value representing the lower limit of the color scale. +Values smaller than vmin are plotted with the same color as vmin. Default NULL

    -
    vmax
    -

    The value representing the upper limit of the color scale. -Values larger than vmax are plotted with the same color as vmax. +

    vmax
    +

    The value representing the upper limit of the color scale. +Values larger than vmax are plotted with the same color as vmax. Default NULL

    -
    colorBarTitle
    +
    colorBarTitle

    Title for the color bar.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
@@ -286,7 +286,7 @@ 
    Examples
    
 sce <- runScanpyUMAP(sce, useReducedDim = "scanpyPCA")
 markers <- c("MALAT1" ,"RPS27" ,"CST3")
 plotScanpyDotPlot(sce, features = markers, groupBy = 'Scanpy_louvain_1')
-}
+} # }
    @@ -301,15 +301,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyEmbedding.html b/docs/reference/plotScanpyEmbedding.html index 4b3dc86f6..18ed609c5 100644 --- a/docs/reference/plotScanpyEmbedding.html +++ b/docs/reference/plotScanpyEmbedding.html @@ -1,9 +1,9 @@ -plotScanpyEmbedding — plotScanpyEmbedding • singleCellTKplotScanpyEmbedding — plotScanpyEmbedding • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,44 +220,44 @@

    plotScanpyEmbedding

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    reducedDimName
    +
    reducedDimName

    Name of reducedDims object containing embeddings. Eg. scanpyUMAP.

    -
    useAssay
    +
    useAssay

    Specify name of assay to use. Default is NULL, which will use scaled assay by default.

    -
    color
    +
    color

    Keys for annotations of observations/cells or variables/genes.

    -
    legend
    -

    Location of legend, either 'on data', 'right margin' or a +

    legend
    +

    Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter of Legend.

    -
    title
    +
    title

    Provide title for panels either as string or list of strings

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
@@ -265,7 +265,7 @@ 
    Examples
    
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
 sce <- runScanpyUMAP(sce, useReducedDim = "scanpyPCA")
 plotScanpyEmbedding(sce, reducedDimName = "scanpyUMAP", color = 'Scanpy_louvain_1')
-}
+} # }
    @@ -280,15 +280,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyHVG.html b/docs/reference/plotScanpyHVG.html index 2c0e3b895..2bddcd3fe 100644 --- a/docs/reference/plotScanpyHVG.html +++ b/docs/reference/plotScanpyHVG.html @@ -1,9 +1,9 @@ -plotScanpyHVG — plotScanpyHVG • singleCellTKplotScanpyHVG — plotScanpyHVG • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,29 +213,29 @@

    plotScanpyHVG

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    log
    +
    log

    Plot on logarithmic axes. Default FALSE.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 plotScanpyHVG(sce)
-}
+} # }
    @@ -250,15 +250,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyHeatmap.html b/docs/reference/plotScanpyHeatmap.html index 20fe35a5c..914c2116d 100644 --- a/docs/reference/plotScanpyHeatmap.html +++ b/docs/reference/plotScanpyHeatmap.html @@ -1,9 +1,9 @@ -plotScanpyHeatmap — plotScanpyHeatmap • singleCellTKplotScanpyHeatmap — plotScanpyHeatmap • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -221,54 +221,54 @@

    plotScanpyHeatmap

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Assay to use for plotting. By default it will use counts assay.

    -
    features
    +
    features

    Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes). The var_names could be a dictionary or a list.

    -
    groupBy
    +
    groupBy

    The key of the observation grouping to consider.

    -
    standardScale
    -

    Whether or not to standardize the given dimension -between 0 and 1, meaning for each variable or group, subtract the minimum and +

    standardScale
    +

    Whether or not to standardize the given dimension +between 0 and 1, meaning for each variable or group, subtract the minimum and divide each by its maximum. Default NULL means that it doesn't perform any scaling.

    -
    vmin
    -

    The value representing the lower limit of the color scale. +

    vmin
    +

    The value representing the lower limit of the color scale. Values smaller than vmin are plotted with the same color as vmin. Default NULL

    -
    vmax
    -

    The value representing the upper limit of the color scale. -Values larger than vmax are plotted with the same color as vmax. +

    vmax
    +

    The value representing the upper limit of the color scale. +Values larger than vmax are plotted with the same color as vmax. Default NULL

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
@@ -277,7 +277,7 @@ 
    Examples
    
 sce <- runScanpyUMAP(sce, useReducedDim = "scanpyPCA")
 markers <- c("MALAT1" ,"RPS27" ,"CST3")
 plotScanpyHeatmap(sce, features = markers, groupBy = 'Scanpy_louvain_1')
-}
+} # }
    @@ -292,15 +292,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyMarkerGenes.html b/docs/reference/plotScanpyMarkerGenes.html index 22b5805e0..9abaa6a6f 100644 --- a/docs/reference/plotScanpyMarkerGenes.html +++ b/docs/reference/plotScanpyMarkerGenes.html @@ -1,9 +1,9 @@ -plotScanpyMarkerGenes — plotScanpyMarkerGenes • singleCellTKplotScanpyMarkerGenes — plotScanpyMarkerGenes • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -219,39 +219,39 @@

    plotScanpyMarkerGenes

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    groups
    +
    groups

    The groups for which to show the gene ranking. Default NULL means that all groups will be considered.

    -
    nGenes
    +
    nGenes

    Number of genes to show. Default 10

    -
    nCols
    +
    nCols

    Number of panels shown per row. Default 4

    -
    sharey
    -

    Controls if the y-axis of each panels should be shared. +

    sharey
    +

    Controls if the y-axis of each panels should be shared. Default FALSE allows each panel to have its own y-axis range.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
@@ -259,7 +259,7 @@ 
    Examples
    
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
 sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
 plotScanpyMarkerGenes(sce, groups = '0')
-}
+} # }
    @@ -274,15 +274,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyMarkerGenesDotPlot.html b/docs/reference/plotScanpyMarkerGenesDotPlot.html index 997c74cc1..37820d416 100644 --- a/docs/reference/plotScanpyMarkerGenesDotPlot.html +++ b/docs/reference/plotScanpyMarkerGenesDotPlot.html @@ -1,9 +1,9 @@ -plotScanpyMarkerGenesDotPlot — plotScanpyMarkerGenesDotPlot • singleCellTKplotScanpyMarkerGenesDotPlot — plotScanpyMarkerGenesDotPlot • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -226,80 +226,80 @@

    plotScanpyMarkerGenesDotPlot

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    groups
    +
    groups

    The groups for which to show the gene ranking. Default NULL means that all groups will be considered.

    -
    nGenes
    +
    nGenes

    Number of genes to show. Default 10

    -
    groupBy
    -

    The key of the observation grouping to consider. By default, +

    groupBy
    +

    The key of the observation grouping to consider. By default, the groupby is chosen from the rank genes groups parameter.

    -
    log2fcThreshold
    +
    log2fcThreshold

    Only output DEGs with the absolute values of log2FC larger than this value. Default NULL.

    -
    parameters
    -

    The options for marker genes results to plot are: +

    parameters
    +

    The options for marker genes results to plot are: ‘scores’, ‘logfoldchanges’, ‘pvals’, ‘pvals_adj’, ‘log10_pvals’, ‘log10_pvals_adj’. If NULL provided then it uses mean gene value to plot.

    -
    standardScale
    -

    Whether or not to standardize the given dimension -between 0 and 1, meaning for each variable or group, subtract the minimum and +

    standardScale
    +

    Whether or not to standardize the given dimension +between 0 and 1, meaning for each variable or group, subtract the minimum and divide each by its maximum. Default NULL means that it doesn't perform any scaling.

    -
    features
    +
    features

    Genes to plot. Sometimes is useful to pass a specific list of -var names (e.g. genes) to check their fold changes or p-values, instead of -the top/bottom genes. The gene names could be a dictionary or a list. +var names (e.g. genes) to check their fold changes or p-values, instead of +the top/bottom genes. The gene names could be a dictionary or a list. Default NULL

    -
    title
    +
    title

    Provide title for the figure.

    -
    vmin
    -

    The value representing the lower limit of the color scale. -Values smaller than vmin are plotted with the same color as vmin. +

    vmin
    +

    The value representing the lower limit of the color scale. +Values smaller than vmin are plotted with the same color as vmin. Default NULL

    -
    vmax
    -

    The value representing the upper limit of the color scale. -Values larger than vmax are plotted with the same color as vmax. +

    vmax
    +

    The value representing the upper limit of the color scale. +Values larger than vmax are plotted with the same color as vmax. Default NULL

    -
    colorBarTitle
    +
    colorBarTitle

    Title for the color bar.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
@@ -307,7 +307,7 @@ 
    Examples
    
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
 sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
 plotScanpyMarkerGenesDotPlot(sce, groupBy = 'Scanpy_louvain_1')
-}
+} # }
    @@ -322,15 +322,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyMarkerGenesHeatmap.html b/docs/reference/plotScanpyMarkerGenesHeatmap.html index 9607aa219..0bc87e819 100644 --- a/docs/reference/plotScanpyMarkerGenesHeatmap.html +++ b/docs/reference/plotScanpyMarkerGenesHeatmap.html @@ -1,9 +1,9 @@ -plotScanpyMarkerGenesHeatmap — plotScanpyMarkerGenesHeatmap • singleCellTKplotScanpyMarkerGenesHeatmap — plotScanpyMarkerGenesHeatmap • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,45 +220,45 @@

    plotScanpyMarkerGenesHeatmap

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    groups
    +
    groups

    The groups for which to show the gene ranking. Default NULL means that all groups will be considered.

    -
    groupBy
    -

    The key of the observation grouping to consider. By default, +

    groupBy
    +

    The key of the observation grouping to consider. By default, the groupby is chosen from the rank genes groups parameter.

    -
    nGenes
    +
    nGenes

    Number of genes to show. Default 10

    -
    features
    +
    features

    Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes). The var_names could be a dictionary or a list.

    -
    log2fcThreshold
    +
    log2fcThreshold

    Only output DEGs with the absolute values of log2FC larger than this value. Default NULL.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
@@ -266,7 +266,7 @@ 
    Examples
    
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
 sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
 plotScanpyMarkerGenesHeatmap(sce, groupBy = 'Scanpy_louvain_1')
-}
+} # }
    @@ -281,15 +281,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyMarkerGenesMatrixPlot.html b/docs/reference/plotScanpyMarkerGenesMatrixPlot.html index 235506221..f544add83 100644 --- a/docs/reference/plotScanpyMarkerGenesMatrixPlot.html +++ b/docs/reference/plotScanpyMarkerGenesMatrixPlot.html @@ -1,9 +1,9 @@ -plotScanpyMarkerGenesMatrixPlot — plotScanpyMarkerGenesMatrixPlot • singleCellTKplotScanpyMarkerGenesMatrixPlot — plotScanpyMarkerGenesMatrixPlot • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -226,80 +226,80 @@

    plotScanpyMarkerGenesMatrixPlot

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    groups
    +
    groups

    The groups for which to show the gene ranking. Default NULL means that all groups will be considered.

    -
    nGenes
    +
    nGenes

    Number of genes to show. Default 10

    -
    groupBy
    -

    The key of the observation grouping to consider. By default, +

    groupBy
    +

    The key of the observation grouping to consider. By default, the groupby is chosen from the rank genes groups parameter.

    -
    log2fcThreshold
    +
    log2fcThreshold

    Only output DEGs with the absolute values of log2FC larger than this value. Default NULL.

    -
    parameters
    -

    The options for marker genes results to plot are: +

    parameters
    +

    The options for marker genes results to plot are: ‘scores’, ‘logfoldchanges’, ‘pvals’, ‘pvals_adj’, ‘log10_pvals’, ‘log10_pvals_adj’. If NULL provided then it uses mean gene value to plot.

    -
    standardScale
    -

    Whether or not to standardize the given dimension -between 0 and 1, meaning for each variable or group, subtract the minimum and +

    standardScale
    +

    Whether or not to standardize the given dimension +between 0 and 1, meaning for each variable or group, subtract the minimum and divide each by its maximum. Default NULL means that it doesn't perform any scaling.

    -
    features
    +
    features

    Genes to plot. Sometimes is useful to pass a specific list of -var names (e.g. genes) to check their fold changes or p-values, instead of -the top/bottom genes. The var_names could be a dictionary or a list. +var names (e.g. genes) to check their fold changes or p-values, instead of +the top/bottom genes. The var_names could be a dictionary or a list. Default NULL

    -
    title
    +
    title

    Provide title for the figure.

    -
    vmin
    -

    The value representing the lower limit of the color scale. -Values smaller than vmin are plotted with the same color as vmin. +

    vmin
    +

    The value representing the lower limit of the color scale. +Values smaller than vmin are plotted with the same color as vmin. Default NULL

    -
    vmax
    -

    The value representing the upper limit of the color scale. -Values larger than vmax are plotted with the same color as vmax. +

    vmax
    +

    The value representing the upper limit of the color scale. +Values larger than vmax are plotted with the same color as vmax. Default NULL

    -
    colorBarTitle
    +
    colorBarTitle

    Title for the color bar.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
@@ -307,7 +307,7 @@ 
    Examples
    
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
 sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
 plotScanpyMarkerGenesMatrixPlot(sce, groupBy = 'Scanpy_louvain_1')
-}
+} # }
    @@ -322,15 +322,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyMarkerGenesViolin.html b/docs/reference/plotScanpyMarkerGenesViolin.html index c9054c860..5590de59a 100644 --- a/docs/reference/plotScanpyMarkerGenesViolin.html +++ b/docs/reference/plotScanpyMarkerGenesViolin.html @@ -1,9 +1,9 @@ -plotScanpyMarkerGenesViolin — plotScanpyMarkerGenesViolin • singleCellTKplotScanpyMarkerGenesViolin — plotScanpyMarkerGenesViolin • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,35 +213,35 @@

    plotScanpyMarkerGenesViolin

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    groups
    +
    groups

    The groups for which to show the gene ranking. Default NULL means that all groups will be considered.

    -
    features
    -

    List of genes to plot. Is only useful if interested in a +

    features
    +

    List of genes to plot. Is only useful if interested in a custom gene list

    -
    nGenes
    +
    nGenes

    Number of genes to show. Default 10

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
@@ -249,7 +249,7 @@ 
    Examples
    
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
 sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
 plotScanpyMarkerGenesViolin(sce, groups = '0')
-}
+} # }
    @@ -264,15 +264,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyMatrixPlot.html b/docs/reference/plotScanpyMatrixPlot.html index d10f2891e..60ced0c1c 100644 --- a/docs/reference/plotScanpyMatrixPlot.html +++ b/docs/reference/plotScanpyMatrixPlot.html @@ -1,9 +1,9 @@ -plotScanpyMatrixPlot — plotScanpyMatrixPlot • singleCellTKplotScanpyMatrixPlot — plotScanpyMatrixPlot • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -223,61 +223,61 @@

    plotScanpyMatrixPlot

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Assay to use for plotting. By default it will use counts assay.

    -
    features
    +
    features

    Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes). The var_names could be a dictionary or a list.

    -
    groupBy
    +
    groupBy

    The key of the observation grouping to consider.

    -
    standardScale
    -

    Whether or not to standardize the given dimension -between 0 and 1, meaning for each variable or group, subtract the minimum and +

    standardScale
    +

    Whether or not to standardize the given dimension +between 0 and 1, meaning for each variable or group, subtract the minimum and divide each by its maximum. Default NULL means that it doesn't perform any scaling.

    -
    title
    +
    title

    Provide title for the figure.

    -
    vmin
    -

    The value representing the lower limit of the color scale. -Values smaller than vmin are plotted with the same color as vmin. +

    vmin
    +

    The value representing the lower limit of the color scale. +Values smaller than vmin are plotted with the same color as vmin. Default NULL

    -
    vmax
    -

    The value representing the upper limit of the color scale. -Values larger than vmax are plotted with the same color as vmax. +

    vmax
    +

    The value representing the upper limit of the color scale. +Values larger than vmax are plotted with the same color as vmax. Default NULL

    -
    colorBarTitle
    +
    colorBarTitle

    Title for the color bar.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
@@ -286,7 +286,7 @@ 
    Examples
    
 sce <- runScanpyUMAP(sce, useReducedDim = "scanpyPCA")
 markers <- c("MALAT1" ,"RPS27" ,"CST3")
 plotScanpyMatrixPlot(sce, features = markers, groupBy = 'Scanpy_louvain_1')
-}
+} # }
    @@ -301,15 +301,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyPCA.html b/docs/reference/plotScanpyPCA.html index 64563ff7b..16b926a9b 100644 --- a/docs/reference/plotScanpyPCA.html +++ b/docs/reference/plotScanpyPCA.html @@ -1,9 +1,9 @@ -plotScanpyPCA — plotScanpyPCA • singleCellTKplotScanpyPCA — plotScanpyPCA • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -219,44 +219,44 @@

    plotScanpyPCA

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    reducedDimName
    +
    reducedDimName

    Name of new reducedDims object containing Scanpy PCA.

    -
    color
    +
    color

    Keys for annotations of observations/cells or variables/genes.

    -
    title
    +
    title

    Provide title for panels either as string or list of strings

    -
    legend
    -

    Location of legend, either 'on data', 'right margin' or a +

    legend
    +

    Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter of Legend.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
 sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
 plotScanpyPCA(sce)
-}
+} # }
    @@ -271,15 +271,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyPCAGeneRanking.html b/docs/reference/plotScanpyPCAGeneRanking.html index b75233886..7b210fe6b 100644 --- a/docs/reference/plotScanpyPCAGeneRanking.html +++ b/docs/reference/plotScanpyPCAGeneRanking.html @@ -1,9 +1,9 @@ -plotScanpyPCAGeneRanking — plotScanpyPCAGeneRanking • singleCellTKplotScanpyPCAGeneRanking — plotScanpyPCAGeneRanking • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,37 +213,37 @@

    plotScanpyPCAGeneRanking

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    PC_comp
    -

    For example, '1,2,3' means [1, 2, 3], first, second, +

    PC_comp
    +

    For example, '1,2,3' means [1, 2, 3], first, second, third principal component.

    -
    includeLowest
    -

    Whether to show the variables with both highest and +

    includeLowest
    +

    Whether to show the variables with both highest and lowest loadings. Default TRUE

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
 sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
 plotScanpyPCAGeneRanking(sce)
-}
+} # }
    @@ -258,15 +258,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyPCAVariance.html b/docs/reference/plotScanpyPCAVariance.html index 8c193449f..12d28189b 100644 --- a/docs/reference/plotScanpyPCAVariance.html +++ b/docs/reference/plotScanpyPCAVariance.html @@ -1,9 +1,9 @@ -plotScanpyPCAVariance — plotScanpyPCAVariance • singleCellTKplotScanpyPCAVariance — plotScanpyPCAVariance • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,35 +213,35 @@

    plotScanpyPCAVariance

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    nPCs
    +
    nPCs

    Number of PCs to show. Default 50.

    -
    log
    +
    log

    Plot on logarithmic scale. Default FALSE

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
 sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
 plotScanpyPCAVariance(sce)
-}
+} # }
    @@ -256,15 +256,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScanpyViolin.html b/docs/reference/plotScanpyViolin.html index 2579f7cdf..75b16e4af 100644 --- a/docs/reference/plotScanpyViolin.html +++ b/docs/reference/plotScanpyViolin.html @@ -1,9 +1,9 @@ -plotScanpyViolin — plotScanpyViolin • singleCellTKplotScanpyViolin — plotScanpyViolin • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,44 +220,44 @@

    plotScanpyViolin

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Assay to use for plotting. By default it will use counts assay.

    -
    features
    +
    features

    Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes). The var_names could be a dictionary or a list.

    -
    groupBy
    +
    groupBy

    The key of the observation grouping to consider.

    -
    xlabel
    +
    xlabel

    Label of the x axis. Defaults to groupBy.

    -
    ylabel
    -

    Label of the y axis. If NULL and groupBy is NULL, +

    ylabel
    +

    Label of the y axis. If NULL and groupBy is NULL, defaults to 'value'. If NULL and groupBy is not NULL, defaults to features.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
@@ -266,7 +266,7 @@ 
    Examples
    
 sce <- runScanpyUMAP(sce, useReducedDim = "scanpyPCA")
 markers <- c("MALAT1" ,"RPS27" ,"CST3")
 plotScanpyViolin(sce, features = markers, groupBy = "Scanpy_louvain_1")
-}
+} # }
    @@ -281,15 +281,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScdsHybridResults-1.png b/docs/reference/plotScdsHybridResults-1.png index e8615395c..2a1c8cda1 100644 Binary files a/docs/reference/plotScdsHybridResults-1.png and b/docs/reference/plotScdsHybridResults-1.png differ diff --git a/docs/reference/plotScdsHybridResults.html b/docs/reference/plotScdsHybridResults.html index 4d46ef1cd..67eff6cac 100644 --- a/docs/reference/plotScdsHybridResults.html +++ b/docs/reference/plotScdsHybridResults.html @@ -1,11 +1,11 @@ -Plots for runCxdsBcdsHybrid outputs. — plotScdsHybridResults • singleCellTKPlots for runCxdsBcdsHybrid outputs. — plotScdsHybridResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -252,170 +252,170 @@

    Plots for runCxdsBcdsHybrid outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runCxdsBcdsHybrid. Required.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to. Default NULL.

    -
    shape
    +
    shape

    If provided, add shapes based on the value.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector equal length to the number of the samples in the SingleCellExperiment object, or can be retrieved from the colData slot. Default NULL.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    violin
    +
    violin

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    +
    boxplot

    Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    reducedDimName
    +
    reducedDimName

    Saved dimension reduction name in the SingleCellExperiment object. Required.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    dim1
    +
    dim1

    1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    dim2
    +
    dim2

    2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    bin
    +
    bin

    Numeric vector. If single value, will divide the numeric values into the `bin` groups. If more than one value, will bin numeric values using values as a cut point.

    -
    binLabel
    +
    binLabel

    Character vector. Labels for the bins created by the `bin` parameter. Default NULL.

    -
    defaultTheme
    +
    defaultTheme

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default NULL.

    -
    summaryTextSize
    +
    summaryTextSize

    The text size of the summary statistic displayed above the violin plot. Default 3.

    -
    transparency
    +
    transparency

    Transparency of the dots, values will be 0-1. Default 1.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    legendSize
    +
    legendSize

    size of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default NULL.

    -
    relHeights
    +
    relHeights

    Relative heights of plots when combine is set.

    -
    relWidths
    +
    relWidths

    Relative widths of plots when combine is set.

    -
    plotNCols
    +
    plotNCols

    Number of columns when plots are combined in a grid.

    -
    plotNRows
    +
    plotNRows

    Number of rows when plots are combined in a grid.

    -
    labelSamples
    +
    labelSamples

    Will label sample name in title of plot if TRUE. Default TRUE.

    -
    samplePerColumn
    +
    samplePerColumn

    If TRUE, when there are multiple samples and combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

    -
    sampleRelHeights
    +
    sampleRelHeights

    If there are multiple samples and combining by "all", the relative heights for each plot.

    -
    sampleRelWidths
    +
    sampleRelWidths

    If there are multiple samples and combining by "all", the relative widths for each plot.

    Value

    - - -

    list of .ggplot objects

    +

    list of .ggplot objects

    @@ -423,9 +423,9 @@

    Examples

    data(scExample, package="singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runQuickUMAP(sce)
-#> Fri May  3 07:17:06 2024 ... Computing Scater UMAP for sample 'pbmc_4k'.
+#> Thu Feb 13 10:30:36 2025 ... Computing Scater UMAP for sample 'pbmc_4k'.
 sce <- runCxdsBcdsHybrid(sce)
-#> Fri May  3 07:17:10 2024 ... Running 'cxds_bcds_hybrid'
+#> Thu Feb 13 10:30:40 2025 ... Running 'cxds_bcds_hybrid'
 plotScdsHybridResults(inSCE=sce, reducedDimName="UMAP")
    @@ -442,15 +442,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotScrubletResults.html b/docs/reference/plotScrubletResults.html index dee8ed44b..aa49cc95e 100644 --- a/docs/reference/plotScrubletResults.html +++ b/docs/reference/plotScrubletResults.html @@ -1,11 +1,11 @@ -Plots for runScrublet outputs. — plotScrubletResults • singleCellTKPlots for runScrublet outputs. — plotScrubletResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -252,182 +252,182 @@

    Plots for runScrublet outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runCxds. Required.

    -
    reducedDimName
    -

    Saved dimension reduction name in inSCE. +

    reducedDimName
    +

    Saved dimension reduction name in inSCE. Default "UMAP".

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    shape
    +
    shape

    If provided, add shapes based on the value. Default NULL.

    -
    groupBy
    +
    groupBy

    Groupings for each numeric value. A user may input a vector -equal length to the number of the samples in inSCE, or can be +equal length to the number of the samples in inSCE, or can be retrieved from the colData slot. Default NULL.

    -
    combinePlot
    -

    Must be either "all", "sample", or -"none". "all" will combine all plots into a single .ggplot -object, while "sample" will output a list of plots separated by +

    combinePlot
    +

    Must be either "all", "sample", or +"none". "all" will combine all plots into a single .ggplot +object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    violin
    -

    Boolean. If TRUE, will plot the violin plot. Default +

    violin
    +

    Boolean. If TRUE, will plot the violin plot. Default TRUE.

    -
    boxplot
    -

    Boolean. If TRUE, will plot boxplots for each violin +

    boxplot
    +

    Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.

    -
    dots
    +
    dots

    Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    dim1
    -

    1st dimension to be used for plotting. Can either be a string -which specifies the name of the dimension to be plotted from reducedDims, or -a numeric value which specifies the index of the dimension to be plotted. +

    dim1
    +

    1st dimension to be used for plotting. Can either be a string +which specifies the name of the dimension to be plotted from reducedDims, or +a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

    -
    dim2
    -

    2nd dimension to be used for plotting. Similar to dim1. +

    dim2
    +

    2nd dimension to be used for plotting. Similar to dim1. Default is NULL.

    -
    bin
    -

    Numeric vector. If single value, will divide the numeric values +

    bin
    +

    Numeric vector. If single value, will divide the numeric values into bin groups. If more than one value, will bin numeric values using values as a cut point. Default NULL.

    -
    binLabel
    +
    binLabel

    Character vector. Labels for the bins created by bin. Default NULL.

    -
    defaultTheme
    -

    Removes grid in plot and sets axis title size to +

    defaultTheme
    +

    Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Size of dots. Default 0.5.

    -
    summary
    +
    summary

    Adds a summary statistic, as well as a crossbar to the -violin plot. Options are "mean" or "median". Default +violin plot. Options are "mean" or "median". Default NULL.

    -
    summaryTextSize
    +
    summaryTextSize

    The text size of the summary statistic displayed above the violin plot. Default 3.

    -
    transparency
    -

    Transparency of the dots, values will be 0-1. Default +

    transparency
    +

    Transparency of the dots, values will be 0-1. Default 1.

    -
    baseSize
    +
    baseSize

    The base font size for all text. Default 12. -Can be overwritten by titleSize, axisSize, and +Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.

    -
    titleSize
    +
    titleSize

    Size of title of plot. Default NULL.

    -
    axisLabelSize
    +
    axisLabelSize

    Size of x/y-axis labels. Default NULL.

    -
    axisSize
    +
    axisSize

    Size of x/y-axis ticks. Default NULL.

    -
    legendSize
    +
    legendSize

    size of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    size of legend title. Default NULL.

    -
    relHeights
    -

    Relative heights of plots when combine is set. Default +

    relHeights
    +

    Relative heights of plots when combine is set. Default 1.

    -
    relWidths
    -

    Relative widths of plots when combine is set. Default +

    relWidths
    +

    Relative widths of plots when combine is set. Default c(1, 1, 1).

    -
    plotNCols
    -

    Number of columns when plots are combined in a grid. Default +

    plotNCols
    +

    Number of columns when plots are combined in a grid. Default NULL.

    -
    plotNRows
    -

    Number of rows when plots are combined in a grid. Default +

    plotNRows
    +

    Number of rows when plots are combined in a grid. Default NULL.

    -
    labelSamples
    -

    Will label sample name in title of plot if TRUE. Default +

    labelSamples
    +

    Will label sample name in title of plot if TRUE. Default TRUE.

    -
    samplePerColumn
    -

    If TRUE, when there are multiple samples and -combining by "all", the output .ggplot will have plots from each +

    samplePerColumn
    +

    If TRUE, when there are multiple samples and +combining by "all", the output .ggplot will have plots from each sample on a single column. Default TRUE.

    -
    sampleRelHeights
    -

    If there are multiple samples and combining by +

    sampleRelHeights
    +

    If there are multiple samples and combining by "all", the relative heights for each plot. Default 1.

    -
    sampleRelWidths
    -

    If there are multiple samples and combining by +

    sampleRelWidths
    +

    If there are multiple samples and combining by "all", the relative widths for each plot. Default 1.

    Value

    - - -

    list of .ggplot objects

    +

    list of .ggplot objects

    See also

    @@ -437,12 +437,12 @@

    See also

    Examples

    data(scExample, package="singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runQuickUMAP(sce)
 sce <- runScrublet(sce)
 plotScrubletResults(inSCE=sce, reducedDimName="UMAP")
-}
+} # }
    @@ -457,15 +457,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSeuratElbow.html b/docs/reference/plotSeuratElbow.html index bd772a950..3e1de1377 100644 --- a/docs/reference/plotSeuratElbow.html +++ b/docs/reference/plotSeuratElbow.html @@ -1,15 +1,11 @@ -plotSeuratElbow -Computes the plot object for elbow plot from the pca slot in the input sce -object — plotSeuratElbow • singleCellTKplotSeuratElbow Computes the plot object for elbow plot from the pca slot in the input sce object — plotSeuratElbow • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    plotSeuratElbow -Computes the plot object for elbow plot from the pca slot in the input sce -object

    +

    plotSeuratElbow Computes the plot object for elbow plot from the pca slot in the input sce object

    Source: R/seuratFunctions.R
    @@ -224,60 +218,60 @@

    plotSeuratElbow reduction = "pca", ndims = 20, externalReduction = NULL, - interactive = TRUE + interactive = FALSE )

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object from which to compute the elbow plot (pca should be computed)

    -
    significantPC
    +
    significantPC

    Number of significant principal components to plot. This is used to alter the color of the points for the corresponding PCs. If NULL, all points will be the same color. Default NULL.

    -
    reduction
    +
    reduction

    Reduction to use for elbow plot generation. Either "pca" or "ica". Default "pca".

    -
    ndims
    +
    ndims

    Number of components to use. Default 20.

    -
    externalReduction
    +
    externalReduction

    Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.

    -
    interactive
    +
    interactive

    Logical value indicating if the returned object should be an interactive plotly object if TRUE or a ggplot object if -set to FALSE. Default is TRUE.

    +set to FALSE. Default is FALSE.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 sce <- runSeuratScaleData(sce, useAssay = "counts")
 sce <- runSeuratPCA(sce, useAssay = "counts")
 plotSeuratElbow(sce)
-}
+} # }
    @@ -292,15 +286,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSeuratGenes.html b/docs/reference/plotSeuratGenes.html index 17854fcda..02d976d51 100644 --- a/docs/reference/plotSeuratGenes.html +++ b/docs/reference/plotSeuratGenes.html @@ -1,9 +1,9 @@ -Compute and plot visualizations for marker genes — plotSeuratGenes • singleCellTKCompute and plot visualizations for marker genes — plotSeuratGenes • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -224,51 +224,53 @@

    Compute and plot visualizations for marker genes

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Specify the name of the assay that will be scaled by this function.

    -
    plotType
    +
    plotType

    Specify the type of the plot to compute. Options are limited to "ridge", "violin", "feature", "dot" and "heatmap".

    -
    features
    +
    features

    Specify the features to compute the plot against.

    -
    groupVariable
    +
    groupVariable

    Specify the column name from the colData slot that should be used as grouping variable.

    -
    reducedDimName
    +
    reducedDimName

    saved dimension reduction name in the SingleCellExperiment object. Default seuratUMAP.

    -
    splitBy
    +
    splitBy

    Specify the column name from the colData slot that should be used to split samples. Default is NULL.

    -
    cols
    +
    cols

    Specify two colors to form a gradient between. Default is c("lightgrey", "blue").

    -
    ncol
    +
    ncol

    Visualizations will be adjusted in "ncol" number of columns. Default is 1.

    -
    combine
    +
    combine

    A logical value that indicates if the plots should be combined together into a single plot if TRUE, else if FALSE returns separate ggplot objects for each feature. Only works when plotType @@ -279,9 +281,7 @@

    Arguments

    Value

    - - -

    Plot object

    +

    Plot object

    @@ -296,15 +296,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSeuratHVG.html b/docs/reference/plotSeuratHVG.html index da483f0a5..e08c5baa7 100644 --- a/docs/reference/plotSeuratHVG.html +++ b/docs/reference/plotSeuratHVG.html @@ -1,15 +1,11 @@ -plotSeuratHVG -Plot highly variable genes from input sce object (must have highly variable -genes computations stored) — plotSeuratHVG • singleCellTKplotSeuratHVG Plot highly variable genes from input sce object (must have highly variable genes computations stored) — plotSeuratHVG • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    plotSeuratHVG -Plot highly variable genes from input sce object (must have highly variable -genes computations stored)

    +

    plotSeuratHVG Plot highly variable genes from input sce object (must have highly variable genes computations stored)

    Source: R/seuratFunctions.R
    @@ -223,12 +217,14 @@

    plotSeuratHVG

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object that contains the highly variable genes computations

    -
    labelPoints
    +
    labelPoints

    Numeric value indicating the number of top genes that should be labeled. Default is 0, which will not label any point.

    @@ -236,19 +232,17 @@

    Arguments

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 plotSeuratHVG(sce)
-}
+} # }

    @@ -263,15 +257,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSeuratHeatmap.html b/docs/reference/plotSeuratHeatmap.html index e0aed65f3..cd335b7a4 100644 --- a/docs/reference/plotSeuratHeatmap.html +++ b/docs/reference/plotSeuratHeatmap.html @@ -1,15 +1,11 @@ -plotSeuratHeatmap -Modifies the heatmap plot object so it contains specified number of heatmaps -in a single plot — plotSeuratHeatmap • singleCellTKplotSeuratHeatmap Modifies the heatmap plot object so it contains specified number of heatmaps in a single plot — plotSeuratHeatmap • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    plotSeuratHeatmap -Modifies the heatmap plot object so it contains specified number of heatmaps -in a single plot

    +

    plotSeuratHeatmap Modifies the heatmap plot object so it contains specified number of heatmaps in a single plot

    Source: R/seuratFunctions.R
    @@ -223,28 +217,28 @@

    plotSeuratHeatmap

    Arguments

    -
    plotObject
    + + +
    plotObject

    plot object computed from runSeuratHeatmap() function

    -
    dims
    +
    dims

    numerical value of how many heatmaps to draw (default is 0)

    -
    ncol
    +
    ncol

    numerical value indicating that in how many columns should the heatmaps be distrbuted (default is 2)

    -
    labels
    +
    labels

    list() of labels to draw on heatmaps

    Value

    - - -

    modified plot object

    +

    modified plot object

    @@ -259,15 +253,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSeuratJackStraw.html b/docs/reference/plotSeuratJackStraw.html index ece74ebc6..5ec5f51d5 100644 --- a/docs/reference/plotSeuratJackStraw.html +++ b/docs/reference/plotSeuratJackStraw.html @@ -1,15 +1,11 @@ -plotSeuratJackStraw -Computes the plot object for jackstraw plot from the pca slot in the input -sce object — plotSeuratJackStraw • singleCellTKplotSeuratJackStraw Computes the plot object for jackstraw plot from the pca slot in the input sce object — plotSeuratJackStraw • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    plotSeuratJackStraw -Computes the plot object for jackstraw plot from the pca slot in the input -sce object

    +

    plotSeuratJackStraw Computes the plot object for jackstraw plot from the pca slot in the input sce object

    Source: R/seuratFunctions.R
    @@ -229,47 +223,47 @@

    plotSeuratJackStraw

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object from which to compute the jackstraw plot (pca should be computed)

    -
    dims
    +
    dims

    Number of components to plot in Jackstraw. If NULL, then all components are plotted Default NULL.

    -
    xmax
    +
    xmax

    X-axis maximum on each QQ plot. Default 0.1.

    -
    ymax
    +
    ymax

    Y-axis maximum on each QQ plot. Default 0.3.

    -
    externalReduction
    +
    externalReduction

    Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 sce <- runSeuratScaleData(sce, useAssay = "counts")
 sce <- runSeuratPCA(sce, useAssay = "counts")
 sce <- runSeuratJackStraw(sce, useAssay = "counts")
 plotSeuratJackStraw(sce)
-}
+} # }

    @@ -284,15 +278,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSeuratReduction.html b/docs/reference/plotSeuratReduction.html index 0f8bdf294..228d96c9b 100644 --- a/docs/reference/plotSeuratReduction.html +++ b/docs/reference/plotSeuratReduction.html @@ -1,12 +1,10 @@ -plotSeuratReduction -Plots the selected dimensionality reduction method — plotSeuratReduction • singleCellTKplotSeuratReduction Plots the selected dimensionality reduction method — plotSeuratReduction • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    plotSeuratReduction -Plots the selected dimensionality reduction method

    +

    plotSeuratReduction Plots the selected dimensionality reduction method

    Source: R/seuratFunctions.R
    @@ -224,48 +221,48 @@

    plotSeuratReduction

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object which has the selected dimensionality reduction algorithm already computed and stored

    -
    useReduction
    +
    useReduction

    Dimentionality reduction to plot. One of "pca", "ica", "tsne", or "umap". Default "umap".

    -
    showLegend
    +
    showLegend

    Select if legends and labels should be shown on the output plot or not. Either "TRUE" or "FALSE". Default FALSE.

    -
    groupBy
    +
    groupBy

    Specify a colData column name that be used for grouping. Default is NULL.

    -
    splitBy
    +
    splitBy

    Specify a colData column name that be used for splitting the output plot. Default is NULL.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 sce <- runSeuratScaleData(sce, useAssay = "counts")
 sce <- runSeuratPCA(sce, useAssay = "counts")
 plotSeuratReduction(sce, useReduction = "pca")
-}
+} # }

    @@ -280,15 +277,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotSoupXResults.html b/docs/reference/plotSoupXResults.html index be138c44b..6ee27da30 100644 --- a/docs/reference/plotSoupXResults.html +++ b/docs/reference/plotSoupXResults.html @@ -1,5 +1,5 @@ -Plot SoupX Result — plotSoupXResults • singleCellTKPlot SoupX Result — plotSoupXResults • singleCellTK - +
    @@ -31,7 +31,7 @@
    - +
    @@ -248,117 +248,117 @@

    Plot SoupX Result

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object. With runSoupX already applied.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to. Default NULL.

    -
    background
    +
    background

    Logical. Whether background was applied when running runSoupX. Default FALSE.

    -
    reducedDimName
    +
    reducedDimName

    Character. The embedding to use for plotting. Leave it NULL for using the sample-specific UMAPs generated when running runSoupX. Default NULL.

    -
    plotNCols
    +
    plotNCols

    Integer. Number of columns for the plot grid per sample. Will determine the number of top markers to show together with plotNRows. Default 3.

    -
    plotNRows
    +
    plotNRows

    Integer. Number of rows for the plot grid per sample. Will determine the number of top markers to show together with plotNCols. Default 2.

    -
    baseSize
    +
    baseSize

    Numeric. The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize. Default 8.

    -
    combinePlot
    +
    combinePlot

    Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "all".

    -
    xlab
    +
    xlab

    Character vector. Label for x-axis. Default NULL.

    -
    ylab
    +
    ylab

    Character vector. Label for y-axis. Default NULL.

    -
    dim1
    +
    dim1

    See plotSCEDimReduceColData. Default NULL.

    -
    dim2
    +
    dim2

    See plotSCEDimReduceColData. Default NULL.

    -
    labelClusters
    +
    labelClusters

    Logical. Whether the cluster labels are plotted. Default FALSE.

    -
    clusterLabelSize
    +
    clusterLabelSize

    Numeric. Determines the size of cluster label when labelClusters is set to TRUE. Default 3.5.

    -
    defaultTheme
    +
    defaultTheme

    Logical. Adds grid to plot when TRUE. Default TRUE.

    -
    dotSize
    +
    dotSize

    Numeric. Size of dots. Default 0.5.

    -
    transparency
    +
    transparency

    Numeric. Transparency of the dots, values will be from 0 to 1. Default 1.

    -
    titleSize
    +
    titleSize

    Numeric. Size of title of plot. Default 15.

    -
    axisLabelSize
    +
    axisLabelSize

    Numeric. Size of x/y-axis labels. Default NULL.

    -
    axisSize
    +
    axisSize

    Numeric. Size of x/y-axis ticks. Default NULL.

    -
    legendSize
    +
    legendSize

    Numeric. Size of legend. Default NULL.

    -
    legendTitleSize
    +
    legendTitleSize

    Numeric. Size of legend title. Default NULL.

    Value

    - - -

    ggplot object of the combination of UMAPs. See description.

    +

    ggplot object of the combination of UMAPs. See description.

    See also

    @@ -367,11 +367,11 @@

    See also

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 sce <- importExampleData("pbmc3k")
 sce <- runSoupX(sce, sample = "sample")
 plotSoupXResults(sce, sample = "sample")
-}
+} # }
    @@ -386,15 +386,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotTSCANClusterDEG.html b/docs/reference/plotTSCANClusterDEG.html index bcf122acd..5e87748b0 100644 --- a/docs/reference/plotTSCANClusterDEG.html +++ b/docs/reference/plotTSCANClusterDEG.html @@ -1,13 +1,11 @@ -Plot features identified by runTSCANClusterDEAnalysis on -cell 2D embedding with MST overlaid — plotTSCANClusterDEG • singleCellTKPlot features identified by runTSCANClusterDEAnalysis on cell 2D embedding with MST overlaid — plotTSCANClusterDEG • singleCellTK - +
    @@ -29,7 +27,7 @@
    - +
    -

    Plot features identified by runTSCANClusterDEAnalysis on -cell 2D embedding with MST overlaid

    +

    Plot features identified by runTSCANClusterDEAnalysis on cell 2D embedding with MST overlaid

    Source: R/runTSCAN.R
    @@ -229,44 +226,46 @@

    Plot features identified by r

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useCluster
    +
    useCluster

    Choose a cluster used for identifying DEG with runTSCANClusterDEAnalysis. Required.

    -
    pathIndex
    +
    pathIndex

    Specifies one of the branching paths from useCluster and plot the top DEGs on this path. Ususally presented by the terminal cluster of a path. By default NULL plot top DEGs of all paths.

    -
    useReducedDim
    +
    useReducedDim

    A single character for the matrix of 2D embedding. Should exist in reducedDims slot. Default "UMAP".

    -
    topN
    +
    topN

    Integer. Use top N genes identified. Default 9.

    -
    useAssay
    +
    useAssay

    A single character for the feature expression matrix. Should exist in assayNames(inSCE). Default NULL for using the one used in runTSCANClusterDEAnalysis.

    -
    featureDisplay
    +
    featureDisplay

    Specify the feature ID type to display. Users can set default value with setSCTKDisplayRow. NULL or "rownames" specifies the rownames of inSCE. Other character values indicates rowData variable.

    -
    combinePlot
    +
    combinePlot

    Must be either "all" or "none". "all" will combine plots of each feature into a single .ggplot object, while "none" will output a list of plots. Default "all".

    @@ -274,9 +273,7 @@

    Arguments

    Value

    - - -

    A .ggplot object of cell scatter plot, colored by the +

    A .ggplot object of cell scatter plot, colored by the expression of a gene identified by runTSCANClusterDEAnalysis, with the layer of trajectory.

    @@ -290,19 +287,19 @@

    Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
 mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                 useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:17:16 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:17:16 2024 ...   Identified 2 clusters
-#> Fri May  3 07:17:16 2024 ... Running TSCAN to estimate pseudotime
+#> Thu Feb 13 10:30:46 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:30:46 2025 ...   Identified 2 clusters
+#> Thu Feb 13 10:30:46 2025 ... Running TSCAN to estimate pseudotime
 #> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
 #> Also defined by ‘spam’
 #> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
 #> Also defined by ‘spam’
-#> Fri May  3 07:17:17 2024 ...   Clusters involved in path index 2 are: 1, 2
-#> Fri May  3 07:17:17 2024 ...   Number of estimated paths is 1
+#> Thu Feb 13 10:30:47 2025 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:30:47 2025 ...   Number of estimated paths is 1
 mouseBrainSubsetSCE <- runTSCANClusterDEAnalysis(inSCE = mouseBrainSubsetSCE,
                                                  useCluster = 1)
-#> Fri May  3 07:17:17 2024 ... Finding DEG between TSCAN branches
-#> Fri May  3 07:17:17 2024 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:30:47 2025 ... Finding DEG between TSCAN branches
+#> Thu Feb 13 10:30:47 2025 ...   Clusters involved in path index 2 are: 1, 2
 plotTSCANClusterDEG(mouseBrainSubsetSCE, useCluster = 1,
                     useReducedDim = "TSNE_logcounts")
 
@@ -320,15 +317,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotTSCANClusterPseudo.html b/docs/reference/plotTSCANClusterPseudo.html index 5202aaae7..727981647 100644 --- a/docs/reference/plotTSCANClusterPseudo.html +++ b/docs/reference/plotTSCANClusterPseudo.html @@ -1,12 +1,12 @@ -Plot TSCAN pseudotime rooted from given cluster — plotTSCANClusterPseudo • singleCellTKPlot TSCAN pseudotime rooted from given cluster — plotTSCANClusterPseudo • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -224,21 +224,23 @@

    Plot TSCAN pseudotime rooted from given cluster

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useCluster
    +
    useCluster

    The cluster to be regarded as the root, has to existing in colData(inSCE)$TSCAN_clusters.

    -
    useReducedDim
    +
    useReducedDim

    Saved dimension reduction name in the SingleCellExperiment object. Required.

    -
    combinePlot
    +
    combinePlot

    Must be either "all" or "none". "all" will combine plots of pseudotime along each path into a single .ggplot object, while "none" will output a list of plots. Default @@ -247,7 +249,9 @@

    Arguments

    Value

    -
    combinePlot = "all"
    + + +
    combinePlot = "all"

    A .ggplot object

    combinePlot = "none"
    @@ -264,11 +268,11 @@

    Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
 mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                 useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:17:20 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:17:21 2024 ...   Identified 2 clusters
-#> Fri May  3 07:17:21 2024 ... Running TSCAN to estimate pseudotime
-#> Fri May  3 07:17:21 2024 ...   Clusters involved in path index 2 are: 1, 2
-#> Fri May  3 07:17:21 2024 ...   Number of estimated paths is 1
+#> Thu Feb 13 10:30:53 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:30:53 2025 ...   Identified 2 clusters
+#> Thu Feb 13 10:30:53 2025 ... Running TSCAN to estimate pseudotime
+#> Thu Feb 13 10:30:53 2025 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:30:53 2025 ...   Number of estimated paths is 1
 plotTSCANClusterPseudo(mouseBrainSubsetSCE, useCluster = 1,
                        useReducedDim = "TSNE_logcounts")
 #> Warning: Removed 1 row containing missing values or values outside the scale range
@@ -288,15 +292,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotTSCANDimReduceFeatures.html b/docs/reference/plotTSCANDimReduceFeatures.html index f550552d4..2cf541e3d 100644 --- a/docs/reference/plotTSCANDimReduceFeatures.html +++ b/docs/reference/plotTSCANDimReduceFeatures.html @@ -1,11 +1,11 @@ -Plot feature expression on cell 2D embedding with MST overlaid — plotTSCANDimReduceFeatures • singleCellTKPlot feature expression on cell 2D embedding with MST overlaid — plotTSCANDimReduceFeatures • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -226,44 +226,46 @@

    Plot feature expression on cell 2D embedding with MST overlaid

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    features
    +
    features

    Choose the feature of interest to explore the expression level on the trajectory. Required.

    -
    useReducedDim
    +
    useReducedDim

    A single character for the matrix of 2D embedding. Should exist in reducedDims slot. Default "UMAP".

    -
    useAssay
    +
    useAssay

    A single character for the feature expression matrix. Should exist in assayNames(inSCE). Default "logcounts".

    -
    by
    +
    by

    Where should features be found? NULL, "rownames" for rownames(inSCE), otherwise will be regarded as rowData variable.

    -
    useCluster
    +
    useCluster

    Choose specific clusters where gene expression needs to be visualized. By default NULL, all clusters are chosen.

    -
    featureDisplay
    +
    featureDisplay

    Specify the feature ID type to display. Users can set default value with setSCTKDisplayRow. NULL or "rownames" specifies the rownames of inSCE. Other character values indicates rowData variable.

    -
    combinePlot
    +
    combinePlot

    Must be either "all" or "none". "all" will combine plots of each feature into a single .ggplot object, while "none" will output a list of plots. Default "all".

    @@ -271,9 +273,7 @@

    Arguments

    Value

    - - -

    A .ggplot object of cell scatter plot, colored by the +

    A .ggplot object of cell scatter plot, colored by the expression of a gene of interest, with the layer of trajectory.

    @@ -286,11 +286,11 @@

    Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
 mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                 useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:17:22 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:17:23 2024 ...   Identified 2 clusters
-#> Fri May  3 07:17:23 2024 ... Running TSCAN to estimate pseudotime
-#> Fri May  3 07:17:23 2024 ...   Clusters involved in path index 2 are: 1, 2
-#> Fri May  3 07:17:23 2024 ...   Number of estimated paths is 1
+#> Thu Feb 13 10:30:54 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:30:55 2025 ...   Identified 2 clusters
+#> Thu Feb 13 10:30:55 2025 ... Running TSCAN to estimate pseudotime
+#> Thu Feb 13 10:30:55 2025 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:30:55 2025 ...   Number of estimated paths is 1
 plotTSCANDimReduceFeatures(inSCE = mouseBrainSubsetSCE,
                            features = "Tshz1",
                            useReducedDim = "TSNE_logcounts")
@@ -309,15 +309,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotTSCANPseudotimeGenes-1.png b/docs/reference/plotTSCANPseudotimeGenes-1.png index 318ee7f52..be7d53b9f 100644 Binary files a/docs/reference/plotTSCANPseudotimeGenes-1.png and b/docs/reference/plotTSCANPseudotimeGenes-1.png differ diff --git a/docs/reference/plotTSCANPseudotimeGenes.html b/docs/reference/plotTSCANPseudotimeGenes.html index 27c1ee1e6..42326a685 100644 --- a/docs/reference/plotTSCANPseudotimeGenes.html +++ b/docs/reference/plotTSCANPseudotimeGenes.html @@ -1,5 +1,5 @@ -Plot expression changes of top features along a TSCAN pseudotime path — plotTSCANPseudotimeGenes • singleCellTKPlot expression changes of top features along a TSCAN pseudotime path — plotTSCANPseudotimeGenes • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -228,35 +228,37 @@

    Plot expression changes of top features along a TSCAN pseudotime path

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    pathIndex
    +
    pathIndex

    Path index for which the pseudotime values should be used. Should have being used in runTSCANDEG.

    -
    direction
    +
    direction

    Should we show features with expression increasing or decreeasing along the increase in TSCAN pseudotime? Choices are "increasing" or "decreasing".

    -
    topN
    +
    topN

    An integer. Only to plot this number of top genes that are increasing/decreasing in expression with increasing pseudotime along the path in the MST. Default 10

    -
    useAssay
    +
    useAssay

    A single character to specify a feature expression matrix in assays slot. The expression of top features from here will be visualized. Default NULL use the one used for runTSCANDEG.

    -
    featureDisplay
    +
    featureDisplay

    Specify the feature ID type to display. Users can set default value with setSCTKDisplayRow. NULL or "rownames" specifies the rownames of inSCE. Other character @@ -265,9 +267,7 @@

    Arguments

    Value

    - - -

    A .ggplot object with the facets of the top genes. Expression +

    A .ggplot object with the facets of the top genes. Expression on y-axis, pseudotime on x-axis.

    @@ -280,11 +280,11 @@

    Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
 mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                 useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:17:24 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:17:25 2024 ...   Identified 2 clusters
-#> Fri May  3 07:17:25 2024 ... Running TSCAN to estimate pseudotime
-#> Fri May  3 07:17:25 2024 ...   Clusters involved in path index 2 are: 1, 2
-#> Fri May  3 07:17:25 2024 ...   Number of estimated paths is 1
+#> Thu Feb 13 10:30:56 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:30:56 2025 ...   Identified 2 clusters
+#> Thu Feb 13 10:30:56 2025 ... Running TSCAN to estimate pseudotime
+#> Thu Feb 13 10:30:57 2025 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:30:57 2025 ...   Number of estimated paths is 1
 terminalNodes <- listTSCANTerminalNodes(mouseBrainSubsetSCE)
 mouseBrainSubsetSCE <- runTSCANDEG(inSCE = mouseBrainSubsetSCE,
                                    pathIndex = terminalNodes[1])
@@ -306,15 +306,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotTSCANPseudotimeHeatmap-1.png b/docs/reference/plotTSCANPseudotimeHeatmap-1.png index 86ad54a70..cb3535981 100644 Binary files a/docs/reference/plotTSCANPseudotimeHeatmap-1.png and b/docs/reference/plotTSCANPseudotimeHeatmap-1.png differ diff --git a/docs/reference/plotTSCANPseudotimeHeatmap.html b/docs/reference/plotTSCANPseudotimeHeatmap.html index c30768e90..9c8e61171 100644 --- a/docs/reference/plotTSCANPseudotimeHeatmap.html +++ b/docs/reference/plotTSCANPseudotimeHeatmap.html @@ -1,5 +1,5 @@ -Plot heatmap of genes with expression change along TSCAN pseudotime — plotTSCANPseudotimeHeatmap • singleCellTKPlot heatmap of genes with expression change along TSCAN pseudotime — plotTSCANPseudotimeHeatmap • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -229,40 +229,42 @@

    Plot heatmap of genes with expression change along TSCAN pseudotime

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    pathIndex
    +
    pathIndex

    Path index for which the pseudotime values should be used. Should have being used in runTSCANDEG.

    -
    direction
    +
    direction

    Should we show features with expression increasing or decreeasing along the increase in TSCAN pseudotime? Choices are "both", "increasing" or "decreasing".

    -
    topN
    +
    topN

    An integer. Only to plot this number of top genes along the path in the MST, in terms of FDR value. Use NULL to cancel the top N subscription. Default 30.

    -
    log2fcThreshold
    +
    log2fcThreshold

    Only output DEGs with the absolute values of log2FC larger than this value. Default NULL.

    -
    useAssay
    +
    useAssay

    A single character to specify a feature expression matrix in assays slot. The expression of top features from here will be visualized. Default NULL use the one used for runTSCANDEG.

    -
    featureDisplay
    +
    featureDisplay

    Whether to display feature ID and what ID type to display. Users can set default ID type by setSCTKDisplayRow. NULL will display when number of features to display is less than 60. @@ -272,9 +274,7 @@

    Arguments

    Value

    - - -

    A ComplexHeatmap in .ggplot class

    +

    A ComplexHeatmap in .ggplot class

    Author

    @@ -286,11 +286,11 @@

    Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
 mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                 useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:17:26 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:17:27 2024 ...   Identified 2 clusters
-#> Fri May  3 07:17:27 2024 ... Running TSCAN to estimate pseudotime
-#> Fri May  3 07:17:28 2024 ...   Clusters involved in path index 2 are: 1, 2
-#> Fri May  3 07:17:28 2024 ...   Number of estimated paths is 1
+#> Thu Feb 13 10:30:58 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:30:58 2025 ...   Identified 2 clusters
+#> Thu Feb 13 10:30:58 2025 ... Running TSCAN to estimate pseudotime
+#> Thu Feb 13 10:30:59 2025 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:30:59 2025 ...   Number of estimated paths is 1
 terminalNodes <- listTSCANTerminalNodes(mouseBrainSubsetSCE)
 mouseBrainSubsetSCE <- runTSCANDEG(inSCE = mouseBrainSubsetSCE,
                                    pathIndex = terminalNodes[1])
@@ -311,15 +311,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotTSCANResults-1.png b/docs/reference/plotTSCANResults-1.png index 867abf43e..aa23b5a8e 100644 Binary files a/docs/reference/plotTSCANResults-1.png and b/docs/reference/plotTSCANResults-1.png differ diff --git a/docs/reference/plotTSCANResults.html b/docs/reference/plotTSCANResults.html index 31c907a7c..30a6fa0b8 100644 --- a/docs/reference/plotTSCANResults.html +++ b/docs/reference/plotTSCANResults.html @@ -1,11 +1,11 @@ -Plot MST pseudotime values on cell 2D embedding — plotTSCANResults • singleCellTKPlot MST pseudotime values on cell 2D embedding — plotTSCANResults • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -217,20 +217,20 @@

    Plot MST pseudotime values on cell 2D embedding

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useReducedDim
    +
    useReducedDim

    Saved dimension reduction name in inSCE object. Required.

    Value

    - - -

    A .ggplot object with the pseudotime ordering of the cells +

    A .ggplot object with the pseudotime ordering of the cells colored on a cell 2D embedding, and the MST path drawn on it.

    @@ -243,11 +243,11 @@

    Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
 mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                 useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:17:29 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:17:30 2024 ...   Identified 2 clusters
-#> Fri May  3 07:17:30 2024 ... Running TSCAN to estimate pseudotime
-#> Fri May  3 07:17:30 2024 ...   Clusters involved in path index 2 are: 1, 2
-#> Fri May  3 07:17:30 2024 ...   Number of estimated paths is 1
+#> Thu Feb 13 10:31:00 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:31:00 2025 ...   Identified 2 clusters
+#> Thu Feb 13 10:31:00 2025 ... Running TSCAN to estimate pseudotime
+#> Thu Feb 13 10:31:01 2025 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:31:01 2025 ...   Number of estimated paths is 1
 plotTSCANResults(inSCE = mouseBrainSubsetSCE,
                  useReducedDim = "TSNE_logcounts")
 #> Scale for colour is already present.
@@ -267,15 +267,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotTSNE-1.png b/docs/reference/plotTSNE-1.png index 63ec9085a..5428b1e07 100644 Binary files a/docs/reference/plotTSNE-1.png and b/docs/reference/plotTSNE-1.png differ diff --git a/docs/reference/plotTSNE.html b/docs/reference/plotTSNE.html index 6845786d4..a5ea49548 100644 --- a/docs/reference/plotTSNE.html +++ b/docs/reference/plotTSNE.html @@ -1,9 +1,9 @@ -Plot t-SNE plot on dimensionality reduction data run from t-SNE method. — plotTSNE • singleCellTKPlot t-SNE plot on dimensionality reduction data run from t-SNE method. — plotTSNE • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,38 +220,38 @@

    Plot t-SNE plot on dimensionality reduction data run from t-SNE method.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    colorBy
    +
    colorBy

    color by condition.

    -
    shape
    +
    shape

    add shape to each distinct label.

    -
    reducedDimName
    +
    reducedDimName

    a name to store the results of the dimension reduction coordinates obtained from this method. This is stored in the SingleCellExperiment object in the reducedDims slot. Required.

    -
    runTSNE
    +
    runTSNE

    Run t-SNE if the reducedDimName does not exist. the Default is FALSE.

    -
    useAssay
    +
    useAssay

    Indicate which assay to use. The default is "logcounts".

    Value

    - - -

    A t-SNE plot

    +

    A t-SNE plot

    @@ -274,15 +274,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotTopHVG-1.png b/docs/reference/plotTopHVG-1.png index 1a4227fa5..1fc5045be 100644 Binary files a/docs/reference/plotTopHVG-1.png and b/docs/reference/plotTopHVG-1.png differ diff --git a/docs/reference/plotTopHVG.html b/docs/reference/plotTopHVG.html index 0a9a29e61..b6731cac4 100644 --- a/docs/reference/plotTopHVG.html +++ b/docs/reference/plotTopHVG.html @@ -1,9 +1,9 @@ -Plot highly variable genes — plotTopHVG • singleCellTKPlot highly variable genes — plotTopHVG • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -223,58 +223,58 @@

    Plot highly variable genes

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object containing the computations.

    -
    method
    +
    method

    Select either "vst", "mean.var.plot", "dispersion" or "modelGeneVar".

    -
    hvgNumber
    +
    hvgNumber

    Specify the number of top genes to highlight in red. Default 2000. See details.

    -
    useFeatureSubset
    +
    useFeatureSubset

    A character string for the rowData variable name to store a logical index of selected features. Default NULL. See details.

    -
    labelsCount
    +
    labelsCount

    Specify the number of data points/genes to label. Should be less than hvgNumber. Default 10. See details.

    -
    featureDisplay
    +
    featureDisplay

    A character string for the rowData variable name to indicate what type of feature ID should be displayed. If set by setSCTKDisplayRow, will by default use it. If NULL, will use rownames(inSCE).

    -
    labelSize
    -

    Numeric, size of the text label on top HVGs. Default +

    labelSize
    +

    Numeric, size of the text label on top HVGs. Default 2.

    -
    dotSize
    +
    dotSize

    Numeric, size of the dots of the features. Default 2.

    -
    textSize
    +
    textSize

    Numeric, size of the text of axis title, axis label, etc. Default 12.

    Value

    - - -

    ggplot of HVG metrics and top HVG labels

    +

    ggplot of HVG metrics and top HVG labels

    Details

    @@ -312,15 +312,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/plotUMAP-1.png b/docs/reference/plotUMAP-1.png index 366aaa8e3..4121c403c 100644 Binary files a/docs/reference/plotUMAP-1.png and b/docs/reference/plotUMAP-1.png differ diff --git a/docs/reference/plotUMAP.html b/docs/reference/plotUMAP.html index 8cdc8b8ab..50d3e9220 100644 --- a/docs/reference/plotUMAP.html +++ b/docs/reference/plotUMAP.html @@ -1,9 +1,9 @@ -Plot UMAP results either on already run results or run first and then plot. — plotUMAP • singleCellTKPlot UMAP results either on already run results or run first and then plot. — plotUMAP • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,38 +220,38 @@

    Plot UMAP results either on already run results or run first and then plot.<

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components. Required

    -
    colorBy
    +
    colorBy

    color by a condition(any column of the annotation data).

    -
    shape
    +
    shape

    add shapes to each condition.

    -
    reducedDimName
    +
    reducedDimName

    saved dimension reduction name in the SingleCellExperiment object. Required.

    -
    runUMAP
    +
    runUMAP

    If the dimension reduction components are already available set this to FALSE, otherwise set to TRUE. Default is False.

    -
    useAssay
    +
    useAssay

    Indicate which assay to use. The default is "logcounts"

    Value

    - - -

    a UMAP plot of the reduced dimensions.

    +

    a UMAP plot of the reduced dimensions.

    @@ -259,7 +259,7 @@

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runQuickUMAP(sce)
-#> Fri May  3 07:17:33 2024 ... Computing Scater UMAP for sample 'pbmc_4k'.
+#> Thu Feb 13 10:31:03 2025 ... Computing Scater UMAP for sample 'pbmc_4k'.
 plotUMAP(sce)
    @@ -276,15 +276,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/qcInputProcess.html b/docs/reference/qcInputProcess.html index 7d1d18f4d..8a5bbbf34 100644 --- a/docs/reference/qcInputProcess.html +++ b/docs/reference/qcInputProcess.html @@ -1,9 +1,9 @@ -Create SingleCellExperiment object from command line input arguments — qcInputProcess • singleCellTKCreate SingleCellExperiment object from command line input arguments — qcInputProcess • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -224,51 +224,51 @@

    Create SingleCellExperiment object from command line input arguments

    Arguments

    -
    preproc
    -

    Method used to preprocess the data. It's one of the path provided in --preproc argument.

    -
    samplename
    -

    The sample name of the data. It's one of the path provided in --sample argument.

    +
    preproc
    +

    Method used to preprocess the data. It's one of the path provided in –preproc argument.

    + + +
    samplename
    +

    The sample name of the data. It's one of the path provided in –sample argument.

    -
    path
    -

    Base path of the dataset. It's one of the path provided in --bash_path argument.

    +
    path
    +

    Base path of the dataset. It's one of the path provided in –bash_path argument.

    -
    raw
    -

    The directory contains droplet matrix, gene and cell barcodes information. It's one of the path provided in --raw_data_path argument.

    +
    raw
    +

    The directory contains droplet matrix, gene and cell barcodes information. It's one of the path provided in –raw_data_path argument.

    -
    fil
    -

    The directory contains cell matrix, gene and cell barcodes information. It's one of the path provided in --cell_data_path argument.

    +
    fil
    +

    The directory contains cell matrix, gene and cell barcodes information. It's one of the path provided in –cell_data_path argument.

    -
    ref
    +
    ref

    The name of reference used by cellranger. Only need for CellrangerV2 data.

    -
    rawFile
    -

    The full path of the RDS file or Matrix file of the raw gene count matrix. It's one of the path provided in --raw_data argument.

    +
    rawFile
    +

    The full path of the RDS file or Matrix file of the raw gene count matrix. It's one of the path provided in –raw_data argument.

    -
    filFile
    -

    The full path of the RDS file or Matrix file of the cell count matrix. It's one of the path provided in --cell_data argument.

    +
    filFile
    +

    The full path of the RDS file or Matrix file of the cell count matrix. It's one of the path provided in –cell_data argument.

    -
    flatFiles
    +
    flatFiles

    The full paths of the matrix, barcode, and features (in that order) files used to construct an SCE object.

    -
    dataType
    -

    Type of the input. It can be "Both", "Droplet" or "Cell". It's one of the path provided in --genome argument.

    +
    dataType
    +

    Type of the input. It can be "Both", "Droplet" or "Cell". It's one of the path provided in –genome argument.

    Value

    - - -

    A list of SingleCellExperiment object containing +

    A list of SingleCellExperiment object containing the droplet or cell data or both,depending on the dataType that users provided.

    @@ -284,15 +284,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/readSingleCellMatrix.html b/docs/reference/readSingleCellMatrix.html index 3fe4010f7..869b6e83d 100644 --- a/docs/reference/readSingleCellMatrix.html +++ b/docs/reference/readSingleCellMatrix.html @@ -1,10 +1,10 @@ -Read single cell expression matrix — readSingleCellMatrix • singleCellTKRead single cell expression matrix — readSingleCellMatrix • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -221,31 +221,33 @@

    Read single cell expression matrix

    Arguments

    -
    file
    + + +
    file

    Path to input file. Supported file endings include .mtx, .txt, .csv, .tab, .tsv, .npz, and their corresponding gzip, bzip2, or xz compressed extensions (*.gz, *.bz2, or *.xz).

    -
    class
    +
    class

    Character. Class of matrix. One of "Matrix" or "matrix". Specifying "Matrix" will convert to a sparse format which should be used for datasets with large numbers of cells. Default "Matrix".

    -
    delayedArray
    +
    delayedArray

    Boolean. Whether to read the expression matrix as DelayedArray object or not. Default TRUE.

    -
    colIndexLocation
    +
    colIndexLocation

    Character. For Optimus output, the path to the barcode index .npy file. Used only if file has .npz extension. Default NULL.

    -
    rowIndexLocation
    +
    rowIndexLocation

    Character. For Optimus output, The path to the feature (gene) index .npy file. Used only if file has .npz extension. Default NULL.

    @@ -253,9 +255,7 @@

    Arguments

    Value

    - - -

    A DelayedArray object or matrix.

    +

    A DelayedArray object or matrix.

    @@ -276,15 +276,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportCellQC.html b/docs/reference/reportCellQC.html index 0ad4b0088..ba9233acc 100644 --- a/docs/reference/reportCellQC.html +++ b/docs/reference/reportCellQC.html @@ -1,9 +1,9 @@ -Get runCellQC .html report — reportCellQC • singleCellTKGet runCellQC .html report — reportCellQC • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,47 +220,47 @@

    Get runCellQC .html report

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object containing the filtered count matrix with the output from runCellQC function

    -
    output_file
    +
    output_file

    Character. The name of the generated file. If NULL/default then the output file name will be based on the name of the Rmarkdown template.

    -
    output_dir
    +
    output_dir

    Character. The name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory

    -
    subTitle
    +
    subTitle

    subtitle of the QC HTML report. Default is NULL.

    -
    studyDesign
    +
    studyDesign

    Character. The description of the data set and experiment design. It would be shown at the top of QC HTML report. Default is NULL.

    -
    useReducedDim
    +
    useReducedDim

    Character. The name of the saved dimension reduction slot including cells from all samples in thenSingleCellExperiment object, Default is NULL

    Value

    - - -

    .html file

    +

    .html file

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runCellQC(sce)
 reportCellQC(inSCE = sce)
-}
+} # }
    @@ -275,15 +275,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportClusterAbundance.html b/docs/reference/reportClusterAbundance.html index 69e61f0b8..d792f7613 100644 --- a/docs/reference/reportClusterAbundance.html +++ b/docs/reference/reportClusterAbundance.html @@ -1,10 +1,10 @@ -Get plotClusterAbundance .html report — reportClusterAbundance • singleCellTKGet plotClusterAbundance .html report — reportClusterAbundance • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -223,48 +223,48 @@

    Get plotClusterAbundance .html report

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    cluster
    +
    cluster

    A single character, specifying the name to store the cluster label in colData.

    -
    variable
    +
    variable

    A single character, specifying the name to store the phenotype labels in colData.

    -
    output_dir
    +
    output_dir

    name of the output directory to save the rendered file. If NULL the file is stored to the current working directory. Default NULL.

    -
    output_file
    +
    output_file

    name of the generated file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is TRUE.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is TRUE.

    Value

    - - -

    An HTML file of the report will be generated at the path specified +

    An HTML file of the report will be generated at the path specified in the arguments.

    @@ -280,15 +280,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportDiffAbundanceFET.html b/docs/reference/reportDiffAbundanceFET.html index 2bc5e9c76..42c858907 100644 --- a/docs/reference/reportDiffAbundanceFET.html +++ b/docs/reference/reportDiffAbundanceFET.html @@ -1,9 +1,9 @@ -Get diffAbundanceFET .html report — reportDiffAbundanceFET • singleCellTKGet diffAbundanceFET .html report — reportDiffAbundanceFET • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -224,63 +224,63 @@

    Get diffAbundanceFET .html report

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    cluster
    +
    cluster

    A single character, specifying the name to store the cluster label in colData.

    -
    variable
    +
    variable

    A single character, specifying the name to store the phenotype labels in colData.

    -
    control
    +
    control

    character. Specifying one or more categories that can be found in the vector specified by variable.

    -
    case
    +
    case

    character. Specifying one or more categories that can be found in the vector specified by variable.

    -
    analysisName
    +
    analysisName

    A single character. Will be used for naming the result table, which will be saved in metadata slot.

    -
    output_dir
    +
    output_dir

    name of the output directory to save the rendered file. If NULL the file is stored to the current working directory. Default NULL.

    -
    output_file
    +
    output_file

    name of the generated file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is TRUE.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is TRUE.

    Value

    - - -

    An HTML file of the report will be generated at the path specified +

    An HTML file of the report will be generated at the path specified in the arguments.

    @@ -296,15 +296,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportDiffExp.html b/docs/reference/reportDiffExp.html index 4a1600af5..704bf080c 100644 --- a/docs/reference/reportDiffExp.html +++ b/docs/reference/reportDiffExp.html @@ -1,10 +1,10 @@ -Get runDEAnalysis .html report — reportDiffExp • singleCellTKGet runDEAnalysis .html report — reportDiffExp • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -222,34 +222,36 @@

    Get runDEAnalysis .html report

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object containing the output from runDEAnalysis function

    -
    study
    +
    study

    The specific analysis to visualize, used as analysisName argument when running differential expression.

    -
    useReducedDim
    +
    useReducedDim

    Specify an embedding for visualizing the relation ship between the conditions.

    -
    featureDisplay
    +
    featureDisplay

    The feature ID type to use for displaying. Should exists as a variable name of rowData. Default NULL use rownames of inSCE.

    -
    output_file
    +
    output_file

    name of the generated file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    output_dir
    +
    output_dir

    name of the output directory to save the rendered file. If NULL the file is stored to the current working directory. Default NULL.

    @@ -257,9 +259,7 @@

    Arguments

    Value

    - - -

    Saves the HTML report in the specified output directory.

    +

    Saves the HTML report in the specified output directory.

    @@ -274,15 +274,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportDropletQC.html b/docs/reference/reportDropletQC.html index a17110c94..23f45680e 100644 --- a/docs/reference/reportDropletQC.html +++ b/docs/reference/reportDropletQC.html @@ -1,9 +1,9 @@ -Get runDropletQC .html report — reportDropletQC • singleCellTKGet runDropletQC .html report — reportDropletQC • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -219,41 +219,41 @@

    Get runDropletQC .html report

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object containing the full droplet count matrix with the output from runDropletQC function

    -
    output_file
    +
    output_file

    name of the generated file. If NULL/default then the output file name will be based on the name of the Rmarkdown template

    -
    output_dir
    +
    output_dir

    name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory

    -
    subTitle
    +
    subTitle

    subtitle of the QC HTML report. Default is NULL.

    -
    studyDesign
    +
    studyDesign

    description of the data set and experiment design. It would be shown at the top of QC HTML report. Default is NULL.

    Value

    - - -

    .html file

    +

    .html file

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runDropletQC(sce)
 reportDropletQC(inSCE = sce)
-}
+} # }
    @@ -268,15 +268,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportFindMarker.html b/docs/reference/reportFindMarker.html index 34e01c198..02c38381e 100644 --- a/docs/reference/reportFindMarker.html +++ b/docs/reference/reportFindMarker.html @@ -1,10 +1,10 @@ -Get runFindMarker .html report — reportFindMarker • singleCellTKGet runFindMarker .html report — reportFindMarker • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -215,18 +215,20 @@

    Get runFindMarker .html report

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object containing the output from runFindMarker function

    -
    output_file
    +
    output_file

    name of the generated file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    output_dir
    +
    output_dir

    name of the output directory to save the rendered file. If NULL the file is stored to the current working directory. Default NULL.

    @@ -234,9 +236,7 @@

    Arguments

    Value

    - - -

    An HTML file of the report will be generated at the path specified +

    An HTML file of the report will be generated at the path specified in the arguments.

    @@ -252,15 +252,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportQCTool.html b/docs/reference/reportQCTool.html index 2f2dca86e..2ecff77b0 100644 --- a/docs/reference/reportQCTool.html +++ b/docs/reference/reportQCTool.html @@ -1,9 +1,9 @@ -Get .html report of the output of the selected QC algorithm — reportQCTool • singleCellTKGet .html report of the output of the selected QC algorithm — reportQCTool • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -219,41 +219,41 @@

    Get .html report of the output of the selected QC algorithm

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object containing the count matrix (full droplets or filtered matrix, depends on the selected QC algorithm) with the output from at least one of these functions: runQCMetrics, runScrublet, runScDblFinder, runCxds, runBcds, runCxdsBcdsHybrid, runDecontX, runBarcodeRankDrops, runEmptyDrops

    -
    algorithm
    +
    algorithm

    Character. Specifies which QC algorithm report to generate. Available options are "BarcodeRankDrops", "EmptyDrops", "QCMetrics", "Scrublet", "ScDblFinder", "Cxds", "Bcds", "CxdsBcdsHybrid", "DoubletFinder", "DecontX" and "SoupX".

    -
    output_file
    +
    output_file

    name of the generated file. If NULL/default then the output file name will be based on the name of the selected QC algorithm name .

    -
    output_dir
    +
    output_dir

    name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory

    Value

    - - -

    .html file

    +

    .html file

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runDecontX(sce)
 sce <- runQuickUMAP(sce)
 reportQCTool(inSCE = sce, algorithm = "DecontX")
-}
+} # }
    @@ -268,15 +268,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportSeurat.html b/docs/reference/reportSeurat.html index 5155b5fcf..d39296459 100644 --- a/docs/reference/reportSeurat.html +++ b/docs/reference/reportSeurat.html @@ -1,12 +1,10 @@ -Generates an HTML report for the complete Seurat workflow and returns the - SCE object with the results computed and stored inside the object. — reportSeurat • singleCellTKGenerates an HTML report for the complete Seurat workflow and returns the SCE object with the results computed and stored inside the object. — reportSeurat • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    Generates an HTML report for the complete Seurat workflow and returns the - SCE object with the results computed and stored inside the object.

    +

    Generates an HTML report for the complete Seurat workflow and returns the SCE object with the results computed and stored inside the object.

    Source: R/htmlReports.R
    @@ -247,150 +244,152 @@

    Generates an HTML report for the complete Seurat workflow and returns the

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    biological.group
    +
    biological.group

    A character value that specifies the name of the colData() column to use as the main biological group in the Seurat report for marker selection and grouping.

    -
    phenotype.groups
    +
    phenotype.groups

    A character vector that specifies the names of the colData() columns to use for differential expression in addition to the biological.group parameter.

    -
    selected.markers
    +
    selected.markers

    A character vector containing the user-specified gene symbols or feature names of marker genes that be used to generate gene plots in addition to the gene markers computed from differential expression.

    -
    clustering.resolution
    +
    clustering.resolution

    A numeric value indicating the user-specified final resolution to use with clustering. Default is 0.8.

    -
    variable.features
    +
    variable.features

    A numeric value indicating the number of top variable features to identify. Default 2000.

    -
    pc.count
    +
    pc.count

    A numeric value indicating the number of principal components to use in the analysis workflow. Default is 50.

    -
    outputFile
    +
    outputFile

    Specify the name of the generated output HTML file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    outputPath
    +
    outputPath

    Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.

    -
    subtitle
    +
    subtitle

    A character value specifying the subtitle to use in the report. Default NULL.

    -
    authors
    +
    authors

    A character value specifying the names of the authors to use in the report. Default NULL.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is FALSE.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.

    -
    runHVG
    +
    runHVG

    A logical value indicating if the feature selection computation should be run or not. Default is TRUE.

    -
    plotHVG
    +
    plotHVG

    A logical value indicating if the plot for the top most variable genes should be visualized in a mean-to-variance plot. Default is TRUE.

    -
    runDimRed
    +
    runDimRed

    A logical value indicating if PCA should be computed. Default is TRUE.

    -
    plotJackStraw
    +
    plotJackStraw

    A logical value indicating if JackStraw plot be visualized for the principal components. Default is FALSE.

    -
    plotElbowPlot
    +
    plotElbowPlot

    A logical value indicating if the ElbowPlot be visualized for the principal components. Default is TRUE.

    -
    plotHeatmaps
    +
    plotHeatmaps

    A logical value indicating if heatmaps should be plotted for the principal components. Default is TRUE.

    -
    runClustering
    +
    runClustering

    A logical value indicating if clustering section should be run in the report. Default is TRUE.

    -
    plotTSNE
    +
    plotTSNE

    A logical value indicating if TSNE plots should be visualized for clustering results. Default is TRUE.

    -
    plotUMAP
    +
    plotUMAP

    A logical value indicating if the UMAP plots should be visualized for the clustering results. Default is TRUE.

    -
    minResolution
    +
    minResolution

    A numeric value indicating the minimum resolution to use for clustering. Default is 0.3.

    -
    maxResolution
    +
    maxResolution

    A numeric value indicating the maximum resolution to use for clustering. Default is 1.5.

    -
    runMSClusters
    +
    runMSClusters

    A logical value indicating if marker selection should be run between clusters. Default is TRUE.

    -
    runMSBioGroup
    +
    runMSBioGroup

    A logical value indicating if marker selection should be run between the biological.group parameter. Default is TRUE.

    -
    numTopFeatures
    +
    numTopFeatures

    A numeric value indicating the number of top features to visualize in each group. Default 10.

    -
    forceRun
    +
    forceRun

    A logical value indicating if all algorithms should be re-run regardless if they have been computed previously in the input object. Default is TRUE.

    @@ -398,9 +397,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with computations stored.

    @@ -416,15 +413,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportSeuratClustering.html b/docs/reference/reportSeuratClustering.html index 3b09fc955..dd80cd5a4 100644 --- a/docs/reference/reportSeuratClustering.html +++ b/docs/reference/reportSeuratClustering.html @@ -1,12 +1,10 @@ -Generates an HTML report for Seurat Clustering and returns the SCE object - with the results computed and stored inside the object. — reportSeuratClustering • singleCellTKGenerates an HTML report for Seurat Clustering and returns the SCE object with the results computed and stored inside the object. — reportSeuratClustering • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    Generates an HTML report for Seurat Clustering and returns the SCE object - with the results computed and stored inside the object.

    +

    Generates an HTML report for Seurat Clustering and returns the SCE object with the results computed and stored inside the object.

    Source: R/htmlReports.R
    @@ -236,90 +233,92 @@

    Generates an HTML report for Seurat Clustering and returns the SCE object

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    biological.group
    +
    biological.group

    A character value that specifies the name of the colData() column to use as the main biological group in the Seurat report for marker selection and grouping.

    -
    phenotype.groups
    +
    phenotype.groups

    A character vector that specifies the names of the colData() columns to use for differential expression in addition to the biological.group parameter.

    -
    runClustering
    +
    runClustering

    A logical value indicating if Clustering should be run or not in the report. Default is TRUE. If FALSE, parameters plotTSNE and plotUMAP are also set to FALSE.

    -
    plotTSNE
    +
    plotTSNE

    A logical value indicating if TSNE plots should be visualized in the clustering section of the report. Default is TRUE.

    -
    plotUMAP
    +
    plotUMAP

    A logical value indicating if UMAP plots should be visualized in the clustering section of the report. Default is TRUE.

    -
    minResolution
    +
    minResolution

    A numeric value indicating the minimum resolution to use for clustering. Default 0.3.

    -
    maxResolution
    +
    maxResolution

    A numeric value indicating the maximum resolution to use for clustering. Default 1.5.

    -
    numClusters
    +
    numClusters

    temp (to remove)

    -
    significant_PC
    +
    significant_PC

    temp (change to pc.use)

    -
    outputFile
    +
    outputFile

    Specify the name of the generated output HTML file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    outputPath
    +
    outputPath

    Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.

    -
    subtitle
    +
    subtitle

    A character value specifying the subtitle to use in the report. Default NULL.

    -
    authors
    +
    authors

    A character value specifying the names of the authors to use in the report. Default NULL.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is FALSE.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.

    -
    forceRun
    +
    forceRun

    A logical value indicating if all computations previously computed should be re-calculated regardless if these computations are available in the input object. Default is TRUE.

    @@ -327,9 +326,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with computations stored.

    @@ -345,15 +342,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportSeuratDimRed.html b/docs/reference/reportSeuratDimRed.html index 1d472be0b..5584f91c7 100644 --- a/docs/reference/reportSeuratDimRed.html +++ b/docs/reference/reportSeuratDimRed.html @@ -1,15 +1,11 @@ -Generates an HTML report for Seurat Dimensionality Reduction - and returns the SCE object with the results computed and stored - inside the object. — reportSeuratDimRed • singleCellTKGenerates an HTML report for Seurat Dimensionality Reduction and returns the SCE object with the results computed and stored inside the object. — reportSeuratDimRed • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    Generates an HTML report for Seurat Dimensionality Reduction - and returns the SCE object with the results computed and stored - inside the object.

    +

    Generates an HTML report for Seurat Dimensionality Reduction and returns the SCE object with the results computed and stored inside the object.

    Source: R/htmlReports.R
    @@ -237,69 +231,71 @@

    Generates an HTML report for Seurat Dimensionality Reduction

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    pc.count
    +
    pc.count

    A numeric value indicating the number of principal components to compute. Default is 50.

    -
    runDimRed
    +
    runDimRed

    A logical value indicating if dimenionality reduction should be computed. Default TRUE.

    -
    plotJackStraw
    +
    plotJackStraw

    A logical value indicating if JackStraw plot should be visualized. Default FALSE.

    -
    plotElbowPlot
    +
    plotElbowPlot

    A logical value indicating if ElbowPlot should be visualized. Default TRUE.

    -
    plotHeatmaps
    +
    plotHeatmaps

    A logical value indicating if heatmaps should be visualized. Default TRUE.

    -
    outputFile
    +
    outputFile

    Specify the name of the generated output HTML file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    outputPath
    +
    outputPath

    Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.

    -
    subtitle
    +
    subtitle

    A character value specifying the subtitle to use in the report. Default NULL.

    -
    authors
    +
    authors

    A character value specifying the names of the authors to use in the report. Default NULL.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is FALSE.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.

    -
    forceRun
    +
    forceRun

    A logical value indicating if all computations previously computed should be re-calculated regardless if these computations are available in the input object. Default is TRUE.

    @@ -307,9 +303,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with computations stored.

    @@ -325,15 +319,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportSeuratFeatureSelection.html b/docs/reference/reportSeuratFeatureSelection.html index afb26f879..b919bbac7 100644 --- a/docs/reference/reportSeuratFeatureSelection.html +++ b/docs/reference/reportSeuratFeatureSelection.html @@ -1,12 +1,10 @@ -Generates an HTML report for Seurat Feature Selection and returns the -SCE object with the results computed and stored inside the object. — reportSeuratFeatureSelection • singleCellTKGenerates an HTML report for Seurat Feature Selection and returns the SCE object with the results computed and stored inside the object. — reportSeuratFeatureSelection • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    Generates an HTML report for Seurat Feature Selection and returns the -SCE object with the results computed and stored inside the object.

    +

    Generates an HTML report for Seurat Feature Selection and returns the SCE object with the results computed and stored inside the object.

    Source: R/htmlReports.R
    @@ -230,59 +227,61 @@

    Generates an HTML report for Seurat Feature Selection and returns the

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    variable.features
    +
    variable.features

    A numeric value indicating the number of top variable features to identify. Default 2000.

    -
    runHVG
    +
    runHVG

    A logical value indicating if the feature selection algorithm should be run or not. Default TRUE.

    -
    plotHVG
    +
    plotHVG

    A logical value indicating if the mean-to-variance plot of the top variable feature should be visualized or not. Default TRUE.

    -
    outputFile
    +
    outputFile

    Specify the name of the generated output HTML file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    outputPath
    +
    outputPath

    Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.

    -
    subtitle
    +
    subtitle

    A character value specifying the subtitle to use in the report. Default NULL.

    -
    authors
    +
    authors

    A character value specifying the names of the authors to use in the report. Default NULL.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is FALSE.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.

    -
    forceRun
    +
    forceRun

    A logical value indicating if all computations previously computed should be re-calculated regardless if these computations are available in the input object. Default is TRUE.

    @@ -290,9 +289,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with computations stored.

    @@ -308,15 +305,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportSeuratMarkerSelection.html b/docs/reference/reportSeuratMarkerSelection.html index 560859a63..1faba93b6 100644 --- a/docs/reference/reportSeuratMarkerSelection.html +++ b/docs/reference/reportSeuratMarkerSelection.html @@ -1,15 +1,11 @@ -Generates an HTML report for Seurat Results (including Clustering & Marker - Selection) and returns the SCE object with the results computed and stored - inside the object. — reportSeuratMarkerSelection • singleCellTKGenerates an HTML report for Seurat Results (including Clustering & Marker Selection) and returns the SCE object with the results computed and stored inside the object. — reportSeuratMarkerSelection • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    Generates an HTML report for Seurat Results (including Clustering & Marker - Selection) and returns the SCE object with the results computed and stored - inside the object.

    +

    Generates an HTML report for Seurat Results (including Clustering & Marker Selection) and returns the SCE object with the results computed and stored inside the object.

    Source: R/htmlReports.R
    @@ -237,82 +231,82 @@

    Generates an HTML report for Seurat Results (including Clustering & Mark

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    biological.group
    +
    biological.group

    A character value that specifies the name of the colData() column to use as the main biological group in the Seurat report for marker selection and grouping.

    -
    phenotype.groups
    +
    phenotype.groups

    A character vector that specifies the names of the colData() columns to use for differential expression in addition to the biological.group parameter.

    -
    selected.markers
    +
    selected.markers

    A character vector containing the user-specified gene symbols or feature names of marker genes that be used to generate gene plots in addition to the gene markers computed from differential expression.

    -
    runMarkerSelection
    +
    runMarkerSelection

    A logical value indicating if the marker selection computation should be run or not. Default TRUE.

    -
    plotMarkerSelection
    +
    plotMarkerSelection

    A logical value indicating if the gene marker plots should be visualized or not. Default TRUE.

    -
    numTopFeatures
    +
    numTopFeatures

    A numeric value indicating the number of top features to visualize in each group. Default 10.

    -
    outputFile
    +
    outputFile

    Specify the name of the generated output HTML file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    outputPath
    +
    outputPath

    Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.

    -
    subtitle
    +
    subtitle

    A character value specifying the subtitle to use in the report. Default NULL.

    -
    authors
    +
    authors

    A character value specifying the names of the authors to use in the report. Default NULL.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is FALSE.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with computations stored.

    @@ -328,15 +322,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportSeuratNormalization.html b/docs/reference/reportSeuratNormalization.html index 96b9f4885..92f118438 100644 --- a/docs/reference/reportSeuratNormalization.html +++ b/docs/reference/reportSeuratNormalization.html @@ -1,15 +1,11 @@ -Generates an HTML report for Seurat Normalization - and returns the SCE object with the results computed and stored - inside the object. — reportSeuratNormalization • singleCellTKGenerates an HTML report for Seurat Normalization and returns the SCE object with the results computed and stored inside the object. — reportSeuratNormalization • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    Generates an HTML report for Seurat Normalization - and returns the SCE object with the results computed and stored - inside the object.

    +

    Generates an HTML report for Seurat Normalization and returns the SCE object with the results computed and stored inside the object.

    Source: R/htmlReports.R
    @@ -232,44 +226,46 @@

    Generates an HTML report for Seurat Normalization

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object previously passed through reportSeuratRun().

    -
    outputFile
    +
    outputFile

    Specify the name of the generated output HTML file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    outputPath
    +
    outputPath

    Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.

    -
    subtitle
    +
    subtitle

    A character value specifying the subtitle to use in the report. Default NULL.

    -
    authors
    +
    authors

    A character value specifying the names of the authors to use in the report. Default NULL.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is FALSE.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.

    -
    forceRun
    +
    forceRun

    A logical value indicating if all computations previously computed should be re-calculated regardless if these computations are available in the input object. Default is TRUE.

    @@ -277,9 +273,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with computations stored.

    @@ -295,15 +289,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportSeuratResults.html b/docs/reference/reportSeuratResults.html index f00e24158..ba13df7eb 100644 --- a/docs/reference/reportSeuratResults.html +++ b/docs/reference/reportSeuratResults.html @@ -1,15 +1,11 @@ -Generates an HTML report for Seurat Results (including Clustering & Marker - Selection) and returns the SCE object with the results computed and stored - inside the object. — reportSeuratResults • singleCellTKGenerates an HTML report for Seurat Results (including Clustering & Marker Selection) and returns the SCE object with the results computed and stored inside the object. — reportSeuratResults • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    Generates an HTML report for Seurat Results (including Clustering & Marker - Selection) and returns the SCE object with the results computed and stored - inside the object.

    +

    Generates an HTML report for Seurat Results (including Clustering & Marker Selection) and returns the SCE object with the results computed and stored inside the object.

    Source: R/htmlReports.R
    @@ -243,106 +237,108 @@

    Generates an HTML report for Seurat Results (including Clustering & Mark

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object previously passed through reportSeuratRun().

    -
    biological.group
    +
    biological.group

    A character value that specifies the name of the colData() column to use as the main biological group in the Seurat report for marker selection and grouping.

    -
    phenotype.groups
    +
    phenotype.groups

    A character vector that specifies the names of the colData() columns to use for differential expression in addition to the biological.group parameter.

    -
    selected.markers
    +
    selected.markers

    A character vector containing the user-specified gene symbols or feature names of marker genes that be used to generate gene plots in addition to the gene markers computed from differential expression.

    -
    clustering.resolution
    +
    clustering.resolution

    A numeric value indicating the user-specified final resolution to use with clustering. Default is 0.8.

    -
    pc.count
    +
    pc.count

    A numeric value indicating the number of principal components to use in the analysis workflow. Default is 50.

    -
    plotTSNE
    +
    plotTSNE

    A logical value indicating if TSNE plots should be visualized in the clustering section of the report. Default is TRUE.

    -
    plotUMAP
    +
    plotUMAP

    A logical value indicating if UMAP plots should be visualized in the clustering section of the report. Default is TRUE.

    -
    runClustering
    +
    runClustering

    A logical value indicating if Clustering should be run or not in the report. Default is TRUE. If FALSE, parameters plotTSNE and plotUMAP are also set to FALSE.

    -
    runMSClusters
    +
    runMSClusters

    A logical value indicating if the marker selection section for identifying marker genes between clusters should be run and visualized in the report. Default TRUE.

    -
    runMSBioGroup
    +
    runMSBioGroup

    A logical value indicating if the marker selection section for identifying marker genes between the biological.group parameter should be run and visualized in the report. Default TRUE.

    -
    numTopFeatures
    +
    numTopFeatures

    A numeric value indicating the number of top features to visualize in each group. Default 10.

    -
    outputFile
    +
    outputFile

    Specify the name of the generated output HTML file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    outputPath
    +
    outputPath

    Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.

    -
    subtitle
    +
    subtitle

    A character value specifying the subtitle to use in the report. Default NULL.

    -
    authors
    +
    authors

    A character value specifying the names of the authors to use in the report. Default NULL.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is FALSE.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.

    -
    forceRun
    +
    forceRun

    A logical value indicating if all computations previously computed should be re-calculated regardless if these computations are available in the input object. Default is TRUE.

    @@ -350,9 +346,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with computations stored.

    @@ -368,15 +362,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportSeuratRun.html b/docs/reference/reportSeuratRun.html index 957792121..5b7e33a87 100644 --- a/docs/reference/reportSeuratRun.html +++ b/docs/reference/reportSeuratRun.html @@ -1,15 +1,11 @@ -Generates an HTML report for Seurat Run (including Normalization, - Feature Selection, Dimensionality Reduction & Clustering) and returns the - SCE object with the results computed and stored inside the object. — reportSeuratRun • singleCellTKGenerates an HTML report for Seurat Run (including Normalization, Feature Selection, Dimensionality Reduction & Clustering) and returns the SCE object with the results computed and stored inside the object. — reportSeuratRun • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    Generates an HTML report for Seurat Run (including Normalization, - Feature Selection, Dimensionality Reduction & Clustering) and returns the - SCE object with the results computed and stored inside the object.

    +

    Generates an HTML report for Seurat Run (including Normalization, Feature Selection, Dimensionality Reduction & Clustering) and returns the SCE object with the results computed and stored inside the object.

    Source: R/htmlReports.R
    @@ -247,122 +241,124 @@

    Generates an HTML report for Seurat Run (including Normalization,

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    biological.group
    +
    biological.group

    A character value that specifies the name of the colData() column to use as the main biological group in the Seurat report for tSNE & UMAP visualization.

    -
    phenotype.groups
    +
    phenotype.groups

    A character value that specifies the name of the colData() column to use as additional phenotype variables in the Seurat report for tSNE & UMAP visualization.

    -
    variable.features
    +
    variable.features

    A numeric value indicating the number of top variable genes to identify in the report. Default is 2000.

    -
    pc.count
    +
    pc.count

    A numeric value indicating the number of principal components to use in the analysis workflow. Default is 50.

    -
    runHVG
    +
    runHVG

    A logical value indicating if feature selection should be run in the report. Default TRUE.

    -
    plotHVG
    +
    plotHVG

    A logical value indicating if the top variable genes should be visualized through a mean-to-variance plot. Default is TRUE.

    -
    runDimRed
    +
    runDimRed

    A logical value indicating if PCA should be computed in the report. Default is TRUE.

    -
    plotJackStraw
    +
    plotJackStraw

    A logical value indicating if the JackStraw plot should be visualized for the principal components. Default is FALSE.

    -
    plotElbowPlot
    +
    plotElbowPlot

    A logical value indicating if the ElbowPlot should be visualized for the principal components. Default is FALSE.

    -
    plotHeatmaps
    +
    plotHeatmaps

    A logical value indicating if the Heatmaps should be visualized for the principal components. Default is FALSE.

    -
    runClustering
    +
    runClustering

    A logical value indicating if Clustering should be run over multiple resolutions as defined by the minResolution and maxResolution parameters. Default is TRUE.

    -
    plotTSNE
    +
    plotTSNE

    A logical value indicating if TSNE plot should be visualized for clusters. Default is TRUE.

    -
    plotUMAP
    +
    plotUMAP

    A logical value indicating if UMAP plot should be visualized for clusters. Default is TRUE.

    -
    minResolution
    +
    minResolution

    A numeric value indicating the minimum resolution to use for clustering. Default 0.3.

    -
    maxResolution
    +
    maxResolution

    A numeric value indicating the maximum resolution to use for clustering. Default 1.5.

    -
    outputFile
    +
    outputFile

    Specify the name of the generated output HTML file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    outputPath
    +
    outputPath

    Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.

    -
    subtitle
    +
    subtitle

    A character value specifying the subtitle to use in the report. Default NULL.

    -
    authors
    +
    authors

    A character value specifying the names of the authors to use in the report. Default NULL.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is FALSE.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.

    -
    forceRun
    +
    forceRun

    A logical value indicating if all computations previously computed should be re-calculated regardless if these computations are available in the input object. Default is TRUE.

    @@ -370,9 +366,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with computations stored.

    @@ -388,15 +382,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/reportSeuratScaling.html b/docs/reference/reportSeuratScaling.html index 3786ab543..a38716068 100644 --- a/docs/reference/reportSeuratScaling.html +++ b/docs/reference/reportSeuratScaling.html @@ -1,15 +1,11 @@ -Generates an HTML report for Seurat Scaling - and returns the SCE object with the results computed and stored - inside the object. — reportSeuratScaling • singleCellTKGenerates an HTML report for Seurat Scaling and returns the SCE object with the results computed and stored inside the object. — reportSeuratScaling • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    Generates an HTML report for Seurat Scaling - and returns the SCE object with the results computed and stored - inside the object.

    +

    Generates an HTML report for Seurat Scaling and returns the SCE object with the results computed and stored inside the object.

    Source: R/htmlReports.R
    @@ -232,44 +226,46 @@

    Generates an HTML report for Seurat Scaling

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    outputFile
    +
    outputFile

    Specify the name of the generated output HTML file. If NULL then the output file name will be based on the name of the Rmarkdown template. Default NULL.

    -
    outputPath
    +
    outputPath

    Specify the name of the output directory to save the rendered HTML file. If NULL the file is stored to the current working directory. Default NULL.

    -
    subtitle
    +
    subtitle

    A character value specifying the subtitle to use in the report. Default NULL.

    -
    authors
    +
    authors

    A character value specifying the names of the authors to use in the report. Default NULL.

    -
    showSession
    +
    showSession

    A logical value indicating if session information should be displayed or not. Default is FALSE.

    -
    pdf
    +
    pdf

    A logical value indicating if a pdf should also be generated for each figure in the report. Default is FALSE.

    -
    forceRun
    +
    forceRun

    A logical value indicating if all computations previously computed should be re-calculated regardless if these computations are available in the input object. Default is TRUE.

    @@ -277,9 +273,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object +

    A SingleCellExperiment object with computations stored.

    @@ -295,15 +289,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/retrieveSCEIndex.html b/docs/reference/retrieveSCEIndex.html index 42cefd326..256a28887 100644 --- a/docs/reference/retrieveSCEIndex.html +++ b/docs/reference/retrieveSCEIndex.html @@ -1,5 +1,5 @@ -Retrieve cell/feature index by giving identifiers saved in col/rowData — retrieveSCEIndex • singleCellTKRetrieve cell/feature index by giving identifiers saved in col/rowData — retrieveSCEIndex • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -228,42 +228,42 @@

    Retrieve cell/feature index by giving identifiers saved in col/rowData

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object. Required

    -
    IDs
    +
    IDs

    Character vector of identifiers for features or cells to find in rowData or colData of inSCE

    -
    axis
    +
    axis

    A character scalar to specify whether to search for features or cells. Use "row", "feature" or "gene" for features; "col" or "cell" for cells.

    -
    by
    +
    by

    Character. In which column to search for features/cells in rowData/colData. Default NULL for search the rownames/colnames

    -
    exactMatch
    +
    exactMatch

    A logical scalar. Whether to only identify exact matches or to identify partial matches using grep. Default TRUE

    -
    firstMatch
    +
    firstMatch

    A logical scalar. Whether to only identify the first matches or to return all plausible matches. Default TRUE

    Value

    - - -

    A unique, non-NA numeric vector of indices for the matching +

    A unique, non-NA numeric vector of indices for the matching features/cells in inSCE.

    @@ -291,15 +291,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runBBKNN.html b/docs/reference/runBBKNN.html index 08182310f..8b73b21cc 100644 --- a/docs/reference/runBBKNN.html +++ b/docs/reference/runBBKNN.html @@ -1,11 +1,11 @@ -Apply BBKNN batch effect correction method to SingleCellExperiment object — runBBKNN • singleCellTKApply BBKNN batch effect correction method to SingleCellExperiment object — runBBKNN • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -223,28 +223,30 @@

    Apply BBKNN batch effect correction method to SingleCellExperiment object

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    useAssay
    +
    useAssay

    A single character indicating the name of the assay requiring batch correction. Default "logcounts".

    -
    batch
    +
    batch

    A single character indicating a field in colData that annotates the batches of each cell; or a vector/factor with the same length as the number of cells. Default "batch".

    -
    reducedDimName
    +
    reducedDimName

    A single character. The name for the corrected low-dimensional representation. Will be saved to reducedDim(inSCE). Default "BBKNN".

    -
    nComponents
    +
    nComponents

    An integer. Number of principle components or the dimensionality, adopted in the pre-PCA-computation step, the BBKNN step (for how many PCs the algorithm takes into account), and the final UMAP @@ -254,9 +256,7 @@

    Arguments

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with reducedDim(inSCE, reducedDimName) updated.

    @@ -266,12 +266,12 @@

    References

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data('sceBatches', package = 'singleCellTK')
 logcounts(sceBatches) <- log1p(counts(sceBatches))
 sceBatches <- runBBKNN(sceBatches, useAssay = "logcounts",
                        nComponents = 10)
-}
+} # }
    @@ -286,15 +286,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runBarcodeRankDrops.html b/docs/reference/runBarcodeRankDrops.html index c263d7936..ac0eac9c3 100644 --- a/docs/reference/runBarcodeRankDrops.html +++ b/docs/reference/runBarcodeRankDrops.html @@ -1,12 +1,12 @@ -Identify empty droplets using barcodeRanks. — runBarcodeRankDrops • singleCellTKIdentify empty droplets using barcodeRanks. — runBarcodeRankDrops • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -208,8 +208,8 @@

    Identify empty droplets using

    Run barcodeRanks on a count matrix -provided in a SingleCellExperiment object. Distinguish between -droplets containing cells and ambient RNA in a droplet-based single-cell RNA +provided in a SingleCellExperiment object. Distinguish between +droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment.

    @@ -226,50 +226,50 @@

    Identify empty droplets using

    Arguments

    -
    inSCE
    -

    A SingleCellExperiment object. Must contain a raw + + +

    inSCE
    +

    A SingleCellExperiment object. Must contain a raw counts matrix before empty droplets have been removed.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    useAssay
    -

    A string specifying which assay in the SCE to use. Default +

    useAssay
    +

    A string specifying which assay in the SCE to use. Default "counts"

    -
    lower
    -

    See barcodeRanks for more information. +

    lower
    +

    See barcodeRanks for more information. Default 100.

    -
    fitBounds
    -

    See barcodeRanks for more information. +

    fitBounds
    +

    See barcodeRanks for more information. Default NULL.

    -
    df
    -

    See barcodeRanks for more information. Default +

    df
    +

    See barcodeRanks for more information. Default 20.

    Value

    - - -

    A SingleCellExperiment object with the +

    A SingleCellExperiment object with the barcodeRanks output table appended to the colData slot. The columns include -dropletUtils_BarcodeRank_Knee and +dropletUtils_BarcodeRank_Knee and dropletUtils_barcodeRank_inflection. Please refer to the documentation of barcodeRanks for details.

    See also

    -

    barcodeRanks, +

    barcodeRanks, runDropletQC, plotBarcodeRankDropsResults

    @@ -277,7 +277,7 @@

    See also

    Examples

    data(scExample, package = "singleCellTK")
 sce <- runBarcodeRankDrops(inSCE = sce)
-#> Fri May  3 07:17:43 2024 ... Running 'barcodeRanks'
+#> Thu Feb 13 10:31:16 2025 ... Running 'barcodeRanks'
    @@ -292,15 +292,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runBcds.html b/docs/reference/runBcds.html index 465385200..74953ca2b 100644 --- a/docs/reference/runBcds.html +++ b/docs/reference/runBcds.html @@ -1,12 +1,12 @@ -Find doublets/multiplets using bcds. — runBcds • singleCellTKFind doublets/multiplets using bcds. — runBcds • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -231,77 +231,75 @@

    Find doublets/multiplets using

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    seed
    +
    seed

    Seed for the random number generator, can be NULL. Default 12345.

    -
    ntop
    +
    ntop

    See bcds for more information. Default 500.

    -
    srat
    +
    srat

    See bcds for more information. Default 1.

    -
    verb
    +
    verb

    See bcds for more information. Default FALSE.

    -
    retRes
    -

    See bcds for more information. Default +

    retRes
    +

    See bcds for more information. Default FALSE.

    -
    nmax
    -

    See bcds for more information. Default +

    nmax
    +

    See bcds for more information. Default "tune".

    -
    varImp
    -

    See bcds for more information. Default +

    varImp
    +

    See bcds for more information. Default FALSE.

    -
    estNdbl
    -

    See bcds for more information. Default +

    estNdbl
    +

    See bcds for more information. Default FALSE.

    -
    useAssay
    +
    useAssay

    A string specifying which assay in inSCE to use. Default "counts"

    Value

    - - -

    A SingleCellExperiment object with bcds

    - - -

    output appended to the colData slot. The columns include -bcds_score and optionally bcds_call. Please refer to the +

    A SingleCellExperiment object with bcds +output appended to the colData slot. The columns include +bcds_score and optionally bcds_call. Please refer to the documentation of bcds for details.

    Details

    When the argument sample is specified, bcds will -be run on cells from each sample separately. If sample = NULL, then +be run on cells from each sample separately. If sample = NULL, then all cells will be processed together.

    See also

    -

    bcds, plotBcdsResults, +

    bcds, plotBcdsResults, runCellQC

    @@ -310,7 +308,7 @@

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runBcds(sce)
-#> Fri May  3 07:17:44 2024 ... Running 'bcds'
+#> Thu Feb 13 10:31:17 2025 ... Running 'bcds'
    @@ -325,15 +323,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runCellQC.html b/docs/reference/runCellQC.html index 36a50bb1f..51a22ba9d 100644 --- a/docs/reference/runCellQC.html +++ b/docs/reference/runCellQC.html @@ -1,11 +1,11 @@ -Perform comprehensive single cell QC — runCellQC • singleCellTKPerform comprehensive single cell QC — runCellQC • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -237,101 +237,99 @@

    Perform comprehensive single cell QC

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    algorithms
    +
    algorithms

    Character vector. Specify which QC algorithms to run. -Available options are "QCMetrics", "scrublet", "doubletFinder", "scDblFinder", +Available options are "QCMetrics", "scrublet", "doubletFinder", "scDblFinder", "cxds", "bcds", "cxds_bcds_hybrid", "decontX" and "soupX".

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to. Algorithms will be run on cells from each sample separately.

    -
    collectionName
    -

    Character. Name of a GeneSetCollection obtained by +

    collectionName
    +

    Character. Name of a GeneSetCollection obtained by using one of the importGeneSet* functions. Default NULL.

    -
    geneSetList
    +
    geneSetList

    See runPerCellQC. Default NULL.

    -
    geneSetListLocation
    +
    geneSetListLocation

    See runPerCellQC. Default NULL.

    -
    geneSetCollection
    +
    geneSetCollection

    See runPerCellQC. Default NULL.

    -
    mitoRef, mitoIDType, mitoPrefix, mitoID, mitoGeneLocation
    -

    Arguments used to -import mitochondrial genes and quantify their expression. Please see +

    mitoRef, mitoIDType, mitoPrefix, mitoID, mitoGeneLocation
    +

    Arguments used to +import mitochondrial genes and quantify their expression. Please see runPerCellQC for detailed information.

    -
    useAssay
    +
    useAssay

    A string specifying which assay contains the count matrix for cells.

    -
    background
    +
    background

    A SingleCellExperiment -with the matrix located in the assay slot under bgAssayName. It should have -the same structure as inSCE except it contains the matrix of empty droplets instead -of cells. When supplied, empirical distribution of transcripts from these -empty droplets will be used as the contamination distribution. It is only used in +with the matrix located in the assay slot under bgAssayName. It should have +the same structure as inSCE except it contains the matrix of empty droplets instead +of cells. When supplied, empirical distribution of transcripts from these +empty droplets will be used as the contamination distribution. It is only used in algorithms "decontX" and "soupX". Default NULL.

    -
    bgAssayName
    -

    Character. Name of the assay to use if background is a +

    bgAssayName
    +

    Character. Name of the assay to use if background is a SingleCellExperiment. If NULL, the function -will use the same value as useAssay. It is only used in algorithms +will use the same value as useAssay. It is only used in algorithms "decontX" and "soupX". Default is NULL.

    -
    bgBatch
    -

    Batch labels for background. If background is a -SingleCellExperiment object, this can be a single -character specifying a name that can be found in colData(background) +

    bgBatch
    +

    Batch labels for background. If background is a +SingleCellExperiment object, this can be a single +character specifying a name that can be found in colData(background) to directly use the barcode annotation Its unique values should be the same -as those in sample, such that each batch of cells have their corresponding +as those in sample, such that each batch of cells have their corresponding batch of empty droplets as background, pointed by this parameter. It is only used in algorithms "decontX" and "soupX". Default to NULL.

    -
    seed
    +
    seed

    Seed for the random number generator. Default 12345.

    -
    paramsList
    +
    paramsList

    A list containing parameters for QC functions. Default NULL.

    Value

    - - -

    SingleCellExperiment object containing the outputs of the - specified algorithms in the colData

    - - -

    of inSCE.

    +

    SingleCellExperiment object containing the outputs of the + specified algorithms in the colData +of inSCE.

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runCellQC(sce)
-}
+} # }
    @@ -346,15 +344,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runComBatSeq.html b/docs/reference/runComBatSeq.html index 806a92508..de2635091 100644 --- a/docs/reference/runComBatSeq.html +++ b/docs/reference/runComBatSeq.html @@ -1,7 +1,5 @@ -Apply ComBat-Seq batch effect correction method to SingleCellExperiment -object — runComBatSeq • singleCellTKApply ComBat-Seq batch effect correction method to SingleCellExperiment object — runComBatSeq • singleCellTK - +
    @@ -31,7 +29,7 @@
    - +
    -

    Apply ComBat-Seq batch effect correction method to SingleCellExperiment -object

    +

    Apply ComBat-Seq batch effect correction method to SingleCellExperiment object

    Source: R/runBatchCorrection.R
    @@ -235,55 +232,57 @@

    Apply ComBat-Seq batch effect correction method to SingleCellExperiment

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    useAssay
    +
    useAssay

    A single character indicating the name of the assay requiring batch correction. Default "counts".

    -
    batch
    +
    batch

    A single character indicating a field in colData that annotates the batches. Default "batch".

    -
    covariates
    +
    covariates

    A character vector indicating the fields in colData that annotates other covariates, such as the cell types. Default NULL.

    -
    bioCond
    +
    bioCond

    A single character indicating a field in colData that annotates the biological conditions. Default NULL.

    -
    useSVA
    +
    useSVA

    A logical scalar. Whether to estimate surrogate variables and use them as an empirical control. Default FALSE.

    -
    assayName
    +
    assayName

    A single characeter. The name for the corrected assay. Will be saved to assay. Default "ComBat".

    -
    shrink
    +
    shrink

    A logical scalar. Whether to apply shrinkage on parameter estimation. Default FALSE.

    -
    shrinkDisp
    +
    shrinkDisp

    A logical scalar. Whether to apply shrinkage on dispersion. Default FALSE.

    -
    nGene
    +
    nGene

    An integer. Number of random genes to use in empirical Bayes estimation, only useful when shrink is set to TRUE. Default NULL.

    @@ -291,9 +290,7 @@

    Arguments

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with assay(inSCE, assayName) updated.

    @@ -343,15 +340,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runCxds.html b/docs/reference/runCxds.html index 62212ca85..9b3c93c71 100644 --- a/docs/reference/runCxds.html +++ b/docs/reference/runCxds.html @@ -1,11 +1,11 @@ -Find doublets/multiplets using cxds. — runCxds • singleCellTKFind doublets/multiplets using cxds. — runCxds • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -227,67 +227,65 @@

    Find doublets/multiplets using

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    seed
    +
    seed

    Seed for the random number generator, can be NULL. Default 12345.

    -
    ntop
    +
    ntop

    See cxds for more information. Default 500.

    -
    binThresh
    -

    See cxds for more information. Default +

    binThresh
    +

    See cxds for more information. Default 0.

    -
    verb
    +
    verb

    See cxds for more information. Default FALSE.

    -
    retRes
    -

    See cxds for more information. Default +

    retRes
    +

    See cxds for more information. Default FALSE.

    -
    estNdbl
    -

    See cxds for more information. Default +

    estNdbl
    +

    See cxds for more information. Default FALSE.

    -
    useAssay
    -

    A string specifying which assay in the SCE to use. Default +

    useAssay
    +

    A string specifying which assay in the SCE to use. Default "counts"

    Value

    - - -

    A SingleCellExperiment object with cxds

    - - -

    output appended to the colData slot. The columns include +

    A SingleCellExperiment object with cxds +output appended to the colData slot. The columns include cxds_score and optionally cxds_call.

    Details

    When the argument sample is specified, cxds will -be run on cells from each sample separately. If sample = NULL, then +be run on cells from each sample separately. If sample = NULL, then all cells will be processed together.

    See also

    -

    cxds, plotCxdsResults, +

    cxds, plotCxdsResults, runCellQC

    @@ -296,7 +294,7 @@

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runCxds(sce)
-#> Fri May  3 07:17:48 2024 ... Running 'cxds'
+#> Thu Feb 13 10:31:21 2025 ... Running 'cxds'
    @@ -311,15 +309,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runCxdsBcdsHybrid.html b/docs/reference/runCxdsBcdsHybrid.html index cfd5613d9..8ac08c6ae 100644 --- a/docs/reference/runCxdsBcdsHybrid.html +++ b/docs/reference/runCxdsBcdsHybrid.html @@ -1,12 +1,12 @@ -Find doublets/multiplets using cxds_bcds_hybrid. — runCxdsBcdsHybrid • singleCellTKFind doublets/multiplets using cxds_bcds_hybrid. — runCxdsBcdsHybrid • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -230,62 +230,59 @@

    Find doublets/multiplets using

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object. Needs counts in assays slot.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to. cxds_bcds_hybrid will be run on cells from each sample separately. If NULL, then all cells will be processed together. Default NULL.

    -
    seed
    +
    seed

    Seed for the random number generator. Default 12345.

    -
    nTop
    +
    nTop

    The number of top varialbe genes to consider. Used in both csds and bcds. Default 500.

    -
    cxdsArgs
    +
    cxdsArgs

    See cxds_bcds_hybrid for more information. Default NULL.

    -
    bcdsArgs
    +
    bcdsArgs

    See cxds_bcds_hybrid for more information. Default NULL.

    -
    verb
    +
    verb

    See cxds_bcds_hybrid for more information. Default FALSE.

    -
    estNdbl
    +
    estNdbl

    See cxds_bcds_hybrid for more information. Default FALSE.

    -
    force
    +
    force

    See cxds_bcds_hybrid for more information. Default FALSE.

    -
    useAssay
    +
    useAssay

    A string specifying which assay in the SCE to use.

    Value

    - - -

    A SingleCellExperiment object with

    -

    -

    cxds_bcds_hybrid output appended to the

    -

    -

    colData slot. The columns include

    -

    -

    hybrid_score and optionally hybrid_call. +

    A SingleCellExperiment object with + cxds_bcds_hybrid output appended to the + colData slot. The columns include + hybrid_score and optionally hybrid_call. Please refer to the documentation of cxds_bcds_hybrid for details.

    @@ -295,7 +292,7 @@

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runCxdsBcdsHybrid(sce)
-#> Fri May  3 07:17:48 2024 ... Running 'cxds_bcds_hybrid'
+#> Thu Feb 13 10:31:22 2025 ... Running 'cxds_bcds_hybrid'
    @@ -310,15 +307,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runDEAnalysis.html b/docs/reference/runDEAnalysis.html index 1479c6f33..1e0b35420 100644 --- a/docs/reference/runDEAnalysis.html +++ b/docs/reference/runDEAnalysis.html @@ -1,9 +1,9 @@ -Perform differential expression analysis on SCE object — runDEAnalysis • singleCellTKPerform differential expression analysis on SCE object — runDEAnalysis • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -335,39 +335,41 @@

    Perform differential expression analysis on SCE object

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    method
    +
    method

    Character. Specify which method to use when using runDEAnalysis(). Choose from "wilcox", "MAST", "DESeq2", "Limma", "ANOVA". Default "wilcox".

    -
    ...
    +
    ...

    Arguments to pass to specific methods when using the generic runDEAnalysis().

    -
    useAssay
    +
    useAssay

    character. A string specifying which assay to use for the DE regression. Ignored when useReducedDim is specified. Default "counts" for DESeq2, "logcounts" for other methods.

    -
    useReducedDim
    +
    useReducedDim

    character. A string specifying which reducedDim to use for DE analysis. Will treat the dimensions as features. Default NULL.

    -
    index1
    +
    index1

    Any type of indices that can subset a SingleCellExperiment inherited object by cells. Specifies which cells are of interests. Default NULL.

    -
    index2
    +
    index2

    Any type of indices that can subset a SingleCellExperiment inherited object by cells. specifies the control group against those specified by index1. If @@ -375,105 +377,103 @@

    Arguments

    compared with all other cells. Default NULL.

    -
    class
    +
    class

    A vector/factor with ncol(inSCE) elements, or a character scalar that specifies a column name of colData(inSCE). Default "cluster".

    -
    classGroup1
    +
    classGroup1

    a vector specifying which "levels" given in class are of interests. Default c(1).

    -
    classGroup2
    +
    classGroup2

    a vector specifying which "levels" given in class is the control group against those specified by classGroup1. If NULL when using annotation specification, classGroup1 cells will be compared with all other cells. Default c(2).

    -
    analysisName
    -

    A character scalar naming the DEG analysis. +

    analysisName
    +

    A character scalar naming the DEG analysis. Default "cluster1_VS_2".

    -
    groupName1
    -

    A character scalar naming the group of interests. +

    groupName1
    +

    A character scalar naming the group of interests. Default "cluster1".

    -
    groupName2
    -

    A character scalar naming the control group. +

    groupName2
    +

    A character scalar naming the control group. Default "cluster2".

    -
    covariates
    +
    covariates

    A character vector of additional covariates to use when building the model. All covariates must exist in names(colData(inSCE)). Default NULL.

    -
    fullReduced
    +
    fullReduced

    Logical, DESeq2 only argument. Whether to apply LRT (Likelihood ratio test) with a 'full' model. Default TRUE.

    -
    onlyPos
    +
    onlyPos

    Whether to only output DEG with positive log2_FC value. Default FALSE.

    -
    log2fcThreshold
    +
    log2fcThreshold

    Only out put DEGs with the absolute values of log2FC greater than this value. Default NULL.

    -
    fdrThreshold
    +
    fdrThreshold

    Only out put DEGs with FDR value less than this value. Default NULL.

    -
    minGroup1MeanExp
    +
    minGroup1MeanExp

    Only out put DEGs with mean expression in group1 greater then this value. Default NULL.

    -
    maxGroup2MeanExp
    +
    maxGroup2MeanExp

    Only out put DEGs with mean expression in group2 less then this value. Default NULL.

    -
    minGroup1ExprPerc
    +
    minGroup1ExprPerc

    Only out put DEGs expressed in greater then this fraction of cells in group1. Default NULL.

    -
    maxGroup2ExprPerc
    +
    maxGroup2ExprPerc

    Only out put DEGs expressed in less then this fraction of cells in group2. Default NULL.

    -
    overwrite
    +
    overwrite

    A logical scalar. Whether to overwrite result if exists. Default FALSE.

    -
    verbose
    +
    verbose

    A logical scalar. Whether to show messages. Default TRUE.

    -
    check_sanity
    +
    check_sanity

    Logical, MAST only argument. Whether to perform MAST's sanity check to see if the counts are logged. Default TRUE.

    Value

    - - -

    The input SingleCellExperiment object, where +

    The input SingleCellExperiment object, where metadata(inSCE)$diffExp is updated with a list named by analysisName, with elements of:

    $groupNames
    @@ -518,7 +518,7 @@

    Examples

    sce <- runDEAnalysis(method = "Limma", inSCE = sce, groupName1 = "group1", groupName2 = "group2", index1 = seq(20), index2 = seq(21,40), analysisName = "Limma") -#> Fri May 3 07:17:50 2024 ... Running DE with limma, Analysis name: Limma +#> Thu Feb 13 10:31:25 2025 ... Running DE with limma, Analysis name: Limma
    @@ -534,15 +534,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runDecontX.html b/docs/reference/runDecontX.html index 84afecbf4..569a6fc58 100644 --- a/docs/reference/runDecontX.html +++ b/docs/reference/runDecontX.html @@ -1,10 +1,10 @@ -Detecting contamination with DecontX. — runDecontX • singleCellTKDetecting contamination with DecontX. — runDecontX • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -233,11 +233,13 @@

    Detecting contamination with DecontX.

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    sample
    +
    sample

    A single character specifying a name that can be found in colData(inSCE) to directly use the cell annotation; or a character vector with as many elements as cells to indicates which sample each cell @@ -245,37 +247,37 @@

    Arguments

    each sample separately.

    -
    useAssay
    +
    useAssay

    A string specifying which assay in the SCE to use. Default 'counts'.

    -
    background
    +
    background

    A SingleCellExperiment -with the matrix located in the assay slot under bgAssayName. It should have -the same structure as inSCE except it contains the matrix of empty droplets instead -of cells. When supplied, empirical distribution of transcripts from these +with the matrix located in the assay slot under bgAssayName. It should have +the same structure as inSCE except it contains the matrix of empty droplets instead +of cells. When supplied, empirical distribution of transcripts from these empty droplets will be used as the contamination distribution. Default NULL.

    -
    bgAssayName
    -

    Character. Name of the assay to use if background is a +

    bgAssayName
    +

    Character. Name of the assay to use if background is a SingleCellExperiment. If NULL, the function will use the same value as useAssay. Default is NULL.

    -
    bgBatch
    -

    Batch labels for background. If background is a -SingleCellExperiment object, this can be a single -character specifying a name that can be found in colData(background) -to directly use the barcode annotation; or a numeric / character vector that has -as many elements as barcodes to indicate which sample each barcode belongs to. Its -unique values should be the same as those in sample, such that each -batch of cells have their corresponding batch of empty droplets as background, +

    bgBatch
    +

    Batch labels for background. If background is a +SingleCellExperiment object, this can be a single +character specifying a name that can be found in colData(background) +to directly use the barcode annotation; or a numeric / character vector that has +as many elements as barcodes to indicate which sample each barcode belongs to. Its +unique values should be the same as those in sample, such that each +batch of cells have their corresponding batch of empty droplets as background, pointed by this parameter. Default to NULL.

    -
    z
    +
    z

    Numeric or character vector. Cell cluster labels. If NULL, PCA will be used to reduce the dimensionality of the dataset initially, 'umap' from the 'uwot' package @@ -284,11 +286,11 @@

    Arguments

    will be used to identify clusters of broad cell types. Default NULL.

    -
    maxIter
    +
    maxIter

    Integer. Maximum iterations of the EM algorithm. Default 500.

    -
    delta
    +
    delta

    Numeric Vector of length 2. Concentration parameters for the Dirichlet prior for the contamination in each cell. The first element is the prior for the native counts while the second element is the prior for @@ -306,58 +308,55 @@

    Arguments

    Default c(10, 10).

    -
    estimateDelta
    +
    estimateDelta

    Boolean. Whether to update delta at each iteration.

    -
    convergence
    +
    convergence

    Numeric. The EM algorithm will be stopped if the maximum difference in the contamination estimates between the previous and current iterations is less than this. Default 0.001.

    -
    iterLogLik
    +
    iterLogLik

    Integer. Calculate log likelihood every iterLogLik iteration. Default 10.

    -
    varGenes
    +
    varGenes

    Integer. The number of variable genes to use in dimensionality reduction before clustering. Variability is calcualted using modelGeneVar function from the 'scran' package. Used only when z is not provided. Default 5000.

    -
    dbscanEps
    +
    dbscanEps

    Numeric. The clustering resolution parameter used in 'dbscan' to estimate broad cell clusters. Used only when z is not provided. Default 1.

    -
    seed
    +
    seed

    Integer. Passed to with_seed. For reproducibility, a default value of 12345 is used. If NULL, no calls to with_seed are made.

    -
    logfile
    +
    logfile

    Character. Messages will be redirected to a file named `logfile`. If NULL, messages will be printed to stdout. Default NULL.

    -
    verbose
    +
    verbose

    Logical. Whether to print log messages. Default TRUE.

    Value

    - - -

    A SingleCellExperiment object with - 'decontX_Contamination' and 'decontX_Clusters' added to the

    -

    -

    colData slot. Additionally, the +

    A SingleCellExperiment object with + 'decontX_Contamination' and 'decontX_Clusters' added to the + colData slot. Additionally, the decontaminated counts will be added as an assay called 'decontXCounts'.

    @@ -366,30 +365,30 @@

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runDecontX(sce[,sample(ncol(sce),20)])
-#> Fri May  3 07:17:51 2024 ... Running 'DecontX'
+#> Thu Feb 13 10:31:25 2025 ... Running 'DecontX'
 #> --------------------------------------------------
 #> Starting DecontX
 #> --------------------------------------------------
-#> Fri May  3 07:17:51 2024 .. Analyzing all cells
-#> Fri May  3 07:17:51 2024 .... Generating UMAP and estimating cell types
-#> Fri May  3 07:17:55 2024 .... Estimating contamination
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 10 | converge: 0.01985
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 20 | converge: 0.01116
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 30 | converge: 0.006593
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 40 | converge: 0.003919
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 50 | converge: 0.002691
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 60 | converge: 0.002093
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 70 | converge: 0.001932
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 80 | converge: 0.001769
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 90 | converge: 0.001605
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 100 | converge: 0.00145
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 110 | converge: 0.001304
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 120 | converge: 0.001168
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 130 | converge: 0.001041
-#> Fri May  3 07:17:55 2024 ...... Completed iteration: 134 | converge: 0.0009927
-#> Fri May  3 07:17:55 2024 .. Calculating final decontaminated matrix
+#> Thu Feb 13 10:31:25 2025 .. Analyzing all cells
+#> Thu Feb 13 10:31:25 2025 .... Generating UMAP and estimating cell types
+#> Thu Feb 13 10:31:29 2025 .... Estimating contamination
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 10 | converge: 0.01985
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 20 | converge: 0.01116
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 30 | converge: 0.006593
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 40 | converge: 0.003919
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 50 | converge: 0.002691
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 60 | converge: 0.002093
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 70 | converge: 0.001932
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 80 | converge: 0.001769
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 90 | converge: 0.001605
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 100 | converge: 0.00145
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 110 | converge: 0.001304
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 120 | converge: 0.001168
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 130 | converge: 0.001041
+#> Thu Feb 13 10:31:29 2025 ...... Completed iteration: 134 | converge: 0.0009927
+#> Thu Feb 13 10:31:29 2025 .. Calculating final decontaminated matrix
 #> --------------------------------------------------
-#> Completed DecontX. Total time: 3.801916 secs
+#> Completed DecontX. Total time: 4.091687 secs
 #> --------------------------------------------------
    @@ -405,15 +404,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runDimReduce.html b/docs/reference/runDimReduce.html index dcb3f96f7..120303492 100644 --- a/docs/reference/runDimReduce.html +++ b/docs/reference/runDimReduce.html @@ -1,9 +1,9 @@ -Generic Wrapper function for running dimensionality reduction — runDimReduce • singleCellTKGeneric Wrapper function for running dimensionality reduction — runDimReduce • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -226,69 +226,69 @@

    Generic Wrapper function for running dimensionality reduction

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    method
    +
    method

    One from "scaterPCA", "seuratPCA", "seuratICA", "rTSNE", "seuratTSNE", "scaterUMAP", "seuratUMAP", "scanpyPCA", "scanpyUMAP" and "scanpyTSNE".

    -
    useAssay
    +
    useAssay

    Assay to use for computation. If useAltExp is specified, useAssay has to exist in assays(altExp(inSCE, useAltExp)). Default "counts".

    -
    useReducedDim
    +
    useReducedDim

    The low dimension representation to use for embedding computation. Default NULL.

    -
    useAltExp
    +
    useAltExp

    The subset to use for computation, usually for the selected variable features. Default NULL.

    -
    reducedDimName
    +
    reducedDimName

    The name of the result matrix. Required.

    -
    nComponents
    +
    nComponents

    Specify the number of dimensions to compute with the selected method in case of PCA/ICA and the number of components to use in the case of TSNE/UMAP methods.

    -
    useFeatureSubset
    +
    useFeatureSubset

    Subset of feature to use for dimension reduction. A character string indicating a rowData variable that stores the logical vector of HVG selection, or a vector that can subset the rows of inSCE. Default NULL.

    -
    scale
    +
    scale

    Logical scalar, whether to standardize the expression values. Default TRUE.

    -
    seed
    +
    seed

    Random seed for reproducibility of results. Default NULL will use global seed in use by the R environment.

    -
    ...
    +
    ...

    The other arguments for running a specific algorithm. Please refer to the one you use.

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with reducedDim updated with the result.

    @@ -314,7 +314,7 @@

    Examples

    sce <- runDimReduce(inSCE = sce, method = "scaterPCA", useAssay = "logcounts", scale = TRUE, reducedDimName = "PCA") -#> Fri May 3 07:17:57 2024 ... Computing Scater PCA. +#> Thu Feb 13 10:31:32 2025 ... Computing Scater PCA.
    @@ -329,15 +329,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runDoubletFinder.html b/docs/reference/runDoubletFinder.html index 1b63830de..1d974845e 100644 --- a/docs/reference/runDoubletFinder.html +++ b/docs/reference/runDoubletFinder.html @@ -1,10 +1,10 @@ -Generates a doublet score for each cell via doubletFinder — runDoubletFinder • singleCellTKGenerates a doublet score for each cell via doubletFinder — runDoubletFinder • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -218,6 +218,7 @@

    Generates a doublet score for each cell via doubletFinder

    seuratNfeatures = 2000, seuratPcs = seq(15), seuratRes = 1.5, + sct = FALSE, formationRate = 0.075, nCores = NULL, verbose = FALSE @@ -226,61 +227,65 @@

    Generates a doublet score for each cell via doubletFinder

    Arguments

    -
    inSCE
    + + +
    inSCE

    inSCE A SingleCellExperiment object.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    useAssay
    -

    A string specifying which assay in the SCE to use. Default +

    useAssay
    +

    A string specifying which assay in the SCE to use. Default "counts".

    -
    seed
    -

    Seed for the random number generator, can be set to NULL. +

    seed
    +

    Seed for the random number generator, can be set to NULL. Default 12345.

    -
    seuratNfeatures
    +
    seuratNfeatures

    Integer. Number of highly variable genes to use. Default 2000.

    -
    seuratPcs
    +
    seuratPcs

    Numeric vector. The PCs used in seurat function to determine number of clusters. Default 1:15.

    -
    seuratRes
    +
    seuratRes

    Numeric vector. The resolution parameter used in Seurat, -which adjusts the number of clusters determined via the algorithm. Default +which adjusts the number of clusters determined via the algorithm. Default 1.5.

    -
    formationRate
    -

    Doublet formation rate used within algorithm. Default +

    sct
    +

    Whether or not to use SCT. Default FALSE.

    + + +
    formationRate
    +

    Doublet formation rate used within algorithm. Default 0.075.

    -
    nCores
    -

    Number of cores used for running the function. Default +

    nCores
    +

    Number of cores used for running the function. Default NULL.

    -
    verbose
    -

    Boolean. Wheter to print messages from Seurat and +

    verbose
    +

    Boolean. Wheter to print messages from Seurat and DoubletFinder. Default FALSE.

    Value

    - - -

    SingleCellExperiment object containing the +

    SingleCellExperiment object containing the doublet_finder_doublet_score variable in colData slot.

    @@ -291,9 +296,10 @@

    See also

    Examples

    data(scExample, package = "singleCellTK")
+options(future.globals.maxSize = 786432000)
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runDoubletFinder(sce)
-#> Fri May  3 07:17:57 2024 ... Running 'doubletFinder'
+#> Thu Feb 13 10:31:33 2025 ... Running 'doubletFinder'
 #> Normalizing layer: counts
 #> Finding variable features for layer counts
 #> Centering and scaling data matrix
@@ -311,15 +317,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runDropletQC.html b/docs/reference/runDropletQC.html index 98d2418f9..52d09e585 100644 --- a/docs/reference/runDropletQC.html +++ b/docs/reference/runDropletQC.html @@ -1,10 +1,10 @@ -Perform comprehensive droplet QC — runDropletQC • singleCellTKPerform comprehensive droplet QC — runDropletQC • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -221,47 +221,45 @@

    Perform comprehensive droplet QC

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object containing the full droplet count matrix

    -
    algorithms
    +
    algorithms

    Character vector. Specify which QC algorithms to run. Available options are "emptyDrops" and "barcodeRanks".

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to. Algorithms will be run on cells from each sample separately.

    -
    useAssay
    +
    useAssay

    A string specifying which assay contains the count matrix for droplets.

    -
    paramsList
    +
    paramsList

    A list containing parameters for QC functions. Default NULL.

    Value

    - - -

    SingleCellExperiment object containing the outputs of the - specified algorithms in the colData

    - - -

    of inSCE.

    +

    SingleCellExperiment object containing the outputs of the + specified algorithms in the colData +of inSCE.

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runDropletQC(sce)
-}
+} # }
    @@ -276,15 +274,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runEmptyDrops.html b/docs/reference/runEmptyDrops.html index b7c66dfd5..3a2e3bb40 100644 --- a/docs/reference/runEmptyDrops.html +++ b/docs/reference/runEmptyDrops.html @@ -1,12 +1,12 @@ -Identify empty droplets using emptyDrops. — runEmptyDrops • singleCellTKIdentify empty droplets using emptyDrops. — runEmptyDrops • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -208,7 +208,7 @@

    Identify empty droplets using

    Run emptyDrops on the count matrix in the -provided \linkS4classSingleCellExperiment object. +provided SingleCellExperiment object. Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment.

    @@ -231,66 +231,66 @@

    Identify empty droplets using

    Arguments

    -
    inSCE
    -

    A SingleCellExperiment object. Must contain a raw + + +

    inSCE
    +

    A SingleCellExperiment object. Must contain a raw counts matrix before empty droplets have been removed.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    useAssay
    -

    A string specifying which assay in the SCE to use. Default +

    useAssay
    +

    A string specifying which assay in the SCE to use. Default "counts"

    -
    lower
    -

    See emptyDrops for more information. +

    lower
    +

    See emptyDrops for more information. Default 100.

    -
    niters
    -

    See emptyDrops for more information. +

    niters
    +

    See emptyDrops for more information. Default 10000.

    -
    testAmbient
    -

    See emptyDrops for more information. +

    testAmbient
    +

    See emptyDrops for more information. Default FALSE.

    -
    ignore
    -

    See emptyDrops for more information. +

    ignore
    +

    See emptyDrops for more information. Default NULL.

    -
    alpha
    -

    See emptyDrops for more information. +

    alpha
    +

    See emptyDrops for more information. Default NULL.

    -
    retain
    -

    See emptyDrops for more information. +

    retain
    +

    See emptyDrops for more information. Default NULL.

    -
    barcodeArgs
    -

    See emptyDrops for more information. +

    barcodeArgs
    +

    See emptyDrops for more information. Default list().

    -
    BPPARAM
    -

    See emptyDrops for more information. +

    BPPARAM
    +

    See emptyDrops for more information. Default BiocParallel::SerialParam().

    Value

    - - -

    A SingleCellExperiment object with the +

    A SingleCellExperiment object with the emptyDrops output table appended to the colData slot. The columns include emptyDrops_total, emptyDrops_logprob, @@ -308,7 +308,7 @@

    See also

    Examples

    data(scExample, package = "singleCellTK")
 sce <- runEmptyDrops(inSCE = sce)
-#> Fri May  3 07:18:21 2024 ... Running 'emptyDrops'
+#> Thu Feb 13 10:32:00 2025 ... Running 'emptyDrops'
    @@ -323,15 +323,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runEnrichR.html b/docs/reference/runEnrichR.html index 346e5adf2..2c5359dbe 100644 --- a/docs/reference/runEnrichR.html +++ b/docs/reference/runEnrichR.html @@ -1,9 +1,9 @@ -Run EnrichR on SCE object — runEnrichR • singleCellTKRun EnrichR on SCE object — runEnrichR • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -220,57 +220,57 @@

    Run EnrichR on SCE object

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    features
    +
    features

    Character vector, selected genes for enrichment analysis.

    -
    analysisName
    +
    analysisName

    A string that identifies each specific analysis.

    -
    db
    -

    Character vector. Selected database name(s) from the enrichR -database list. If NULL then EnrichR will be run on all the available +

    db
    +

    Character vector. Selected database name(s) from the enrichR +database list. If NULL then EnrichR will be run on all the available databases on the enrichR database. See details. Default NULL

    -
    by
    -

    Character. From where should we find the features? +

    by
    +

    Character. From where should we find the features? "rownames" for from rownames(inSCE), otherwise, from a column -of feature metadata (rowData(inSCE)[[by]]). See details. Default +of feature metadata (rowData(inSCE)[[by]]). See details. Default "rownames".

    -
    featureName
    +
    featureName

    Character. Indicates the actual feature identifiers to be -passed to EnrichR. Can be "rownames", a column in feature metadata +passed to EnrichR. Can be "rownames", a column in feature metadata (rowData(inSCE)[[featureName]]), or a character vector with its length equals to nrow(inSCE). See details. Default "rownames".

    Value

    - - -

    Updates inSCE metadata with a data.frame of enrichment terms +

    Updates inSCE metadata with a data.frame of enrichment terms overlapping in the respective databases along with p-values, z-scores etc.

    Details

    -

    EnrichR works by querying the specified features to its online +

    EnrichR works by querying the specified features to its online databases, thus it requires the Internet connection.

    -

    Available db options could be shown by running +

    Available db options could be shown by running enrichR::listEnrichrDbs()$libraryName

    -

    This function checks for the existence of features in the SCE object. When -features do not have a match in rownames(inSCE), users may +

    This function checks for the existence of features in the SCE object. When +features do not have a match in rownames(inSCE), users may try to specify by to pass the check.

    -

    EnrichR expects gene symbols/names as the input (i.e. Ensembl ID might not -work). When specified features are not qualified for this, users may -try to specify featureName to change the identifier type to pass to +

    EnrichR expects gene symbols/names as the input (i.e. Ensembl ID might not +work). When specified features are not qualified for this, users may +try to specify featureName to change the identifier type to pass to EnrichR.

    @@ -304,15 +304,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runFastMNN.html b/docs/reference/runFastMNN.html index 33b0a62e2..9be2fe959 100644 --- a/docs/reference/runFastMNN.html +++ b/docs/reference/runFastMNN.html @@ -1,12 +1,10 @@ -Apply a fast version of the mutual nearest neighbors (MNN) batch effect -correction method to SingleCellExperiment object — runFastMNN • singleCellTKApply a fast version of the mutual nearest neighbors (MNN) batch effect correction method to SingleCellExperiment object — runFastMNN • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    Apply a fast version of the mutual nearest neighbors (MNN) batch effect -correction method to SingleCellExperiment object

    +

    Apply a fast version of the mutual nearest neighbors (MNN) batch effect correction method to SingleCellExperiment object

    Source: R/runBatchCorrection.R
    @@ -232,81 +229,81 @@

    Apply a fast version of the mutual nearest neighbors (MNN) batch effect

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    useAssay
    +
    useAssay

    A single character indicating the name of the assay requiring batch correction. Default "logcounts".

    -
    useReducedDim
    +
    useReducedDim

    A single character indicating the dimension reduction used for batch correction. Will ignore useAssay when using. Default NULL.

    -
    batch
    +
    batch

    A single character indicating a field in colData that annotates the batches of each cell; or a vector/factor with the same length as the number of cells. Default "batch".

    -
    reducedDimName
    +
    reducedDimName

    A single character. The name for the corrected low-dimensional representation. Default "fastMNN".

    -
    k
    +
    k

    An integer scalar specifying the number of nearest neighbors to consider when identifying MNNs. See "See Also". Default 20.

    -
    propK
    +
    propK

    A numeric scalar in (0, 1) specifying the proportion of cells in each dataset to use for mutual nearest neighbor searching. See "See Also". Default NULL.

    -
    ndist
    +
    ndist

    A numeric scalar specifying the threshold beyond which neighbours are to be ignored when computing correction vectors. See "See Also". Default 3.

    -
    minBatchSkip
    +
    minBatchSkip

    Numeric scalar specifying the minimum relative magnitude of the batch effect, below which no correction will be performed at a given merge step. See "See Also". Default 0.

    -
    cosNorm
    +
    cosNorm

    A logical scalar indicating whether cosine normalization should be performed on useAssay prior to PCA. See "See Also". Default TRUE.

    -
    nComponents
    +
    nComponents

    An integer scalar specifying the number of dimensions to produce. See "See Also". Default 50.

    -
    weights
    +
    weights

    The weighting scheme to use. Passed to multiBatchPCA. Default NULL.

    -
    BPPARAM
    +
    BPPARAM

    A BiocParallelParam object specifying whether the SVD should be parallelized.

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with reducedDim(inSCE, reducedDimName) updated.

    @@ -339,15 +336,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runFeatureSelection.html b/docs/reference/runFeatureSelection.html index ff1f47ad4..befe435ed 100644 --- a/docs/reference/runFeatureSelection.html +++ b/docs/reference/runFeatureSelection.html @@ -1,17 +1,17 @@ -Run Variable Feature Detection Methods — runFeatureSelection • singleCellTK - +
    @@ -33,7 +33,7 @@
    - +
    @@ -212,13 +212,13 @@

    Run Variable Feature Detection Methods

    -

    Wrapper function to run all of the feature selection methods +

    Wrapper function to run all of the feature selection methods integrated within the singleCellTK package including three methods from -Seurat ("vst", "mean.var.plot" or dispersion) and the +Seurat ("vst", "mean.var.plot" or dispersion) and the Scran modelGeneVar method.

    -

    This function does not return the names of the variable features but only +

    This function does not return the names of the variable features but only computes the metrics, which will be stored in the rowData slot. To set -a HVG list for downstream use, users should call setTopHVG +a HVG list for downstream use, users should call setTopHVG after computing the metrics. To get the names of the variable features, users should call getTopHVG function after computing the metrics.

    @@ -229,16 +229,18 @@

    Run Variable Feature Detection Methods

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Specify the name of the assay that should be used. Should use raw counts for "vst" method, or a normalized assay for other methods.

    -
    method
    +
    method

    Specify the method to use for variable gene selection. Options include "vst", "mean.var.plot" or "dispersion" from Seurat and "modelGeneVar" from Scran. Default "vst"

    @@ -246,9 +248,7 @@

    Arguments

    Value

    - - -

    The input SingleCellExperiment object that contains +

    The input SingleCellExperiment object that contains the computed statistics in the rowData slot

    @@ -278,15 +278,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runFindMarker.html b/docs/reference/runFindMarker.html index cb255e250..0a70e46fa 100644 --- a/docs/reference/runFindMarker.html +++ b/docs/reference/runFindMarker.html @@ -1,12 +1,12 @@ -Find the marker gene set for each cluster — runFindMarker • singleCellTKFind the marker gene set for each cluster — runFindMarker • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -247,69 +247,71 @@

    Find the marker gene set for each cluster

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object.

    -
    useAssay
    +
    useAssay

    character. A string specifying which assay to use for the MAST calculations. Default "logcounts".

    -
    useReducedDim
    +
    useReducedDim

    character. A string specifying which reducedDim to use for MAST calculations. Set useAssay to NULL when using. Required.

    -
    method
    +
    method

    A single character for specific differential expression analysis method. Choose from 'wilcox', 'MAST', 'DESeq2', 'Limma', and 'ANOVA'. Default "wilcox".

    -
    cluster
    +
    cluster

    One single character to specify a column in colData(inSCE) for the clustering label. Alternatively, a vector or a factor is also acceptable. Default "cluster".

    -
    covariates
    +
    covariates

    A character vector of additional covariates to use when building the model. All covariates must exist in names(colData(inSCE)). Not applicable when method is "MAST" method. Default NULL.

    -
    log2fcThreshold
    +
    log2fcThreshold

    Only out put DEGs with the absolute values of log2FC larger than this value. Default NULL

    -
    fdrThreshold
    +
    fdrThreshold

    Only out put DEGs with FDR value smaller than this value. Default NULL

    -
    minClustExprPerc
    +
    minClustExprPerc

    A numeric scalar. The minimum cutoff of the percentage of cells in the cluster of interests that expressed the marker gene. From 0 to 1. Default NULL.

    -
    maxCtrlExprPerc
    +
    maxCtrlExprPerc

    A numeric scalar. The maximum cutoff of the percentage of cells out of the cluster (control group) that expressed the marker gene. From 0 to 1. Default NULL.

    -
    minMeanExpr
    +
    minMeanExpr

    A numeric scalar. The minimum cutoff of the mean expression value of the marker in the cluster of interests. Default NULL.

    -
    detectThresh
    +
    detectThresh

    A numeric scalar, above which a matrix value will be treated as expressed when calculating cluster/control expression percentage. Default 0.

    @@ -317,9 +319,7 @@

    Arguments

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with metadata(inSCE)$findMarker updated with a data.table of the up- regulated DEGs for each cluster.

    @@ -348,9 +348,9 @@

    Examples

    mouseBrainSubsetSCE <- runFindMarker(mouseBrainSubsetSCE, useAssay = "logcounts", cluster = "level1class") -#> Fri May 3 07:18:31 2024 ... Identifying markers for cluster 'microglia', using DE method 'wilcox' -#> Fri May 3 07:18:32 2024 ... Identifying markers for cluster 'oligodendrocytes', using DE method 'wilcox' -#> Fri May 3 07:18:33 2024 ... Organizing findMarker result +#> Thu Feb 13 10:32:10 2025 ... Identifying markers for cluster 'microglia', using DE method 'wilcox' +#> Thu Feb 13 10:32:10 2025 ... Identifying markers for cluster 'oligodendrocytes', using DE method 'wilcox' +#> Thu Feb 13 10:32:11 2025 ... Organizing findMarker result
    @@ -365,15 +365,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runGSVA.html b/docs/reference/runGSVA.html index 8b7c804a0..44874ea83 100644 --- a/docs/reference/runGSVA.html +++ b/docs/reference/runGSVA.html @@ -1,9 +1,9 @@ -Run GSVA analysis on a SingleCellExperiment object — runGSVA • singleCellTKRun GSVA analysis on a SingleCellExperiment object — runGSVA • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -219,37 +219,37 @@

    Run GSVA analysis on a SingleCellExperiment object

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Indicate which assay to use. The default is "logcounts"

    -
    resultNamePrefix
    -

    Character. Prefix to the name the GSVA results -which will be stored in the reducedDim slot of inSCE. The names of the -output matrix will be resultNamePrefix_Scores. If this parameter is -set to NULL, then "GSVA_geneSetCollectionName_" will be used. Default +

    resultNamePrefix
    +

    Character. Prefix to the name the GSVA results +which will be stored in the reducedDim slot of inSCE. The names of the +output matrix will be resultNamePrefix_Scores. If this parameter is +set to NULL, then "GSVA_geneSetCollectionName_" will be used. Default NULL.

    -
    geneSetCollectionName
    -

    Character. The name of the gene set collection +

    geneSetCollectionName
    +

    Character. The name of the gene set collection to use.

    -
    ...
    +
    ...

    Parameters to pass to gsva()

    Value

    - - -

    A SingleCellExperiment object with pathway activity -scores from GSVA stored in reducedDim as +

    A SingleCellExperiment object with pathway activity +scores from GSVA stored in reducedDim as GSVA_geneSetCollectionName_Scores.

    @@ -267,13 +267,17 @@

    Examples

    sce <- runGSVA(inSCE = sce, geneSetCollectionName = "GeneSetCollection", useAssay = "logcounts") -#> Fri May 3 07:18:34 2024 ... Running GSVA -#> No annotation package name available in the input data object. -#> Attempting to directly match identifiers in data to gene sets. -#> Estimating GSVA scores for 2 gene sets. -#> Estimating ECDFs with Gaussian kernels -#> | | | 0% | |=================================== | 50% | |======================================================================| 100% -#> +#> Thu Feb 13 10:32:12 2025 ... Running GSVA +#> ℹ GSVA version 2.0.5 +#> ℹ Calculating GSVA ranks +#> ℹ kcdf='auto' (default) +#> ℹ GSVA dense (classical) algorithm +#> ℹ Row-wise ECDF estimation with Gaussian kernels +#> ℹ Calculating GSVA column ranks +#> ! No annotation metadata available in the input expression data object +#> ! Attempting to directly match identifiers in expression data to gene sets +#> ℹ Calculating GSVA scores +#> ✔ Calculations finished
    @@ -288,15 +292,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runHarmony.html b/docs/reference/runHarmony.html index a5d363a3e..777b9c045 100644 --- a/docs/reference/runHarmony.html +++ b/docs/reference/runHarmony.html @@ -1,11 +1,11 @@ -Apply Harmony batch effect correction method to SingleCellExperiment object — runHarmony • singleCellTKApply Harmony batch effect correction method to SingleCellExperiment object — runHarmony • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -231,82 +231,82 @@

    Apply Harmony batch effect correction method to SingleCellExperiment object<

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    useAssay
    +
    useAssay

    A single character indicating the name of the assay requiring batch correction. Default NULL. It is recommended to use a reducedDim such as PCA through the `useReducedDim` parameter of this function.

    -
    useReducedDim
    +
    useReducedDim

    A single character indicating the name of the reducedDim -to be used. It is recommended to use a reducedDim instead of a full assay as +to be used. It is recommended to use a reducedDim instead of a full assay as using an assay might cause the algorithm to not converge and throw error. Specifying this will ignore useAssay. Default NULL.

    -
    batch
    +
    batch

    A single character indicating a field in colData that annotates the batches of each cell; or a vector/factor with the same length as the number of cells. Default "batch".

    -
    reducedDimName
    +
    reducedDimName

    A single character. The name for the corrected low-dimensional representation. Will be saved to reducedDim(inSCE). Default "HARMONY".

    -
    nComponents
    +
    nComponents

    An integer. The number of PCs to use and generate. Default 50L.

    -
    lambda
    +
    lambda

    A Numeric scalar. Ridge regression penalty parameter. Must be strictly positive. Smaller values result in more aggressive correction. Default 0.1.

    -
    theta
    +
    theta

    A Numeric scalar. Diversity clustering penalty parameter. Larger values of theta result in more diverse clusters. theta=0 does not encourage any diversity. Default 5.

    -
    sigma
    +
    sigma

    A Numeric scalar. Width of soft kmeans clusters. Larger values of sigma result in cells assigned to more clusters. Smaller values of sigma make soft kmeans cluster approach hard clustering. Default 0.1.

    -
    nIter
    +
    nIter

    An integer. The max number of iterations to perform. Default 10L.

    -
    seed
    +
    seed

    Set seed for reproducibility. Default is 12345.

    -
    verbose
    +
    verbose

    Whether to print progress messages. Default TRUE.

    -
    ...
    +
    ...

    Other arguments passed to HarmonyMatrix. See details.

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with reducedDim(inSCE, reducedDimName) updated.

    @@ -326,10 +326,10 @@

    References

    Examples

    data('sceBatches', package = 'singleCellTK')
 logcounts(sceBatches) <- log1p(counts(sceBatches))
-if (FALSE) {
-if (require("harmony"))
+if (FALSE) { # \dontrun{
+if (require("harmony"))
     sceCorr <- runHarmony(sceBatches)
-}
+} # }

    @@ -344,15 +344,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runKMeans.html b/docs/reference/runKMeans.html index f51121810..9db234c69 100644 --- a/docs/reference/runKMeans.html +++ b/docs/reference/runKMeans.html @@ -1,10 +1,10 @@ -Get clustering with KMeans — runKMeans • singleCellTKGet clustering with KMeans — runKMeans • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -225,46 +225,48 @@

    Get clustering with KMeans

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    nCenters
    +
    nCenters

    An integer, the number of centroids (clusters).

    -
    useReducedDim
    +
    useReducedDim

    A single character, specifying which low-dimension representation to perform the clustering algorithm on. Default "PCA".

    -
    clusterName
    +
    clusterName

    A single character, specifying the name to store the cluster label in colData. Default "KMeans_cluster".

    -
    nComp
    +
    nComp

    An integer. The number of components to use for K-Means. Default 10. See Detail.

    -
    nIter
    +
    nIter

    An integer, the maximum number of iterations allowed. Default 10.

    -
    nStart
    +
    nStart

    An integer, the number of random sets to choose. Default 1.

    -
    seed
    +
    seed

    An integer. The seed for the random number generator. Default 12345.

    -
    algorithm
    +
    algorithm

    A single character. Choose from "Hartigan-Wong", "Lloyd", "MacQueen". May be abbreviated. Default "Hartigan-Wong".

    @@ -272,9 +274,7 @@

    Arguments

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with factor cluster labeling updated in colData(inSCE)[[clusterName]].

    @@ -285,8 +285,8 @@

    Examples

    mouseBrainSubsetSCE <- runKMeans(mouseBrainSubsetSCE, useReducedDim = "PCA_logcounts", nCenters = 2) -#> Fri May 3 07:18:36 2024 ... Running 'KMeans clustering' with Hartigan-Wong algorithm. -#> Fri May 3 07:18:36 2024 ... Identified 2 clusters +#> Thu Feb 13 10:32:14 2025 ... Running 'KMeans clustering' with Hartigan-Wong algorithm. +#> Thu Feb 13 10:32:14 2025 ... Identified 2 clusters
    @@ -301,15 +301,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runLimmaBC.html b/docs/reference/runLimmaBC.html index 7d7143d2a..9665b8b1c 100644 --- a/docs/reference/runLimmaBC.html +++ b/docs/reference/runLimmaBC.html @@ -1,10 +1,10 @@ -Apply Limma's batch effect correction method to SingleCellExperiment object — runLimmaBC • singleCellTKApply Limma's batch effect correction method to SingleCellExperiment object — runLimmaBC • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -215,22 +215,24 @@

    Apply Limma's batch effect correction method to SingleCellExperiment object<

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    useAssay
    +
    useAssay

    A single character indicating the name of the assay requiring batch correction. Default "logcounts".

    -
    assayName
    +
    assayName

    A single characeter. The name for the corrected assay. Will be saved to assay. Default "LIMMA".

    -
    batch
    +
    batch

    A single character indicating a field in colData that annotates the batches of each cell; or a vector/factor with the same length as the number of cells. Default "batch".

    @@ -238,9 +240,7 @@

    Arguments

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with assay(inSCE, assayName) updated.

    @@ -267,15 +267,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runMNNCorrect.html b/docs/reference/runMNNCorrect.html index 88f702622..6cea72062 100644 --- a/docs/reference/runMNNCorrect.html +++ b/docs/reference/runMNNCorrect.html @@ -1,7 +1,5 @@ -Apply the mutual nearest neighbors (MNN) batch effect correction method to -SingleCellExperiment object — runMNNCorrect • singleCellTKApply the mutual nearest neighbors (MNN) batch effect correction method to SingleCellExperiment object — runMNNCorrect • singleCellTK - +
    @@ -31,7 +29,7 @@
    - +
    -

    Apply the mutual nearest neighbors (MNN) batch effect correction method to -SingleCellExperiment object

    +

    Apply the mutual nearest neighbors (MNN) batch effect correction method to SingleCellExperiment object

    Source: R/runBatchCorrection.R
    @@ -236,71 +233,71 @@

    Apply the mutual nearest neighbors (MNN) batch effect correction method to

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    useAssay
    +
    useAssay

    A single character indicating the name of the assay requiring batch correction. Default "logcounts".

    -
    batch
    +
    batch

    A single character indicating a field in colData that annotates the batches of each cell; or a vector/factor with the same length as the number of cells. Default "batch".

    -
    assayName
    +
    assayName

    A single characeter. The name for the corrected assay. Will be saved to assay. Default "MNN".

    -
    k
    +
    k

    An integer scalar specifying the number of nearest neighbors to consider when identifying MNNs. See "See Also". Default 20.

    -
    propK
    +
    propK

    A numeric scalar in (0, 1) specifying the proportion of cells in each dataset to use for mutual nearest neighbor searching. See "See Also". Default NULL.

    -
    sigma
    +
    sigma

    A numeric scalar specifying the bandwidth of the Gaussian smoothing kernel used to compute the correction vector for each cell. See "See Also". Default 0.1.

    -
    cosNormIn
    +
    cosNormIn

    A logical scalar indicating whether cosine normalization should be performed on the input data prior to calculating distances between cells. See "See Also". Default TRUE.

    -
    cosNormOut
    +
    cosNormOut

    A logical scalar indicating whether cosine normalization should be performed prior to computing corrected expression values. See "See Also". Default TRUE.

    -
    varAdj
    +
    varAdj

    A logical scalar indicating whether variance adjustment should be performed on the correction vectors. See "See Also". Default TRUE.

    -
    BPPARAM
    +
    BPPARAM

    A BiocParallelParam object specifying whether the PCA and nearest-neighbor searches should be parallelized.

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with assay(inSCE, assayName) updated.

    @@ -331,15 +328,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runModelGeneVar.html b/docs/reference/runModelGeneVar.html index cf2d28439..13d6a1ef8 100644 --- a/docs/reference/runModelGeneVar.html +++ b/docs/reference/runModelGeneVar.html @@ -1,13 +1,13 @@ -Calculate Variable Genes with Scran modelGeneVar — runModelGeneVar • singleCellTKCalculate Variable Genes with Scran modelGeneVar — runModelGeneVar • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -208,10 +208,10 @@

    Calculate Variable Genes with Scran modelGeneVar

    -

    Generates and stores variability data in the input -SingleCellExperiment object, using +

    Generates and stores variability data in the input +SingleCellExperiment object, using modelGeneVar method.

    -

    Also selects a specified number of top HVGs and store the logical selection +

    Also selects a specified number of top HVGs and store the logical selection in rowData.

    @@ -221,22 +221,20 @@

    Calculate Variable Genes with Scran modelGeneVar

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object

    -
    useAssay
    -

    A character string to specify an assay to compute variable +

    useAssay
    +

    A character string to specify an assay to compute variable features from. Default "logcounts".

    Value

    - - -

    inSCE updated with variable feature metrics in rowData

    - - +

    inSCE updated with variable feature metrics in rowData

    See also

    @@ -270,15 +268,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runNormalization.html b/docs/reference/runNormalization.html index d15162a80..922d3355a 100644 --- a/docs/reference/runNormalization.html +++ b/docs/reference/runNormalization.html @@ -1,5 +1,5 @@ -Run normalization/transformation with various methods — runNormalization • singleCellTKRun normalization/transformation with various methods — runNormalization • singleCellTK - +
    @@ -30,7 +30,7 @@
    - +
    @@ -235,72 +235,72 @@

    Run normalization/transformation with various methods

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Specify the name of the assay that should be used.

    -
    outAssayName
    +
    outAssayName

    Specify the name of the new output assay.

    -
    normalizationMethod
    +
    normalizationMethod

    Specify a normalization method from `LogNormalize`, `CLR`, `RC` and `SCTransform` from Seurat or `logNormCounts` and `CPM` from scater packages. Default NULL is set which will not run any normalization method.

    -
    scale
    +
    scale

    Logical value indicating if the data should be scaled using Z.Score. Default FALSE.

    -
    seuratScaleFactor
    +
    seuratScaleFactor

    Specify the `scaleFactor` argument if a Seurat normalization method is selected. Default is 10000. This parameter will not be used if methods other than seurat are selected.

    -
    transformation
    +
    transformation

    Specify the transformation options to run on the selected assay. Options include `log2` (base 2 log transformation), `log1p` (natural log + 1 transformation) and `sqrt` (square root). Default value is NULL, which will not run any transformation.

    -
    pseudocountsBeforeNorm
    +
    pseudocountsBeforeNorm

    Specify a numeric pseudo value that should be added to the assay before normalization is performed. Default is NULL, which will not add any value.

    -
    pseudocountsBeforeTransform
    +
    pseudocountsBeforeTransform

    Specify a numeric pseudo value that should be added to the assay before transformation is run. Default is NULL, which will not add any value.

    -
    trim
    +
    trim

    Specify a vector of two numeric values that should be used as the upper and lower trim values to trim the assay between these two values. For example, c(10,-10) will trim the values between 10 and -10. Default is NULL, which will not trim the data assay.

    -
    verbose
    +
    verbose

    Logical value indicating if progress messages should be displayed to the user. Default is TRUE.

    Value

    - - -

    Output SCE object with new normalized/transformed assay stored.

    +

    Output SCE object with new normalized/transformed assay stored.

    @@ -327,15 +327,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runPerCellQC.html b/docs/reference/runPerCellQC.html index 88f49fd23..a0a87e618 100644 --- a/docs/reference/runPerCellQC.html +++ b/docs/reference/runPerCellQC.html @@ -1,10 +1,10 @@ -Wrapper for calculating QC metrics with scater. — runPerCellQC • singleCellTKWrapper for calculating QC metrics with scater. — runPerCellQC • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -232,149 +232,149 @@

    Wrapper for calculating QC metrics with scater.

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    A string specifying which assay in the SCE to use. Default "counts".

    -
    mitoGeneLocation
    +
    mitoGeneLocation

    Character. Describes the location within inSCE where the gene identifiers in the mitochondrial gene sets should be located. -If set to "rownames" then the features will be searched for among -rownames(inSCE). This can also be set to one of the column names of -rowData(inSCE) in which case the gene identifies will be mapped to -that column in the rowData of inSCE. See +If set to "rownames" then the features will be searched for among +rownames(inSCE). This can also be set to one of the column names of +rowData(inSCE) in which case the gene identifies will be mapped to +that column in the rowData of inSCE. See featureIndex for more information. If this parameter is set to NULL, then no mitochondrial metrics will be calculated. Default "rownames".

    -
    mitoRef
    -

    Character. The species used to extract mitochondrial genes ID -from build-in mitochondrial geneset in SCTK. Available species options are +

    mitoRef
    +

    Character. The species used to extract mitochondrial genes ID +from build-in mitochondrial geneset in SCTK. Available species options are "human" and "mouse". Default is "human".

    -
    mitoIDType
    -

    Character. Types of mitochondrial gene id. SCTK supports -"symbol", "entrez", "ensembl" and -"ensemblTranscriptID". It is used with mitoRef to extract -mitochondrial genes from build-in mitochondrial geneset in SCTK. Default +

    mitoIDType
    +

    Character. Types of mitochondrial gene id. SCTK supports +"symbol", "entrez", "ensembl" and +"ensemblTranscriptID". It is used with mitoRef to extract +mitochondrial genes from build-in mitochondrial geneset in SCTK. Default NULL.

    -
    mitoPrefix
    -

    Character. The prefix used to get mitochondrial gene from -either rownames(inSCE) or columns of rowData(inSCE) specified -by mitoGeneLocation. This parameter is usually used to extract mitochondrial -genes from the gene symbol. For example, mitoPrefix = "^MT-" can be used +

    mitoPrefix
    +

    Character. The prefix used to get mitochondrial gene from +either rownames(inSCE) or columns of rowData(inSCE) specified +by mitoGeneLocation. This parameter is usually used to extract mitochondrial +genes from the gene symbol. For example, mitoPrefix = "^MT-" can be used to detect mito gene symbols like "MT-ND4". Note that case is ignored so "mt-" will still match "MT-ND4". Default "^MT-".

    -
    mitoID
    +
    mitoID

    Character. A vector of mitochondrial genes to be quantified.

    -
    collectionName
    +
    collectionName

    Character. Name of a GeneSetCollection obtained by using one of the importGeneSet* functions. Default NULL.

    -
    geneSetList
    +
    geneSetList

    List of gene sets to be quantified. The genes in the assays will be matched to the genes in the list based on geneSetListLocation. Default NULL.

    -
    geneSetListLocation
    -

    Character or numeric vector. If set to -'rownames', then the genes in geneSetList will be looked up in -rownames(inSCE). If another character is supplied, then genes will be -looked up in the column names of rowData(inSCE). A character vector -with the same length as geneSetList can be supplied if the IDs for -different gene sets are found in different places, including a mixture of +

    geneSetListLocation
    +

    Character or numeric vector. If set to +'rownames', then the genes in geneSetList will be looked up in +rownames(inSCE). If another character is supplied, then genes will be +looked up in the column names of rowData(inSCE). A character vector +with the same length as geneSetList can be supplied if the IDs for +different gene sets are found in different places, including a mixture of 'rownames' and rowData(inSCE). An integer or integer vector can -be supplied to denote the column index in rowData(inSCE). Default +be supplied to denote the column index in rowData(inSCE). Default 'rownames'.

    -
    geneSetCollection
    +
    geneSetCollection

    Class of GeneSetCollection from package GSEABase. The location of the gene IDs in inSCE should be in the description slot of each gene set and should follow the -same notation as geneSetListLocation. The function -getGmt can be used to read in gene sets from a GMT -file. If reading a GMT file, the second column for each gene set should be -the description denoting the location of the gene IDs in inSCE. These -gene sets will be included with those from geneSetList if both +same notation as geneSetListLocation. The function +getGmt can be used to read in gene sets from a GMT +file. If reading a GMT file, the second column for each gene set should be +the description denoting the location of the gene IDs in inSCE. These +gene sets will be included with those from geneSetList if both parameters are provided.

    -
    percent_top
    +
    percent_top

    An integer vector. Each element is treated as a number of -top genes to compute the percentage of library size occupied by the most +top genes to compute the percentage of library size occupied by the most highly expressed genes in each cell. Default c(50, 100, 200, 500).

    -
    use_altexps
    +
    use_altexps

    Logical scalar indicating whether QC statistics should -be computed for alternative Experiments in inSCE -(altExps(inSCE)). If TRUE, statistics are computed for all -alternative experiments. Alternatively, an integer or character vector -specifying the alternative Experiments to use to compute QC statistics. -Alternatively NULL, in which case alternative experiments are not +be computed for alternative Experiments in inSCE +(altExps(inSCE)). If TRUE, statistics are computed for all +alternative experiments. Alternatively, an integer or character vector +specifying the alternative Experiments to use to compute QC statistics. +Alternatively NULL, in which case alternative experiments are not used. Default FALSE.

    -
    flatten
    +
    flatten

    Logical scalar indicating whether the nested -DataFrame-class in the output should be flattened. Default +DataFrame-class in the output should be flattened. Default TRUE.

    -
    detectionLimit
    +
    detectionLimit

    A numeric scalar specifying the lower detection limit for expression. Default 0

    -
    BPPARAM
    +
    BPPARAM

    A BiocParallelParam object specifying whether the QC -calculations should be parallelized. Default +calculations should be parallelized. Default BiocParallel::SerialParam().

    Value

    - - -

    A SingleCellExperiment object with +

    A SingleCellExperiment object with cell QC metrics added to the colData slot.

    Details

    -

    This function allows multiple ways to import mitochondrial genes and quantify +

    This function allows multiple ways to import mitochondrial genes and quantify their expression in cells. mitoGeneLocation is required for all methods to point to the location within inSCE object that stores the -mitochondrial gene IDs or Symbols. The various ways mito genes can be -specified are:

    • A combination of mitoRef and mitoIDType +mitochondrial gene IDs or Symbols. The various ways mito genes can be +specified are:

      • A combination of mitoRef and mitoIDType parameters can be used to load pre-built mitochondrial gene sets stored in the SCTK package. These parameters are used in the importMitoGeneSet function.

      • The mitoPrefix parameter can be used to search for features - matching a particular pattern. The default pattern is an "MT-" + matching a particular pattern. The default pattern is an "MT-" at the beginning of the ID.

        • -

      • The mitoID parameter can be used to directy supply a vector of +

      • The mitoID parameter can be used to directy supply a vector of mitochondrial gene IDs or names. Only features that exactly match items in this vector will be included in the mitochondrial gene set.

    See also

    -

    addPerCellQC, +

    addPerCellQC, link{plotRunPerCellQCResults}, runCellQC

    @@ -384,8 +384,8 @@

    Examples

    mito.ix = grep("^MT-", rowData(sce)$feature_name) geneSet <- list("Mito"=rownames(sce)[mito.ix]) sce <- runPerCellQC(sce, geneSetList = geneSet) -#> Fri May 3 07:18:40 2024 ... Running 'perCellQCMetrics' -#> Fri May 3 07:18:40 2024 ...... Attempting to find mitochondrial genes by identifying features in 'rownames' that match mitochondrial genes from reference 'human' and ID type 'ensembl'. +#> Thu Feb 13 10:32:19 2025 ... Running 'perCellQCMetrics' +#> Thu Feb 13 10:32:19 2025 ...... Attempting to find mitochondrial genes by identifying features in 'rownames' that match mitochondrial genes from reference 'human' and ID type 'ensembl'.
    @@ -400,15 +400,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSCANORAMA.html b/docs/reference/runSCANORAMA.html index d61506424..ae95ecde1 100644 --- a/docs/reference/runSCANORAMA.html +++ b/docs/reference/runSCANORAMA.html @@ -1,13 +1,11 @@ -Apply the mutual nearest neighbors (MNN) batch effect correction method to -SingleCellExperiment object — runSCANORAMA • singleCellTKApply the mutual nearest neighbors (MNN) batch effect correction method to SingleCellExperiment object — runSCANORAMA • singleCellTK - +
    @@ -29,7 +27,7 @@
    - +
    -

    Apply the mutual nearest neighbors (MNN) batch effect correction method to -SingleCellExperiment object

    +

    Apply the mutual nearest neighbors (MNN) batch effect correction method to SingleCellExperiment object

    Source: R/runBatchCorrection.R
    @@ -229,53 +226,53 @@

    Apply the mutual nearest neighbors (MNN) batch effect correction method to

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    useAssay
    +
    useAssay

    A single character indicating the name of the assay requiring batch correction. Scanorama requires a transformed normalized expression assay. Default "logcounts".

    -
    batch
    +
    batch

    A single character indicating a field in colData that annotates the batches of each cell; or a vector/factor with the same length as the number of cells. Default "batch".

    -
    assayName
    +
    assayName

    A single characeter. The name for the corrected assay. Will be saved to assay. Default "SCANORAMA".

    -
    SIGMA
    +
    SIGMA

    A numeric scalar. Algorithmic parameter, correction smoothing parameter on Gaussian kernel. Default 15.

    -
    ALPHA
    +
    ALPHA

    A numeric scalar. Algorithmic parameter, alignment score minimum cutoff. Default 0.1.

    -
    KNN
    +
    KNN

    An integer. Algorithmic parameter, number of nearest neighbors to use for matching. Default 20.

    -
    approx
    +
    approx

    Boolean. Use approximate nearest neighbors, greatly speeds up matching runtime. Default TRUE.

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with assay(inSCE, assayName) updated.

    @@ -285,11 +282,11 @@

    References

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 data('sceBatches', package = 'singleCellTK')
 logcounts(sceBatches) <- log1p(counts(sceBatches))
 sceCorr <- runSCANORAMA(sceBatches, "ScaterLogNormCounts")
-}
+} # }
    @@ -304,15 +301,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSCMerge.html b/docs/reference/runSCMerge.html index 7273bc0e0..cd6eddef1 100644 --- a/docs/reference/runSCMerge.html +++ b/docs/reference/runSCMerge.html @@ -1,11 +1,11 @@ -Apply scMerge batch effect correction method to SingleCellExperiment object — runSCMerge • singleCellTKApply scMerge batch effect correction method to SingleCellExperiment object — runSCMerge • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -227,32 +227,34 @@

    Apply scMerge batch effect correction method to SingleCellExperiment object<

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    useAssay
    +
    useAssay

    A single character indicating the name of the assay requiring batch correction. Default "logcounts".

    -
    batch
    +
    batch

    A single character indicating a field in colData that annotates the batches. Default "batch".

    -
    assayName
    +
    assayName

    A single characeter. The name for the corrected assay. Will be saved to assay. Default "scMerge".

    -
    hvgExprs
    +
    hvgExprs

    A single characeter. The assay that to be used for highly variable genes identification. Default "counts".

    -
    seg
    +
    seg

    A vector of gene names or indices that specifies SEG (Stably Expressed Genes) set as negative control. Pre-defined dataset with human and mouse SEG lists is available with segList or @@ -261,30 +263,28 @@

    Arguments

    scSEGIndex.

    -
    kmeansK
    +
    kmeansK

    An integer vector. Indicating the kmeans' K-value for each batch (i.e. how many subclusters in each batch should exist), in order to -construct pseudo-replicates. The length of codekmeansK needs to be the same +construct pseudo-replicates. The length of kmeansK needs to be the same as the number of batches. Default NULL, and this value will be auto-detected by default, depending on cellType.

    -
    cellType
    +
    cellType

    A single character. A string indicating a field in colData(inSCE) that defines different cell types. Default 'cell_type'.

    -
    BPPARAM
    +
    BPPARAM

    A BiocParallelParam object specifying whether should be parallelized. Default BiocParallel::SerialParam().

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with assay(inSCE, assayName) updated.

    @@ -295,10 +295,10 @@

    References

    Examples

    data('sceBatches', package = 'singleCellTK')
-if (FALSE) {
+if (FALSE) { # \dontrun{
 logcounts(sceBatches) <- log1p(counts(sceBatches))
 sceCorr <- runSCMerge(sceBatches)
-}
+} # }
    @@ -313,15 +313,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScDblFinder.html b/docs/reference/runScDblFinder.html index 7c8c39f1c..d7fc45166 100644 --- a/docs/reference/runScDblFinder.html +++ b/docs/reference/runScDblFinder.html @@ -1,11 +1,11 @@ -Detect doublet cells using scDblFinder. — runScDblFinder • singleCellTKDetect doublet cells using scDblFinder. — runScDblFinder • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -225,54 +225,54 @@

    Detect doublet cells using

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    useAssay
    -

    A string specifying which assay in the SCE to use. Default +

    useAssay
    +

    A string specifying which assay in the SCE to use. Default "counts".

    -
    nNeighbors
    +
    nNeighbors

    Number of nearest neighbors used to calculate density for doublet detection. Default 50.

    -
    simDoublets
    -

    Number of simulated doublets created for doublet +

    simDoublets
    +

    Number of simulated doublets created for doublet detection. Default 10000.

    -
    seed
    -

    Seed for the random number generator, can be set to NULL. +

    seed
    +

    Seed for the random number generator, can be set to NULL. Default 12345.

    -
    BPPARAM
    -

    A BiocParallelParam-class object -specifying whether the neighbour searches should be parallelized. Default +

    BPPARAM
    +

    A BiocParallelParam-class object +specifying whether the neighbour searches should be parallelized. Default BiocParallel::SerialParam().

    Value

    - - -

    A SingleCellExperiment object with the +

    A SingleCellExperiment object with the scDblFinder QC outputs added to the colData slot.

    Details

    -

    This function is a wrapper function for -scDblFinder. runScDblFinder runs -scDblFinder for each sample within inSCE -iteratively. The resulting doublet scores for all cells will be appended to +

    This function is a wrapper function for +scDblFinder. runScDblFinder runs +scDblFinder for each sample within inSCE +iteratively. The resulting doublet scores for all cells will be appended to the colData of inSCE.

    @@ -282,7 +282,7 @@

    References

    See also

    -

    scDblFinder, +

    scDblFinder, plotScDblFinderResults, runCellQC

    @@ -291,7 +291,7 @@

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runScDblFinder(sce)
-#> Fri May  3 07:18:48 2024 ... Running 'scDblFinder'
+#> Thu Feb 13 10:32:24 2025 ... Running 'scDblFinder'
    @@ -306,15 +306,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScanpyFindClusters.html b/docs/reference/runScanpyFindClusters.html index 0a5caece0..414edcf44 100644 --- a/docs/reference/runScanpyFindClusters.html +++ b/docs/reference/runScanpyFindClusters.html @@ -1,15 +1,11 @@ -runScanpyFindClusters -Computes the clusters from the input sce object and stores them back in sce -object — runScanpyFindClusters • singleCellTKrunScanpyFindClusters Computes the clusters from the input sce object and stores them back in sce object — runScanpyFindClusters • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runScanpyFindClusters -Computes the clusters from the input sce object and stores them back in sce -object

    +

    runScanpyFindClusters Computes the clusters from the input sce object and stores them back in sce object

    Source: R/scanpyFunctions.R
    @@ -239,99 +233,99 @@

    runScanpyFindClusters

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object from which clusters should be computed and stored in

    -
    useAssay
    +
    useAssay

    Assay containing scaled counts to use for clustering.

    -
    useReducedDim
    -

    Reduction method to use for computing clusters. +

    useReducedDim
    +

    Reduction method to use for computing clusters. Default "scanpyPCA".

    -
    nNeighbors
    -

    The size of local neighborhood (in terms of number of -neighboring data points) used for manifold approximation. Larger values -result in more global views of the manifold, while smaller values result in +

    nNeighbors
    +

    The size of local neighborhood (in terms of number of +neighboring data points) used for manifold approximation. Larger values +result in more global views of the manifold, while smaller values result in more local data being preserved. Default 10.

    -
    dims
    +
    dims

    numeric value of how many components to use for computing clusters. Default 40.

    -
    method
    +
    method

    selected method to compute clusters. One of "louvain", and "leiden". Default louvain.

    -
    colDataName
    -

    Specify the name to give to this clustering result. +

    colDataName
    +

    Specify the name to give to this clustering result. Default is NULL that will generate a meaningful name automatically.

    -
    resolution
    -

    A parameter value controlling the coarseness of the +

    resolution
    +

    A parameter value controlling the coarseness of the clustering. Higher values lead to more clusters Default 1.

    -
    niterations
    -

    How many iterations of the Leiden clustering method to -perform. Positive values above 2 define the total number of iterations to +

    niterations
    +

    How many iterations of the Leiden clustering method to +perform. Positive values above 2 define the total number of iterations to perform, -1 has the method run until it reaches its optimal clustering. Default -1.

    -
    flavor
    +
    flavor

    Choose between to packages for computing the clustering. Default vtraag

    -
    use_weights
    +
    use_weights

    Boolean. Use weights from knn graph. Default FALSE

    -
    cor_method
    -

    correlation method to use. Options are ‘pearson’, +

    cor_method
    +

    correlation method to use. Options are ‘pearson’, ‘kendall’, and ‘spearman’. Default pearson.

    -
    inplace
    -

    If True, adds dendrogram information to annData object, +

    inplace
    +

    If True, adds dendrogram information to annData object, else this function returns the information. Default TRUE

    -
    externalReduction
    +
    externalReduction

    Pass DimReduce object if PCA computed through other libraries. Default NULL.

    -
    seed
    +
    seed

    Specify numeric value to set as a seed. Default 12345.

    Value

    - - -

    Updated sce object which now contains the computed clusters

    +

    Updated sce object which now contains the computed clusters

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
 sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
-}
+} # }

    @@ -346,15 +340,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScanpyFindHVG.html b/docs/reference/runScanpyFindHVG.html index 750aeed34..776e398c7 100644 --- a/docs/reference/runScanpyFindHVG.html +++ b/docs/reference/runScanpyFindHVG.html @@ -1,12 +1,10 @@ -runScanpyFindHVG -Find highly variable genes and store in the input sce object — runScanpyFindHVG • singleCellTKrunScanpyFindHVG Find highly variable genes and store in the input sce object — runScanpyFindHVG • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    runScanpyFindHVG -Find highly variable genes and store in the input sce object

    +

    runScanpyFindHVG Find highly variable genes and store in the input sce object

    Source: R/scanpyFunctions.R
    @@ -229,81 +226,79 @@

    runScanpyFindHVG

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object to compute highly variable genes from and to store back to it

    -
    useAssay
    +
    useAssay

    Specify the name of the assay to use for computation -of variable genes. It is recommended to use log normalized data, except when +of variable genes. It is recommended to use log normalized data, except when flavor='seurat_v3', in which counts data is expected.

    -
    method
    +
    method

    selected method to use for computation of highly variable genes. One of 'seurat', 'cell_ranger', or 'seurat_v3'. Default "seurat".

    -
    altExpName
    +
    altExpName

    Character. Name of the alternative experiment object to add if returnAsAltExp = TRUE. Default featureSubset.

    -
    altExp
    +
    altExp

    Logical value indicating if the input object is an altExperiment. Default FALSE.

    -
    hvgNumber
    +
    hvgNumber

    numeric value of how many genes to select as highly variable. Default 2000

    -
    minMean
    -

    If n_top_genes unequals None, this and all other cutoffs for -the means and the normalized dispersions are ignored. Ignored if +

    minMean
    +

    If n_top_genes unequals None, this and all other cutoffs for +the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'. Default 0.0125

    -
    maxMean
    -

    If n_top_genes unequals None, this and all other cutoffs for -the means and the normalized dispersions are ignored. Ignored if +

    maxMean
    +

    If n_top_genes unequals None, this and all other cutoffs for +the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'. Default 3

    -
    minDisp
    -

    If n_top_genes unequals None, this and all other cutoffs for -the means and the normalized dispersions are ignored. Ignored if +

    minDisp
    +

    If n_top_genes unequals None, this and all other cutoffs for +the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'. Default 0.5

    -
    maxDisp
    -

    If n_top_genes unequals None, this and all other cutoffs for -the means and the normalized dispersions are ignored. Ignored if +

    maxDisp
    +

    If n_top_genes unequals None, this and all other cutoffs for +the means and the normalized dispersions are ignored. Ignored if flavor='seurat_v3'. Default Inf

    Value

    - - -

    Updated SingleCellExperiment object with highly variable genes +

    Updated SingleCellExperiment object with highly variable genes computation stored getTopHVG, plotTopHVG

    - -

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 g <- getTopHVG(sce, method = "seurat", hvgNumber = 500)
-}
+} # }

    @@ -318,15 +313,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScanpyFindMarkers.html b/docs/reference/runScanpyFindMarkers.html index c2c718a30..38669dd48 100644 --- a/docs/reference/runScanpyFindMarkers.html +++ b/docs/reference/runScanpyFindMarkers.html @@ -1,9 +1,9 @@ -runScanpyFindMarkers — runScanpyFindMarkers • singleCellTKrunScanpyFindMarkers — runScanpyFindMarkers • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -222,64 +222,64 @@

    runScanpyFindMarkers

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    nGenes
    -

    The number of genes that appear in the returned tables. +

    nGenes
    +

    The number of genes that appear in the returned tables. Defaults to all genes.

    -
    useAssay
    +
    useAssay

    Specify the name of the assay to use for computation of marker genes. It is recommended to use log normalized assay.

    -
    colDataName
    -

    colData to use as the key of the observations grouping to +

    colDataName
    +

    colData to use as the key of the observations grouping to consider.

    -
    group1
    -

    Name of group1. Subset of groups, to which comparison shall be +

    group1
    +

    Name of group1. Subset of groups, to which comparison shall be restricted, or 'all' (default), for all groups.

    -
    group2
    -

    Name of group2. If 'rest', compare each group to the union of -the rest of the group. If a group identifier, compare with respect to this +

    group2
    +

    Name of group2. If 'rest', compare each group to the union of +the rest of the group. If a group identifier, compare with respect to this group. Default is 'rest'

    -
    test
    +
    test

    Test to use for DE. Default "t-test".

    -
    corr_method
    -

    p-value correction method. Used only for 't-test', +

    corr_method
    +

    p-value correction method. Used only for 't-test', 't-test_overestim_var', and 'wilcoxon'.

    Value

    - - -

    A SingleCellExperiment object that contains marker genes +

    A SingleCellExperiment object that contains marker genes populated in a data.frame stored inside metadata slot.

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
 sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
 sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
-}
+} # }
    @@ -294,15 +294,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScanpyNormalizeData.html b/docs/reference/runScanpyNormalizeData.html index a5597327e..335588741 100644 --- a/docs/reference/runScanpyNormalizeData.html +++ b/docs/reference/runScanpyNormalizeData.html @@ -1,15 +1,11 @@ -runScanpyNormalizeData -Wrapper for NormalizeData() function from scanpy library -Normalizes the sce object according to the input parameters — runScanpyNormalizeData • singleCellTKrunScanpyNormalizeData Wrapper for NormalizeData() function from scanpy library Normalizes the sce object according to the input parameters — runScanpyNormalizeData • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runScanpyNormalizeData -Wrapper for NormalizeData() function from scanpy library -Normalizes the sce object according to the input parameters

    +

    runScanpyNormalizeData Wrapper for NormalizeData() function from scanpy library Normalizes the sce object according to the input parameters

    Source: R/scanpyFunctions.R
    @@ -229,35 +223,35 @@

    runScanpyNormalizeData

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object to normalize

    -
    useAssay
    +
    useAssay

    Assay containing raw counts to use for normalization.

    -
    targetSum
    -

    If NULL, after normalization, each observation (cell) has a -total count equal to the median of total counts for observations (cells) +

    targetSum
    +

    If NULL, after normalization, each observation (cell) has a +total count equal to the median of total counts for observations (cells) before normalization. Default 1e4

    -
    maxFraction
    -

    Include cells that have more counts than max_fraction of +

    maxFraction
    +

    Include cells that have more counts than max_fraction of the original total counts in at least one cell. Default 0.05

    -
    normAssayName
    +
    normAssayName

    Name of new assay containing normalized data. Default scanpyNormData.

    Value

    - - -

    Normalized SingleCellExperiment object

    +

    Normalized SingleCellExperiment object

    @@ -265,9 +259,9 @@

    Examples

    data(scExample, package = "singleCellTK")
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 rownames(sce) <- rowData(sce)$feature_name
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
-}
+} # }

    @@ -282,15 +276,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScanpyPCA.html b/docs/reference/runScanpyPCA.html index aced39b28..902663731 100644 --- a/docs/reference/runScanpyPCA.html +++ b/docs/reference/runScanpyPCA.html @@ -1,15 +1,11 @@ -runScanpyPCA -Computes PCA on the input sce object and stores the calculated principal -components within the sce object — runScanpyPCA • singleCellTKrunScanpyPCA Computes PCA on the input sce object and stores the calculated principal components within the sce object — runScanpyPCA • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runScanpyPCA -Computes PCA on the input sce object and stores the calculated principal -components within the sce object

    +

    runScanpyPCA Computes PCA on the input sce object and stores the calculated principal components within the sce object

    Source: R/scanpyFunctions.R
    @@ -231,57 +225,57 @@

    runScanpyPCA

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object on which to compute PCA

    -
    useAssay
    +
    useAssay

    Assay containing scaled counts to use in PCA. Default "scanpyScaledData".

    -
    reducedDimName
    +
    reducedDimName

    Name of new reducedDims object containing Scanpy PCA. Default scanpyPCA.

    -
    nPCs
    +
    nPCs

    numeric value of how many components to compute. Default 50.

    -
    method
    -

    selected method to use for computation of pca. +

    method
    +

    selected method to use for computation of pca. One of 'arpack', 'randomized', 'auto' or 'lobpcg'. Default "arpack".

    -
    use_highly_variable
    -

    boolean value of whether to use highly variable +

    use_highly_variable
    +

    boolean value of whether to use highly variable genes only. By default uses them if they have been determined beforehand.

    -
    seed
    +
    seed

    Specify numeric value to set as a seed. Default 12345.

    Value

    - - -

    Updated SingleCellExperiment object which now contains the +

    Updated SingleCellExperiment object which now contains the computed principal components

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
 sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
-}
+} # }

    @@ -296,15 +290,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScanpyScaleData.html b/docs/reference/runScanpyScaleData.html index 586ae8224..b642f558d 100644 --- a/docs/reference/runScanpyScaleData.html +++ b/docs/reference/runScanpyScaleData.html @@ -1,12 +1,10 @@ -runScanpyScaleData -Scales the input sce object according to the input parameters — runScanpyScaleData • singleCellTKrunScanpyScaleData Scales the input sce object according to the input parameters — runScanpyScaleData • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    runScanpyScaleData -Scales the input sce object according to the input parameters

    +

    runScanpyScaleData Scales the input sce object according to the input parameters

    Source: R/scanpyFunctions.R
    @@ -222,33 +219,33 @@

    runScanpyScaleData

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object to scale

    -
    useAssay
    +
    useAssay

    Assay containing normalized counts to scale.

    -
    scaledAssayName
    +
    scaledAssayName

    Name of new assay containing scaled data. Default scanpyScaledData.

    Value

    - - -

    Scaled SingleCellExperiment object

    +

    Scaled SingleCellExperiment object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
-}
+} # }

    @@ -263,15 +260,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScanpyTSNE.html b/docs/reference/runScanpyTSNE.html index d9a37e421..9a511d889 100644 --- a/docs/reference/runScanpyTSNE.html +++ b/docs/reference/runScanpyTSNE.html @@ -1,15 +1,11 @@ -runScanpyTSNE -Computes tSNE from the given sce object and stores the tSNE computations back -into the sce object — runScanpyTSNE • singleCellTKrunScanpyTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object — runScanpyTSNE • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runScanpyTSNE -Computes tSNE from the given sce object and stores the tSNE computations back -into the sce object

    +

    runScanpyTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object

    Source: R/scanpyFunctions.R
    @@ -232,62 +226,62 @@

    runScanpyTSNE

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object on which to compute the tSNE

    -
    useAssay
    +
    useAssay

    Specify name of assay to use. Default is NULL, so useReducedDim param will be used instead.

    -
    useReducedDim
    +
    useReducedDim

    selected reduction method to use for computing tSNE. Default "scanpyPCA".

    -
    reducedDimName
    +
    reducedDimName

    Name of new reducedDims object containing Scanpy tSNE Default scanpyTSNE.

    -
    dims
    +
    dims

    Number of reduction components to use for tSNE computation. Default 40.

    -
    perplexity
    +
    perplexity

    Adjust the perplexity tuneable parameter for the underlying tSNE call. Default 30.

    -
    externalReduction
    +
    externalReduction

    Pass DimReduc object if PCA computed through other libraries. Default NULL.

    -
    seed
    +
    seed

    Specify numeric value to set as a seed. Default 12345.

    Value

    - - -

    Updated sce object with tSNE computations stored

    +

    Updated sce object with tSNE computations stored

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
 sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
 sce <- runScanpyTSNE(sce, useReducedDim = "scanpyPCA")
-}
+} # }

    @@ -302,15 +296,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScanpyUMAP.html b/docs/reference/runScanpyUMAP.html index 07e941a45..1ffee8ba4 100644 --- a/docs/reference/runScanpyUMAP.html +++ b/docs/reference/runScanpyUMAP.html @@ -1,15 +1,11 @@ -runScanpyUMAP -Computes UMAP from the given sce object and stores the UMAP computations back -into the sce object — runScanpyUMAP • singleCellTKrunScanpyUMAP Computes UMAP from the given sce object and stores the UMAP computations back into the sce object — runScanpyUMAP • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runScanpyUMAP -Computes UMAP from the given sce object and stores the UMAP computations back -into the sce object

    +

    runScanpyUMAP Computes UMAP from the given sce object and stores the UMAP computations back into the sce object

    Source: R/scanpyFunctions.R
    @@ -236,82 +230,82 @@

    runScanpyUMAP

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object on which to compute the UMAP

    -
    useAssay
    +
    useAssay

    Specify name of assay to use. Default is NULL, so useReducedDim param will be used instead.

    -
    useReducedDim
    -

    Reduction to use for computing UMAP. +

    useReducedDim
    +

    Reduction to use for computing UMAP. Default is "scanpyPCA".

    -
    reducedDimName
    +
    reducedDimName

    Name of new reducedDims object containing Scanpy UMAP Default scanpyUMAP.

    -
    dims
    +
    dims

    Numerical value of how many reduction components to use for UMAP computation. Default 40.

    -
    minDist
    +
    minDist

    Sets the "min_dist" parameter to the underlying UMAP call. Default 0.5.

    -
    nNeighbors
    +
    nNeighbors

    Sets the "n_neighbors" parameter to the underlying UMAP call. Default 10.

    -
    spread
    +
    spread

    Sets the "spread" parameter to the underlying UMAP call. Default 1.

    -
    alpha
    +
    alpha

    Sets the "alpha" parameter to the underlying UMAP call. Default 1.

    -
    gamma
    +
    gamma

    Sets the "gamma" parameter to the underlying UMAP call. Default 1.

    -
    externalReduction
    +
    externalReduction

    Pass DimReduce object if PCA computed through other libraries. Default NULL.

    -
    seed
    +
    seed

    Specify numeric value to set as a seed. Default 12345.

    Value

    - - -

    Updated sce object with UMAP computations stored

    +

    Updated sce object with UMAP computations stored

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
 sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
 sce <- runScanpyUMAP(sce, useReducedDim = "scanpyPCA")
-}
+} # }

    @@ -326,15 +320,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScranSNN.html b/docs/reference/runScranSNN.html index b2f558c88..1ce795790 100644 --- a/docs/reference/runScranSNN.html +++ b/docs/reference/runScranSNN.html @@ -1,12 +1,12 @@ -Get clustering with SNN graph — runScranSNN • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -235,66 +235,68 @@

    Get clustering with SNN graph

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    useReducedDim
    +
    useReducedDim

    A single character, specifying which low-dimension representation (reducedDim) to perform the clustering algorithm on. Default "PCA".

    -
    useAssay
    +
    useAssay

    A single character, specifying which assay to perform the clustering algorithm on. Default NULL.

    -
    useAltExp
    +
    useAltExp

    A single character, specifying the assay which altExp to perform the clustering algorithm on. Default NULL.

    -
    altExpAssay
    +
    altExpAssay

    A single character, specifying which assay in the chosen altExp to work on. Only used when useAltExp is set. Default "counts".

    -
    altExpRedDim
    +
    altExpRedDim

    A single character, specifying which reducedDim within the altExp specified by useAltExp to use. Only used when useAltExp is set. Default NULL.

    -
    clusterName
    +
    clusterName

    A single character, specifying the name to store the cluster label in colData. Default "cluster".

    -
    k
    +
    k

    An integer, the number of nearest neighbors used to construct the graph. Smaller value indicates higher resolution and larger number of clusters. Default 14.

    -
    nComp
    +
    nComp

    An integer. The number of components to use for graph construction. Default 10. See Detail.

    -
    weightType
    +
    weightType

    A single character, that specifies the edge weighing scheme when constructing the Shared Nearest-Neighbor (SNN) graph. Choose from "rank", "number", "jaccard". Default "jaccard".

    -
    algorithm
    +
    algorithm

    A single character, that specifies the community detection algorithm to work on the SNN graph. Choose from "leiden", "louvain", "walktrap", "infomap", "fastGreedy", @@ -302,26 +304,24 @@

    Arguments

    Detail.

    -
    BPPARAM
    +
    BPPARAM

    A BiocParallelParam object to use for processing the SNN graph generation step in parallel.

    -
    seed
    +
    seed

    Random seed for reproducibility of results. Default NULL will use global seed in use by the R environment.

    -
    ...
    +
    ...

    Other optional parameters passed to the igraph clustering functions. See Details.

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with factor cluster labeling updated in colData(inSCE)[[clusterName]].

    @@ -359,8 +359,8 @@

    Examples

    data("mouseBrainSubsetSCE")
 mouseBrainSubsetSCE <- runScranSNN(mouseBrainSubsetSCE,
                                    useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:19:05 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:19:06 2024 ...   Identified 2 clusters
+#> Thu Feb 13 10:32:46 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:32:46 2025 ...   Identified 2 clusters
    @@ -375,15 +375,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runScrublet.html b/docs/reference/runScrublet.html index 1a3348ff8..defab85b3 100644 --- a/docs/reference/runScrublet.html +++ b/docs/reference/runScrublet.html @@ -1,5 +1,5 @@ -Find doublets using scrublet. — runScrublet • singleCellTKFind doublets using scrublet. — runScrublet • singleCellTK - +
    @@ -31,7 +31,7 @@
    - +
    @@ -249,47 +249,49 @@

    Find doublets using scrublet.

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    sample
    -

    Character vector or colData variable name. Indicates which +

    sample
    +

    Character vector or colData variable name. Indicates which sample each cell belongs to. Default NULL.

    -
    useAssay
    -

    A string specifying which assay in the SCE to use. Default +

    useAssay
    +

    A string specifying which assay in the SCE to use. Default "counts".

    -
    simDoubletRatio
    +
    simDoubletRatio

    Numeric. Number of doublets to simulate relative to the number of observed transcriptomes. Default 2.0.

    -
    nNeighbors
    +
    nNeighbors

    Integer. Number of neighbors used to construct the KNN graph of observed transcriptomes and simulated doublets. If NULL, this is set to round(0.5 * sqrt(n_cells)). Default NULL.

    -
    minDist
    -

    Float Determines how tightly UMAP packs points together. If +

    minDist
    +

    Float Determines how tightly UMAP packs points together. If NULL, this is set to 0.1. Default NULL.

    -
    expectedDoubletRate
    +
    expectedDoubletRate

    The estimated doublet rate for the experiment. Default 0.1.

    -
    stdevDoubletRate
    -

    Uncertainty in the expected doublet rate. Default +

    stdevDoubletRate
    +

    Uncertainty in the expected doublet rate. Default 0.02.

    -
    syntheticDoubletUmiSubsampling
    +
    syntheticDoubletUmiSubsampling

    Numeric. Rate for sampling UMIs when creating synthetic doublets. If 1.0, each doublet is created by simply adding the UMIs from two randomly sampled observed transcriptomes. For @@ -297,104 +299,102 @@

    Arguments

    the specified rate. Defuault 1.0.

    -
    useApproxNeighbors
    +
    useApproxNeighbors

    Boolean. Use approximate nearest neighbor method (annoy) for the KNN classifier. Default TRUE.

    -
    distanceMetric
    +
    distanceMetric

    Character. Distance metric used when finding nearest neighbors. See detail. Default "euclidean".

    -
    getDoubletNeighborParents
    +
    getDoubletNeighborParents

    Boolean. If TRUE, return the parent transcriptomes that generated the doublet neighbors of each observed transcriptome. This information can be used to infer the cell states that generated a given doublet state. Default FALSE.

    -
    minCounts
    +
    minCounts

    Numeric. Used for gene filtering prior to PCA. Genes expressed at fewer than minCounts in fewer than minCells are excluded. Default 3.

    -
    minCells
    +
    minCells

    Integer. Used for gene filtering prior to PCA. Genes -expressed at fewer than minCounts in fewer than minCells are +expressed at fewer than minCounts in fewer than minCells are excluded. Default 3.

    -
    minGeneVariabilityPctl
    +
    minGeneVariabilityPctl

    Numeric. Used for gene filtering prior to PCA. Keep the most highly variable genes (in the top minGeneVariabilityPctl percentile), as measured by the v-statistic (Klein et al., Cell 2015). Default 85.

    -
    logTransform
    +
    logTransform

    Boolean. If TRUE, log-transform the counts matrix (log1p(TPM)). sklearn.decomposition.TruncatedSVD will be used for -dimensionality reduction, unless meanCenter is TRUE. Default +dimensionality reduction, unless meanCenter is TRUE. Default FALSE.

    -
    meanCenter
    +
    meanCenter

    If TRUE, center the data such that each gene has a mean of 0. sklearn.decomposition.PCA will be used for dimensionality reduction. Default TRUE.

    -
    normalizeVariance
    +
    normalizeVariance

    Boolean. If TRUE, normalize the data such that each gene has a variance of 1. sklearn.decomposition.TruncatedSVD will be used for dimensionality reduction, unless meanCenter is TRUE. Default TRUE.

    -
    nPrinComps
    +
    nPrinComps

    Integer. Number of principal components used to embed the transcriptomes prior to k-nearest-neighbor graph construction. Default 30.

    -
    tsneAngle
    +
    tsneAngle

    Float. Determines angular size of a distant node as measured -from a point in the t-SNE plot. If NULL, it is set to 0.5. +from a point in the t-SNE plot. If NULL, it is set to 0.5. Default NULL.

    -
    tsnePerplexity
    +
    tsnePerplexity

    Integer. The number of nearest neighbors that is used -in other manifold learning algorithms. If NULL, it is set to 30. +in other manifold learning algorithms. If NULL, it is set to 30. Default NULL.

    -
    verbose
    +
    verbose

    Boolean. If TRUE, print progress updates. Default TRUE.

    -
    seed
    -

    Seed for the random number generator, can be set to NULL. +

    seed
    +

    Seed for the random number generator, can be set to NULL. Default 12345.

    Value

    - - -

    A SingleCellExperiment object with +

    A SingleCellExperiment object with scrub_doublets output appended to the colData slot. The columns include scrublet_score and scrublet_call.

    Details

    -

    For the list of valid values for distanceMetric, see the -documentation for -annoy (if -useApproxNeighbors is TRUE) or +

    For the list of valid values for distanceMetric, see the +documentation for +annoy (if +useApproxNeighbors is TRUE) or sklearn.neighbors.NearestNeighbors (if useApproxNeighbors is FALSE).

    @@ -406,10 +406,10 @@

    See also

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
 sce <- runScrublet(sce)
-}
+} # }
    @@ -424,15 +424,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratFindClusters.html b/docs/reference/runSeuratFindClusters.html index 69832fa75..10815f1b4 100644 --- a/docs/reference/runSeuratFindClusters.html +++ b/docs/reference/runSeuratFindClusters.html @@ -1,15 +1,11 @@ -runSeuratFindClusters -Computes the clusters from the input sce object and stores them back in sce -object — runSeuratFindClusters • singleCellTKrunSeuratFindClusters Computes the clusters from the input sce object and stores them back in sce object — runSeuratFindClusters • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runSeuratFindClusters -Computes the clusters from the input sce object and stores them back in sce -object

    +

    runSeuratFindClusters Computes the clusters from the input sce object and stores them back in sce object

    Source: R/seuratFunctions.R
    @@ -234,73 +228,73 @@

    runSeuratFindClusters

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object from which clusters should be computed and stored in

    -
    useAssay
    +
    useAssay

    Assay containing scaled counts to use for clustering.

    -
    useReduction
    +
    useReduction

    Reduction method to use for computing clusters. One of "pca" or "ica". Default "pca".

    -
    dims
    +
    dims

    numeric value of how many components to use for computing clusters. Default 10.

    -
    algorithm
    +
    algorithm

    selected algorithm to compute clusters. One of "louvain", "multilevel", or "SLM". Use louvain for "original Louvain algorithm" and multilevel for "Louvain algorithm with multilevel refinement". Default louvain.

    -
    groupSingletons
    +
    groupSingletons

    boolean if singletons should be grouped together or not. Default TRUE.

    -
    resolution
    +
    resolution

    Set the resolution parameter to find larger (value above 1) or smaller (value below 1) number of communities. Default 0.8.

    -
    seed
    +
    seed

    Specify the seed value. Default 12345.

    -
    externalReduction
    +
    externalReduction

    Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.

    -
    verbose
    +
    verbose

    Logical value indicating if informative messages should be displayed. Default is TRUE.

    Value

    - - -

    Updated sce object which now contains the computed clusters

    +

    Updated sce object which now contains the computed clusters

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 sce <- runSeuratScaleData(sce, useAssay = "counts")
 sce <- runSeuratPCA(sce, useAssay = "counts")
 sce <- runSeuratFindClusters(sce, useAssay = "counts")
-}
+} # }

    @@ -315,15 +309,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratFindHVG.html b/docs/reference/runSeuratFindHVG.html index b357b2a83..949aec744 100644 --- a/docs/reference/runSeuratFindHVG.html +++ b/docs/reference/runSeuratFindHVG.html @@ -1,12 +1,10 @@ -runSeuratFindHVG -Find highly variable genes and store in the input sce object — runSeuratFindHVG • singleCellTKrunSeuratFindHVG Find highly variable genes and store in the input sce object — runSeuratFindHVG • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    runSeuratFindHVG -Find highly variable genes and store in the input sce object

    +

    runSeuratFindHVG Find highly variable genes and store in the input sce object

    Source: R/seuratFunctions.R
    @@ -226,52 +223,52 @@

    runSeuratFindHVG

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object to compute highly variable genes from and to store back to it

    -
    useAssay
    +
    useAssay

    Specify the name of the assay to use for computation of variable genes. It is recommended to use a raw counts assay with the "vst" method and normalized assay with all other methods. Default is "counts".

    -
    method
    +
    method

    selected method to use for computation of highly variable genes. One of 'vst', 'dispersion', or 'mean.var.plot'. Default "vst" which uses the raw counts. All other methods use normalized counts.

    -
    hvgNumber
    +
    hvgNumber

    numeric value of how many genes to select as highly variable. Default 2000

    -
    createFeatureSubset
    +
    createFeatureSubset

    Specify a name of the subset to create for the identified variable features. Default is "hvf". Leave it NULL if you do not want to create a subset of variable features.

    -
    altExp
    +
    altExp

    Logical value indicating if the input object is an altExperiment. Default FALSE.

    -
    verbose
    +
    verbose

    Logical value indicating if informative messages should be displayed. Default is TRUE.

    Value

    - - -

    Updated SingleCellExperiment object with highly variable genes +

    Updated SingleCellExperiment object with highly variable genes computation stored

    @@ -285,7 +282,7 @@

    Examples

    data(scExample, package = "singleCellTK")
 sce <- runSeuratFindHVG(sce)
 #> Finding variable features for layer counts
-#> Fri May  3 07:19:08 2024 ... Feature subset variable 'hvf' created.
+#> Thu Feb 13 10:32:49 2025 ... Feature subset variable 'hvf' created.

    @@ -300,15 +297,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratFindMarkers.html b/docs/reference/runSeuratFindMarkers.html index a4c3c0aa5..7952d6f1b 100644 --- a/docs/reference/runSeuratFindMarkers.html +++ b/docs/reference/runSeuratFindMarkers.html @@ -1,9 +1,9 @@ -runSeuratFindMarkers — runSeuratFindMarkers • singleCellTKrunSeuratFindMarkers — runSeuratFindMarkers • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -226,65 +226,65 @@

    runSeuratFindMarkers

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    cells1
    +
    cells1

    A list of sample names included in group1.

    -
    cells2
    +
    cells2

    A list of sample names included in group2.

    -
    group1
    +
    group1

    Name of group1.

    -
    group2
    +
    group2

    Name of group2.

    -
    allGroup
    +
    allGroup

    Name of all groups.

    -
    conserved
    +
    conserved

    Logical value indicating if markers conserved between two groups should be identified. Default is FALSE.

    -
    test
    +
    test

    Test to use for DE. Default "wilcox".

    -
    onlyPos
    +
    onlyPos

    Logical value indicating if only positive markers should be returned.

    -
    minPCT
    +
    minPCT

    Numeric value indicating the minimum fraction of min.pct cells in which genes are detected. Default is 0.1.

    -
    threshUse
    +
    threshUse

    Numeric value indicating the logFC threshold value on which on average, at least X-fold difference (log-scale) between the two groups of cells exists. Default is 0.25.

    -
    verbose
    +
    verbose

    Logical value indicating if informative messages should be displayed. Default is TRUE.

    Value

    - - -

    A SingleCellExperiment object that contains marker genes +

    A SingleCellExperiment object that contains marker genes populated in a data.frame stored inside metadata slot.

    @@ -300,15 +300,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratHeatmap.html b/docs/reference/runSeuratHeatmap.html index 2f04bfea0..cb3b8827f 100644 --- a/docs/reference/runSeuratHeatmap.html +++ b/docs/reference/runSeuratHeatmap.html @@ -1,12 +1,10 @@ -runSeuratHeatmap -Computes the heatmap plot object from the pca slot in the input sce object — runSeuratHeatmap • singleCellTKrunSeuratHeatmap Computes the heatmap plot object from the pca slot in the input sce object — runSeuratHeatmap • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    runSeuratHeatmap -Computes the heatmap plot object from the pca slot in the input sce object

    +

    runSeuratHeatmap Computes the heatmap plot object from the pca slot in the input sce object

    Source: R/seuratFunctions.R
    @@ -231,86 +228,86 @@

    runSeuratHeatmap

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object from which to compute heatmap (pca should be computed)

    -
    useAssay
    +
    useAssay

    Specify name of the assay that will be scaled by this function. The output scaled assay will be used for computation of the heatmap.

    -
    useReduction
    +
    useReduction

    Reduction method to use for computing clusters. One of "pca" or "ica". Default "pca".

    -
    dims
    +
    dims

    Number of components to generate heatmap plot objects. If NULL, a heatmap will be generated for all components. Default NULL.

    -
    nfeatures
    +
    nfeatures

    Number of features to include in the heatmap. Default 30.

    -
    cells
    +
    cells

    Numeric value indicating the number of top cells to plot. Default is NULL which indicates all cells.

    -
    ncol
    +
    ncol

    Numeric value indicating the number of columns to use for plot. Default is NULL which will automatically compute accordingly.

    -
    balanced
    +
    balanced

    Plot equal number of genes with positive and negative scores. Default is TRUE.

    -
    fast
    +
    fast

    See DimHeatmap for more information. Default TRUE.

    -
    combine
    +
    combine

    See DimHeatmap for more information. Default TRUE.

    -
    raster
    +
    raster

    See DimHeatmap for more information. Default TRUE.

    -
    externalReduction
    +
    externalReduction

    Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.

    Value

    - - -

    plot object

    +

    plot object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 sce <- runSeuratScaleData(sce, useAssay = "counts")
 sce <- runSeuratPCA(sce, useAssay = "counts")
 heatmap <- runSeuratHeatmap(sce, useAssay = "counts")
 plotSeuratHeatmap(heatmap)
-}
+} # }

    @@ -325,15 +322,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratICA.html b/docs/reference/runSeuratICA.html index af9ff65cb..4fbef18ae 100644 --- a/docs/reference/runSeuratICA.html +++ b/docs/reference/runSeuratICA.html @@ -1,15 +1,11 @@ -runSeuratICA -Computes ICA on the input sce object and stores the calculated independent -components within the sce object — runSeuratICA • singleCellTKrunSeuratICA Computes ICA on the input sce object and stores the calculated independent components within the sce object — runSeuratICA • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runSeuratICA -Computes ICA on the input sce object and stores the calculated independent -components within the sce object

    +

    runSeuratICA Computes ICA on the input sce object and stores the calculated independent components within the sce object

    Source: R/seuratFunctions.R
    @@ -232,50 +226,50 @@

    runSeuratICA

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object on which to compute ICA

    -
    useAssay
    +
    useAssay

    Assay containing scaled counts to use in ICA.

    -
    useFeatureSubset
    +
    useFeatureSubset

    Subset of feature to use for dimension reduction. A character string indicating a rowData variable that stores the logical vector of HVG selection, or a vector that can subset the rows of inSCE. Default NULL.

    -
    scale
    +
    scale

    Logical scalar, whether to standardize the expression values using ScaleData. Default TRUE.

    -
    reducedDimName
    +
    reducedDimName

    Name of new reducedDims object containing Seurat ICA Default seuratICA.

    -
    nics
    +
    nics

    Number of independent components to compute. Default 20.

    -
    seed
    +
    seed

    Random seed for reproducibility of results. Default NULL will use global seed in use by the R environment.

    -
    verbose
    +
    verbose

    Logical value indicating if informative messages should be displayed. Default is TRUE.

    Value

    - - -

    Updated SingleCellExperiment object which now contains the +

    Updated SingleCellExperiment object which now contains the computed independent components

    @@ -293,12 +287,12 @@

    Details

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 sce <- runSeuratScaleData(sce, useAssay = "counts")
 sce <- runSeuratICA(sce, useAssay = "counts")
-}
+} # }
    @@ -313,15 +307,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratIntegration.html b/docs/reference/runSeuratIntegration.html index 378f9190b..1eb79e0c3 100644 --- a/docs/reference/runSeuratIntegration.html +++ b/docs/reference/runSeuratIntegration.html @@ -1,12 +1,10 @@ -runSeuratIntegration -A wrapper function to Seurat Batch-Correction/Integration workflow. — runSeuratIntegration • singleCellTKrunSeuratIntegration A wrapper function to Seurat Batch-Correction/Integration workflow. — runSeuratIntegration • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    runSeuratIntegration -A wrapper function to Seurat Batch-Correction/Integration workflow.

    +

    runSeuratIntegration A wrapper function to Seurat Batch-Correction/Integration workflow.

    Source: R/seuratFunctions.R
    @@ -227,48 +224,48 @@

    runSeuratIntegration

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object that contains the assay to batch-correct.

    -
    useAssay
    +
    useAssay

    Assay to batch-correct.

    -
    batch
    +
    batch

    Batch variable from colData slot of SingleCellExperiment object.

    -
    newAssayName
    +
    newAssayName

    Assay name for the batch-corrected output assay.

    -
    kAnchor
    +
    kAnchor

    Number of neighbours to use for finding the anchors in the FindIntegrationAnchors function.

    -
    kFilter
    +
    kFilter

    Number of neighbours to use for filtering the anchors in the FindIntegrationAnchors function.

    -
    kWeight
    +
    kWeight

    Number of neighbours to use when weigthing the anchors in the IntegrateData function.

    -
    ndims
    +
    ndims

    Number of dimensions to use. Default 10.

    Value

    - - -

    A SingleCellExperiment object that contains the +

    A SingleCellExperiment object that contains the batch-corrected assay inside the altExp slot of the object

    @@ -284,15 +281,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratJackStraw.html b/docs/reference/runSeuratJackStraw.html index abbeebd95..84a404f88 100644 --- a/docs/reference/runSeuratJackStraw.html +++ b/docs/reference/runSeuratJackStraw.html @@ -1,12 +1,10 @@ -runSeuratJackStraw -Compute jackstraw plot and store the computations in the input sce object — runSeuratJackStraw • singleCellTKrunSeuratJackStraw Compute jackstraw plot and store the computations in the input sce object — runSeuratJackStraw • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    runSeuratJackStraw -Compute jackstraw plot and store the computations in the input sce object

    +

    runSeuratJackStraw Compute jackstraw plot and store the computations in the input sce object

    Source: R/seuratFunctions.R
    @@ -225,57 +222,57 @@

    runSeuratJackStraw

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object on which to compute and store jackstraw plot

    -
    useAssay
    +
    useAssay

    Specify name of the assay to use for scaling. Assay name provided against this parameter is scaled by the function and used for the computation of JackStraw scores along with the reduced dimensions specified by the dims parameter.

    -
    dims
    +
    dims

    Number of components to test in Jackstraw. If NULL, then all components are used. Default NULL.

    -
    numReplicate
    +
    numReplicate

    Numeric value indicating the number of replicate samplings to perform. Default value is 100.

    -
    propFreq
    +
    propFreq

    Numeric value indicating the proportion of data to randomly permute for each replicate. Default value is 0.025.

    -
    externalReduction
    +
    externalReduction

    Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.

    Value

    - - -

    Updated SingleCellExperiment object with jackstraw +

    Updated SingleCellExperiment object with jackstraw computations stored in it

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 sce <- runSeuratScaleData(sce, useAssay = "counts")
 sce <- runSeuratPCA(sce, useAssay = "counts")
 sce <- runSeuratJackStraw(sce, useAssay = "counts")
-}
+} # }

    @@ -290,15 +287,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratNormalizeData.html b/docs/reference/runSeuratNormalizeData.html index b2855a926..dcd041a72 100644 --- a/docs/reference/runSeuratNormalizeData.html +++ b/docs/reference/runSeuratNormalizeData.html @@ -1,15 +1,11 @@ -runSeuratNormalizeData -Wrapper for NormalizeData() function from seurat library -Normalizes the sce object according to the input parameters — runSeuratNormalizeData • singleCellTKrunSeuratNormalizeData Wrapper for NormalizeData() function from seurat library Normalizes the sce object according to the input parameters — runSeuratNormalizeData • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runSeuratNormalizeData -Wrapper for NormalizeData() function from seurat library -Normalizes the sce object according to the input parameters

    +

    runSeuratNormalizeData Wrapper for NormalizeData() function from seurat library Normalizes the sce object according to the input parameters

    Source: R/seuratFunctions.R
    @@ -230,47 +224,47 @@

    runSeuratNormalizeData

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object to normalize

    -
    useAssay
    +
    useAssay

    Assay containing raw counts to use for normalization.

    -
    normAssayName
    +
    normAssayName

    Name of new assay containing normalized data. Default seuratNormData.

    -
    normalizationMethod
    +
    normalizationMethod

    selected normalization method. Default "LogNormalize".

    -
    scaleFactor
    +
    scaleFactor

    numeric value that represents the scaling factor. Default 10000.

    -
    verbose
    +
    verbose

    Logical value indicating if informative messages should be displayed. Default is TRUE.

    Value

    - - -

    Normalized SingleCellExperiment object

    +

    Normalized SingleCellExperiment object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
-}
+} # }

    @@ -285,15 +279,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratPCA.html b/docs/reference/runSeuratPCA.html index e4ec173a2..04a117add 100644 --- a/docs/reference/runSeuratPCA.html +++ b/docs/reference/runSeuratPCA.html @@ -1,15 +1,11 @@ -runSeuratPCA -Computes PCA on the input sce object and stores the calculated principal -components within the sce object — runSeuratPCA • singleCellTKrunSeuratPCA Computes PCA on the input sce object and stores the calculated principal components within the sce object — runSeuratPCA • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runSeuratPCA -Computes PCA on the input sce object and stores the calculated principal -components within the sce object

    +

    runSeuratPCA Computes PCA on the input sce object and stores the calculated principal components within the sce object

    Source: R/seuratFunctions.R
    @@ -232,52 +226,52 @@

    runSeuratPCA

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object on which to compute PCA

    -
    useAssay
    +
    useAssay

    Assay containing scaled counts to use in PCA. Default "seuratNormData".

    -
    useFeatureSubset
    +
    useFeatureSubset

    Subset of feature to use for dimension reduction. A character string indicating a rowData variable that stores the logical vector of HVG selection, or a vector that can subset the rows of inSCE. Default "hvf".

    -
    scale
    +
    scale

    Logical scalar, whether to standardize the expression values using ScaleData. Default TRUE.

    -
    reducedDimName
    +
    reducedDimName

    Name of new reducedDims object containing Seurat PCA. Default seuratPCA.

    -
    nPCs
    +
    nPCs

    numeric value of how many components to compute. Default 20.

    -
    seed
    +
    seed

    Random seed for reproducibility of results. Default NULL will use global seed in use by the R environment.

    -
    verbose
    +
    verbose

    Logical value indicating if informative messages should be displayed. Default is TRUE.

    Value

    - - -

    Updated SingleCellExperiment object which now contains the +

    Updated SingleCellExperiment object which now contains the computed principal components

    @@ -295,13 +289,13 @@

    Details

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 sce <- setTopHVG(sce, method = "vst", featureSubsetName = "hvf")
 sce <- runSeuratScaleData(sce, useAssay = "counts")
 sce <- runSeuratPCA(sce, useAssay = "counts")
-}
+} # }
    @@ -316,15 +310,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratSCTransform.html b/docs/reference/runSeuratSCTransform.html index 514155e47..d19e570df 100644 --- a/docs/reference/runSeuratSCTransform.html +++ b/docs/reference/runSeuratSCTransform.html @@ -1,15 +1,11 @@ -runSeuratSCTransform -Runs the SCTransform function to transform/normalize the input -data — runSeuratSCTransform • singleCellTKrunSeuratSCTransform Runs the SCTransform function to transform/normalize the input data — runSeuratSCTransform • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runSeuratSCTransform -Runs the SCTransform function to transform/normalize the input -data

    +

    runSeuratSCTransform Runs the SCTransform function to transform/normalize the input data

    Source: R/seuratFunctions.R
    @@ -228,29 +222,29 @@

    runSeuratSCTransform

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    normAssayName
    +
    normAssayName

    Name for the output data assay. Default "SCTCounts".

    -
    useAssay
    +
    useAssay

    Name for the input data assay. Default "counts".

    -
    verbose
    +
    verbose

    Logical value indicating if informative messages should be displayed. Default is TRUE.

    Value

    - - -

    Updated SingleCellExperiment object containing the transformed data

    +

    Updated SingleCellExperiment object containing the transformed data

    @@ -271,11 +265,11 @@

    Examples

    #> Model formula is y ~ log_umi #> Get Negative Binomial regression parameters per gene #> Using 2000 genes, 30 cells -#> Found 96 outliers - those will be ignored in fitting/regularization step +#> Found 95 outliers - those will be ignored in fitting/regularization step #> Second step: Get residuals using fitted parameters for 2282 genes #> Computing corrected count matrix for 2282 genes #> Calculating gene attributes -#> Wall clock passed: Time difference of 21.10225 secs +#> Wall clock passed: Time difference of 35.05846 secs #> Determine variable features #> Centering data matrix #> Set default assay to SCTransform @@ -293,15 +287,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratScaleData.html b/docs/reference/runSeuratScaleData.html index e1d450e47..6a2a69ce2 100644 --- a/docs/reference/runSeuratScaleData.html +++ b/docs/reference/runSeuratScaleData.html @@ -1,12 +1,10 @@ -runSeuratScaleData -Scales the input sce object according to the input parameters — runSeuratScaleData • singleCellTKrunSeuratScaleData Scales the input sce object according to the input parameters — runSeuratScaleData • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    runSeuratScaleData -Scales the input sce object according to the input parameters

    +

    runSeuratScaleData Scales the input sce object according to the input parameters

    Source: R/seuratFunctions.R
    @@ -227,56 +224,56 @@

    runSeuratScaleData

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object to scale

    -
    useAssay
    +
    useAssay

    Assay containing normalized counts to scale.

    -
    scaledAssayName
    +
    scaledAssayName

    Name of new assay containing scaled data. Default seuratScaledData.

    -
    model
    +
    model

    selected model to use for scaling data. Default "linear".

    -
    scale
    +
    scale

    boolean if data should be scaled or not. Default TRUE.

    -
    center
    +
    center

    boolean if data should be centered or not. Default TRUE

    -
    scaleMax
    +
    scaleMax

    maximum numeric value to return for scaled data. Default 10.

    -
    verbose
    +
    verbose

    Logical value indicating if informative messages should be displayed. Default is TRUE.

    Value

    - - -

    Scaled SingleCellExperiment object

    +

    Scaled SingleCellExperiment object

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 sce <- runSeuratScaleData(sce, useAssay = "counts")
-}
+} # }

    @@ -291,15 +288,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratTSNE.html b/docs/reference/runSeuratTSNE.html index ed0956141..9e35c1046 100644 --- a/docs/reference/runSeuratTSNE.html +++ b/docs/reference/runSeuratTSNE.html @@ -1,15 +1,11 @@ -runSeuratTSNE -Computes tSNE from the given sce object and stores the tSNE computations back -into the sce object — runSeuratTSNE • singleCellTKrunSeuratTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object — runSeuratTSNE • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runSeuratTSNE -Computes tSNE from the given sce object and stores the tSNE computations back -into the sce object

    +

    runSeuratTSNE Computes tSNE from the given sce object and stores the tSNE computations back into the sce object

    Source: R/seuratFunctions.R
    @@ -231,45 +225,45 @@

    runSeuratTSNE

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object on which to compute the tSNE

    -
    useReduction
    +
    useReduction

    selected reduction algorithm to use for computing tSNE. One of "pca" or "ica". Default "pca".

    -
    reducedDimName
    +
    reducedDimName

    Name of new reducedDims object containing Seurat tSNE Default seuratTSNE.

    -
    dims
    +
    dims

    Number of reduction components to use for tSNE computation. Default 10.

    -
    perplexity
    +
    perplexity

    Adjust the perplexity tuneable parameter for the underlying tSNE call. Default 30.

    -
    externalReduction
    +
    externalReduction

    Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.

    -
    seed
    +
    seed

    Random seed for reproducibility of results. Default 1.

    Value

    - - -

    Updated sce object with tSNE computations stored

    +

    Updated sce object with tSNE computations stored

    @@ -284,15 +278,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSeuratUMAP.html b/docs/reference/runSeuratUMAP.html index 91e864a8f..bb11fd40a 100644 --- a/docs/reference/runSeuratUMAP.html +++ b/docs/reference/runSeuratUMAP.html @@ -1,15 +1,11 @@ -runSeuratUMAP -Computes UMAP from the given sce object and stores the UMAP computations back -into the sce object — runSeuratUMAP • singleCellTKrunSeuratUMAP Computes UMAP from the given sce object and stores the UMAP computations back into the sce object — runSeuratUMAP • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    runSeuratUMAP -Computes UMAP from the given sce object and stores the UMAP computations back -into the sce object

    +

    runSeuratUMAP Computes UMAP from the given sce object and stores the UMAP computations back into the sce object

    Source: R/seuratFunctions.R
    @@ -234,74 +228,74 @@

    runSeuratUMAP

    Arguments

    -
    inSCE
    + + +
    inSCE

    (sce) object on which to compute the UMAP

    -
    useReduction
    +
    useReduction

    Reduction to use for computing UMAP. One of "pca" or "ica". Default is "pca".

    -
    reducedDimName
    +
    reducedDimName

    Name of new reducedDims object containing Seurat UMAP Default seuratUMAP.

    -
    dims
    +
    dims

    Numerical value of how many reduction components to use for UMAP computation. Default 10.

    -
    minDist
    +
    minDist

    Sets the "min.dist" parameter to the underlying UMAP call. See RunUMAP for more information. Default 0.3.

    -
    nNeighbors
    +
    nNeighbors

    Sets the "n.neighbors" parameter to the underlying UMAP call. See RunUMAP for more information. Default 30L.

    -
    spread
    +
    spread

    Sets the "spread" parameter to the underlying UMAP call. See RunUMAP for more information. Default 1.

    -
    externalReduction
    +
    externalReduction

    Pass DimReduc object if PCA/ICA computed through other libraries. Default NULL.

    -
    seed
    +
    seed

    Random seed for reproducibility of results. Default 42.

    -
    verbose
    +
    verbose

    Logical value indicating if informative messages should be displayed. Default is TRUE.

    Value

    - - -

    Updated sce object with UMAP computations stored

    +

    Updated sce object with UMAP computations stored

    Examples

    data(scExample, package = "singleCellTK")
-if (FALSE) {
+if (FALSE) { # \dontrun{
 sce <- runSeuratNormalizeData(sce, useAssay = "counts")
 sce <- runSeuratFindHVG(sce, useAssay = "counts")
 sce <- runSeuratScaleData(sce, useAssay = "counts")
 sce <- runSeuratPCA(sce, useAssay = "counts")
 sce <- runSeuratFindClusters(sce, useAssay = "counts")
 sce <- runSeuratUMAP(sce, useReduction = "pca")
-}
+} # }

    @@ -316,15 +310,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSingleR.html b/docs/reference/runSingleR.html index 50443abd5..af841acee 100644 --- a/docs/reference/runSingleR.html +++ b/docs/reference/runSingleR.html @@ -1,12 +1,12 @@ -Label cell types with SingleR — runSingleR • singleCellTKLabel cell types with SingleR — runSingleR • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -228,46 +228,48 @@

    Label cell types with SingleR

    Arguments

    -
    inSCE
    + + +
    inSCE

    SingleCellExperiment inherited object. Required.

    -
    useAssay
    +
    useAssay

    character. A string specifying which assay to use for expression profile identification. Required.

    -
    useSCERef
    +
    useSCERef

    SingleCellExperiment inherited object. An optional customized reference dataset. Default NULL.

    -
    labelColName
    +
    labelColName

    A single character. A string specifying the column in colData(useSCERef) that stores the cell type labeling. Default NULL.

    -
    useBltinRef
    +
    useBltinRef

    A single character. A string that specifies a reference provided by SingleR. Choose from "hpca", "bpe", "mp", "dice", "immgen", "mouse", "zeisel". See detail. Default "hpca".

    -
    level
    +
    level

    A string for cell type labeling level. Used only when using some of the SingleR built-in references. Choose from "main", "fine", "ont". Default "fine".

    -
    featureType
    +
    featureType

    A string for whether to use gene symbols or Ensembl IDs when using a SingleR built-in reference. Should be set based on the type of rownames of inSCE. Choose from "symbol", "ensembl". Default "symbol".

    -
    labelByCluster
    +
    labelByCluster

    A single character. A string specifying the column name in colData(inSCE) that stores clustering labels. Use this when users want to only label cells on cluster level, instead of performing calculation @@ -276,9 +278,7 @@

    Arguments

    Value

    - - -

    Input SCE object with cell type labeling updated in +

    Input SCE object with cell type labeling updated in colData(inSCE), together with scoring metrics.

    @@ -301,15 +301,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runSoupX.html b/docs/reference/runSoupX.html index 63dc956ee..2407cd730 100644 --- a/docs/reference/runSoupX.html +++ b/docs/reference/runSoupX.html @@ -1,5 +1,5 @@ -Detecting and correct contamination with SoupX — runSoupX • singleCellTKDetecting and correct contamination with SoupX — runSoupX • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -243,11 +243,13 @@

    Detecting and correct contamination with SoupX

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    -
    sample
    +
    sample

    A single character specifying a name that can be found in colData(inSCE) to directly use the cell annotation; or a character vector with as many elements as cells to indicates which sample each cell @@ -255,68 +257,68 @@

    Arguments

    NULL.

    -
    useAssay
    +
    useAssay

    A single character string specifying which assay in inSCE to use. Default 'counts'.

    -
    background
    +
    background

    A numeric matrix of counts or a SingleCellExperiment object with the matrix in assay slot. It should have the same structure as inSCE except it contains the matrix including empty droplets. Default NULL.

    -
    bgAssayName
    +
    bgAssayName

    A single character string specifying which assay in background to use when background is a SingleCellExperiment object. If NULL, the function will use the same value as useAssay. Default NULL.

    -
    bgBatch
    +
    bgBatch

    The same thing as sample but for background. Can be a single character only when background is a SingleCellExperiment object. Default NULL.

    -
    assayName
    +
    assayName

    A single character string of the output corrected matrix. Default "SoupX" when not using a background, otherwise, "SoupX_bg".

    -
    cluster
    +
    cluster

    Prior knowledge of clustering labels on cells. A single character string for specifying clustering label stored in colData(inSCE), or a character vector with as many elements as cells. When not supplied, quickCluster method will be applied.

    -
    reducedDimName
    +
    reducedDimName

    A single character string of the prefix of output corrected embedding matrix for each sample. Default "SoupX_UMAP_" when not using a background, otherwise, "SoupX_bg_UMAP_".

    -
    tfidfMin
    +
    tfidfMin

    Numeric. Minimum value of tfidf to accept for a marker gene. Default 1. See ?SoupX::autoEstCont.

    -
    soupQuantile
    +
    soupQuantile

    Numeric. Only use genes that are at or above this expression quantile in the soup. This prevents inaccurate estimates due to using genes with poorly constrained contribution to the background. Default 0.9. See ?SoupX::autoEstCont.

    -
    maxMarkers
    +
    maxMarkers

    Integer. If we have heaps of good markers, keep only the best maxMarkers of them. Default 100. See ?SoupX::autoEstCont.

    -
    contaminationRange
    +
    contaminationRange

    Numeric vector of two elements. This constrains the contamination fraction to lie within this range. Must be between 0 and 1. The high end of this range is passed to @@ -325,47 +327,47 @@

    Arguments

    ?SoupX::autoEstCont.

    -
    rhoMaxFDR
    +
    rhoMaxFDR

    Numeric. False discovery rate passed to estimateNonExpressingCells, to test if rho is less than maximumContamination. Default 0.2. See ?SoupX::autoEstCont.

    -
    priorRho
    +
    priorRho

    Numeric. Mode of gamma distribution prior on contamination fraction. Default 0.05. See ?SoupX::autoEstCont.

    -
    priorRhoStdDev
    +
    priorRhoStdDev

    Numeric. Standard deviation of gamma distribution prior on contamination fraction. Default 0.1. See ?SoupX::autoEstCont.

    -
    forceAccept
    +
    forceAccept

    Logical. Should we allow very high contamination fractions to be used. Passed to setContaminationFraction. Default FALSE. See ?SoupX::autoEstCont.

    -
    adjustMethod
    +
    adjustMethod

    Character. Method to use for correction. One of 'subtraction', 'soupOnly', or 'multinomial'. Default 'subtraction'. See ?SoupX::adjustCounts.

    -
    roundToInt
    +
    roundToInt

    Logical. Should the resulting matrix be rounded to integers? Default FALSE. See ?SoupX::adjustCounts.

    -
    tol
    +
    tol

    Numeric. Allowed deviation from expected number of soup counts. Don't change this. Default 0.001. See ?SoupX::adjustCounts.

    -
    pCut
    +
    pCut

    Numeric. The p-value cut-off used when method = 'soupOnly'. Default 0.01. See ?SoupX::adjustCounts.

    @@ -373,18 +375,12 @@

    Arguments

    Value

    - - -

    The input inSCE object with soupX_nUMIs, -soupX_clustrers, soupX_contamination appended to colData

    - - -

    slot; soupX_{sample}_est and soupX_{sample}_counts for each +

    The input inSCE object with soupX_nUMIs, +soupX_clustrers, soupX_contamination appended to colData +slot; soupX_{sample}_est and soupX_{sample}_counts for each sample appended to rowData slot; and other computational metrics at -getSoupX(inSCE). Replace "soupX" to "soupX_bg" when background

    - - -

    is used.

    +getSoupX(inSCE). Replace "soupX" to "soupX_bg" when background +is used.

    See also

    @@ -397,12 +393,12 @@

    Author

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 # SoupX does not work for toy example,
 sce <- importExampleData("pbmc3k")
 sce <- runSoupX(sce, sample = "sample")
 plotSoupXResults(sce, sample = "sample")
-}
+} # }
    @@ -417,15 +413,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runTSCAN.html b/docs/reference/runTSCAN.html index e78fa6022..b884bb4a0 100644 --- a/docs/reference/runTSCAN.html +++ b/docs/reference/runTSCAN.html @@ -1,10 +1,10 @@ -Run TSCAN to obtain pseudotime values for cells — runTSCAN • singleCellTKRun TSCAN to obtain pseudotime values for cells — runTSCAN • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -221,38 +221,38 @@

    Run TSCAN to obtain pseudotime values for cells

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useReducedDim
    +
    useReducedDim

    Character. A low-dimension representation in reducedDims, will be used for both clustering if cluster not specified and MST construction. Default "PCA".

    -
    cluster
    +
    cluster

    Grouping for each cell in inSCE. A vector with equal length to the number of the cells in inSCE, or a single character for retriving colData variable. Default NULL, will run runScranSNN to obtain.

    -
    starter
    +
    starter

    Character. Specifies the starting node from which to compute the pseudotime. Default NULL, will select an arbitrary node.

    -
    seed
    +
    seed

    An integer. Random seed for clustering if cluster is not specified. Default 12345.

    Value

    - - -

    The input inSCE object with pseudotime ordering of the cells +

    The input inSCE object with pseudotime ordering of the cells along the paths and the cluster label stored in colData, and other unstructured information in metadata.

    @@ -266,11 +266,11 @@

    Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
 mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                 useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:19:36 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:19:37 2024 ...   Identified 2 clusters
-#> Fri May  3 07:19:37 2024 ... Running TSCAN to estimate pseudotime
-#> Fri May  3 07:19:37 2024 ...   Clusters involved in path index 2 are: 1, 2
-#> Fri May  3 07:19:37 2024 ...   Number of estimated paths is 1
+#> Thu Feb 13 10:33:34 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:33:34 2025 ...   Identified 2 clusters
+#> Thu Feb 13 10:33:34 2025 ... Running TSCAN to estimate pseudotime
+#> Thu Feb 13 10:33:35 2025 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:33:35 2025 ...   Number of estimated paths is 1
    @@ -285,15 +285,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runTSCANClusterDEAnalysis.html b/docs/reference/runTSCANClusterDEAnalysis.html index a79bb6b7d..a609dc55c 100644 --- a/docs/reference/runTSCANClusterDEAnalysis.html +++ b/docs/reference/runTSCANClusterDEAnalysis.html @@ -1,5 +1,5 @@ -Find DE genes between all TSCAN paths rooted from given cluster — runTSCANClusterDEAnalysis • singleCellTKFind DE genes between all TSCAN paths rooted from given cluster — runTSCANClusterDEAnalysis • singleCellTK - +
    @@ -30,7 +30,7 @@
    - +
    @@ -228,30 +228,30 @@

    Find DE genes between all TSCAN paths rooted from given cluster

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useCluster
    +
    useCluster

    The cluster to be regarded as the root, has to existing in colData(inSCE)$TSCAN_clusters.

    -
    useAssay
    +
    useAssay

    Character. The name of the assay to use. This assay should contain log normalized counts. Default "logcounts".

    -
    fdrThreshold
    +
    fdrThreshold

    Only out put DEGs with FDR value smaller than this value. Default 0.05.

    Value

    - - -

    The input inSCE with results updated in metadata.

    +

    The input inSCE with results updated in metadata.

    Author

    @@ -263,15 +263,15 @@

    Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
 mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                 useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:19:38 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:19:38 2024 ...   Identified 2 clusters
-#> Fri May  3 07:19:38 2024 ... Running TSCAN to estimate pseudotime
-#> Fri May  3 07:19:39 2024 ...   Clusters involved in path index 2 are: 1, 2
-#> Fri May  3 07:19:39 2024 ...   Number of estimated paths is 1
+#> Thu Feb 13 10:33:35 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:33:36 2025 ...   Identified 2 clusters
+#> Thu Feb 13 10:33:36 2025 ... Running TSCAN to estimate pseudotime
+#> Thu Feb 13 10:33:36 2025 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:33:36 2025 ...   Number of estimated paths is 1
 mouseBrainSubsetSCE <- runTSCANClusterDEAnalysis(inSCE = mouseBrainSubsetSCE,
                                          useCluster = 1)
-#> Fri May  3 07:19:39 2024 ... Finding DEG between TSCAN branches
-#> Fri May  3 07:19:39 2024 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:33:36 2025 ... Finding DEG between TSCAN branches
+#> Thu Feb 13 10:33:36 2025 ...   Clusters involved in path index 2 are: 1, 2
    @@ -286,15 +286,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runTSCANDEG.html b/docs/reference/runTSCANDEG.html index b6e15476a..00de942d4 100644 --- a/docs/reference/runTSCANDEG.html +++ b/docs/reference/runTSCANDEG.html @@ -1,10 +1,10 @@ -Test gene expression changes along a TSCAN trajectory path — runTSCANDEG • singleCellTKTest gene expression changes along a TSCAN trajectory path — runTSCANDEG • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -215,32 +215,32 @@

    Test gene expression changes along a TSCAN trajectory path

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    pathIndex
    +
    pathIndex

    Path index for which the pseudotime values should be used. This corresponds to the terminal node of specific path from the root node to the terminal node. Run listTSCANTerminalNodes(inSCE) for available options.

    -
    useAssay
    +
    useAssay

    Character. The name of the assay to use for testing the expression change. Should be log-normalized. Default "logcounts"

    -
    discardCluster
    +
    discardCluster

    Cluster(s) which are not of use or masks other interesting effects can be discarded. Default NULL.

    Value

    - - -

    The input inSCE with results updated in metadata.

    +

    The input inSCE with results updated in metadata.

    Author

    @@ -252,11 +252,11 @@

    Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
 mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                 useReducedDim = "PCA_logcounts")
-#> Fri May  3 07:19:39 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
-#> Fri May  3 07:19:40 2024 ...   Identified 2 clusters
-#> Fri May  3 07:19:40 2024 ... Running TSCAN to estimate pseudotime
-#> Fri May  3 07:19:40 2024 ...   Clusters involved in path index 2 are: 1, 2
-#> Fri May  3 07:19:40 2024 ...   Number of estimated paths is 1
+#> Thu Feb 13 10:33:37 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
+#> Thu Feb 13 10:33:37 2025 ...   Identified 2 clusters
+#> Thu Feb 13 10:33:37 2025 ... Running TSCAN to estimate pseudotime
+#> Thu Feb 13 10:33:37 2025 ...   Clusters involved in path index 2 are: 1, 2
+#> Thu Feb 13 10:33:37 2025 ...   Number of estimated paths is 1
 terminalNodes <- listTSCANTerminalNodes(mouseBrainSubsetSCE)
 mouseBrainSubsetSCE <- runTSCANDEG(inSCE = mouseBrainSubsetSCE,
                                    pathIndex = terminalNodes[1])
@@ -274,15 +274,15 @@ 
    Examples
    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runTSNE.html b/docs/reference/runTSNE.html index 115bb350e..1ce510fe2 100644 --- a/docs/reference/runTSNE.html +++ b/docs/reference/runTSNE.html @@ -1,5 +1,5 @@ -Run t-SNE embedding with Rtsne method — runTSNE • singleCellTKRun t-SNE embedding with Rtsne method — runTSNE • singleCellTK - +
    @@ -32,7 +32,7 @@
    - +
    @@ -269,110 +269,110 @@

    Run t-SNE embedding with Rtsne method

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useReducedDim
    +
    useReducedDim

    The low dimension representation to use for UMAP computation. Default "PCA".

    -
    useAssay
    +
    useAssay

    Assay to use for tSNE computation. If useAltExp is specified, useAssay has to exist in assays(altExp(inSCE, useAltExp)). Default NULL.

    -
    useAltExp
    +
    useAltExp

    The subset to use for tSNE computation, usually for the selected.variable features. Default NULL.

    -
    reducedDimName
    +
    reducedDimName

    a name to store the results of the dimension reductions. Default "TSNE".

    -
    logNorm
    +
    logNorm

    Whether the counts will need to be log-normalized prior to generating the tSNE via scaterlogNormCounts. Ignored when using useReducedDim. Default TRUE.

    -
    useFeatureSubset
    +
    useFeatureSubset

    Subset of feature to use for dimension reduction. A character string indicating a rowData variable that stores the logical vector of HVG selection, or a vector that can subset the rows of inSCE. Default NULL.

    -
    nTop
    +
    nTop

    Automatically detect this number of variable features to use for dimension reduction. Ignored when using useReducedDim or using useFeatureSubset. Default 2000.

    -
    center
    +
    center

    Whether data should be centered before PCA is applied. Ignored when using useReducedDim. Default TRUE.

    -
    scale
    +
    scale

    Whether data should be scaled before PCA is applied. Ignored when using useReducedDim. Default TRUE.

    -
    pca
    +
    pca

    Whether an initial PCA step should be performed. Ignored when using useReducedDim. Default TRUE.

    -
    partialPCA
    +
    partialPCA

    Whether truncated PCA should be used to calculate principal components (requires the irlba package). This is faster for large input matrices. Ignored when using useReducedDim. Default FALSE.

    -
    initialDims
    +
    initialDims

    Number of dimensions from PCA to use as input in tSNE. Default 25.

    -
    theta
    +
    theta

    Numeric value for speed/accuracy trade-off (increase for less accuracy), set to 0.0 for exact TSNE. Default 0.5.

    -
    perplexity
    +
    perplexity

    perplexity parameter. Should not be bigger than 3 * perplexity < ncol(inSCE) - 1. Default 30. See Rtsne details for interpretation.

    -
    nIterations
    +
    nIterations

    maximum iterations. Default 1000.

    -
    numThreads
    +
    numThreads

    Integer, number of threads to use using OpenMP, Default 1. 0 corresponds to using all available cores.

    -
    seed
    +
    seed

    Random seed for reproducibility of tSNE results. Default NULL will use global seed in use by the R environment.

    -
    ...
    +
    ...

    Other parameters to be passed to runTSNE

    Value

    - - -

    A SingleCellExperiment object with tSNE computation +

    A SingleCellExperiment object with tSNE computation updated in reducedDim(inSCE, reducedDimName).

    @@ -382,8 +382,8 @@

    Examples

    sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") # Run from raw counts sce <- runQuickTSNE(sce) -#> Fri May 3 07:19:41 2024 ... Computing Rtsne. -if (FALSE) { +#> Thu Feb 13 10:33:38 2025 ... Computing Rtsne. +if (FALSE) { # \dontrun{ # Run from PCA sce <- scaterlogNormCounts(sce, "logcounts") sce <- runModelGeneVar(sce) @@ -392,7 +392,7 @@

    Examples

    sce <- scaterPCA(sce, useAssay = "logcounts", useFeatureSubset = "HVG_modelGeneVar2000", scale = TRUE) sce <- runTSNE(sce, useReducedDim = "PCA") -} +} # }
    @@ -407,15 +407,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runUMAP-1.png b/docs/reference/runUMAP-1.png index 3fe2410fc..97bbaf9e0 100644 Binary files a/docs/reference/runUMAP-1.png and b/docs/reference/runUMAP-1.png differ diff --git a/docs/reference/runUMAP.html b/docs/reference/runUMAP.html index 71647f061..d3b20ba04 100644 --- a/docs/reference/runUMAP.html +++ b/docs/reference/runUMAP.html @@ -1,10 +1,10 @@ -Run UMAP embedding with scater method — runUMAP • singleCellTKRun UMAP embedding with scater method — runUMAP • singleCellTK - +
    @@ -35,7 +35,7 @@
    - +
    @@ -215,11 +215,11 @@

    Run UMAP embedding with scater method

    Uniform Manifold Approximation and Projection (UMAP) algorithm -is commonly for 2D visualization of single-cell data. These functions wrap +is commonly for 2D visualization of single-cell data. These functions wrap the scater calculateUMAP function.

    Users can use runQuickUMAP to directly create UMAP embedding from raw count matrix, with necessary preprocessing including normalization, variable -feature selection, scaling, dimension reduction all automated. Therefore, +feature selection, scaling, dimension reduction all automated. Therefore, useReducedDim is disabled for runQuickUMAP.

    In a complete analysis, we still recommend having dimension reduction such as PCA created beforehand and select proper numbers of dimensions for using @@ -278,91 +278,93 @@

    Run UMAP embedding with scater method

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useReducedDim
    +
    useReducedDim

    The low dimension representation to use for UMAP computation. If useAltExp is specified, useReducedDim has to exist in reducedDims(altExp(inSCE, useAltExp)). Default "PCA".

    -
    useAssay
    +
    useAssay

    Assay to use for UMAP computation. If useAltExp is specified, useAssay has to exist in assays(altExp(inSCE, useAltExp)). Ignored when using useReducedDim. Default NULL.

    -
    useAltExp
    +
    useAltExp

    The subset to use for UMAP computation, usually for the selected variable features. Default NULL.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to. If given a single character, will take the annotation from colData. Default NULL.

    -
    reducedDimName
    +
    reducedDimName

    A name to store the results of the UMAP embedding coordinates obtained from this method. Default "UMAP".

    -
    logNorm
    +
    logNorm

    Whether the counts will need to be log-normalized prior to generating the UMAP via scaterlogNormCounts. Ignored when using useReducedDim. Default TRUE.

    -
    useFeatureSubset
    +
    useFeatureSubset

    Subset of feature to use for dimension reduction. A character string indicating a rowData variable that stores the logical vector of HVG selection, or a vector that can subset the rows of inSCE. Default NULL.

    -
    nTop
    +
    nTop

    Automatically detect this number of variable features to use for dimension reduction. Ignored when using useReducedDim or using useFeatureSubset. Default 2000.

    -
    scale
    +
    scale

    Whether useAssay matrix will need to be standardized. Default TRUE.

    -
    pca
    +
    pca

    Logical. Whether to perform dimension reduction with PCA before UMAP. Ignored when using useReducedDim. Default TRUE.

    -
    initialDims
    +
    initialDims

    Number of dimensions from PCA to use as input in UMAP. Default 10.

    -
    nNeighbors
    +
    nNeighbors

    The size of local neighborhood used for manifold approximation. Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. Default 30. See calculateUMAP for more information.

    -
    nIterations
    +
    nIterations

    The number of iterations performed during layout optimization. Default is 200.

    -
    alpha
    +
    alpha

    The initial value of "learning rate" of layout optimization. Default is 1.

    -
    minDist
    +
    minDist

    The effective minimum distance between embedded points. Smaller values will result in a more clustered/clumped embedding where nearby points on the manifold are drawn closer together, while larger values will @@ -370,36 +372,34 @@

    Arguments

    calculateUMAP for more information.

    -
    spread
    +
    spread

    The effective scale of embedded points. In combination with minDist, this determines how clustered/clumped the embedded points are. Default 1. See calculateUMAP for more information.

    -
    seed
    +
    seed

    Random seed for reproducibility of UMAP results. Default NULL will use global seed in use by the R environment.

    -
    verbose
    +
    verbose

    Logical. Whether to print log messages. Default TRUE.

    -
    BPPARAM
    +
    BPPARAM

    A BiocParallelParam object specifying whether the PCA should be parallelized.

    -
    ...
    +
    ...

    Parameters passed to runUMAP

    Value

    - - -

    A SingleCellExperiment object with UMAP computation +

    A SingleCellExperiment object with UMAP computation updated in reducedDim(inSCE, reducedDimName).

    @@ -409,7 +409,7 @@

    Examples

    sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") # Run from raw counts sce <- runQuickUMAP(sce) -#> Fri May 3 07:19:42 2024 ... Computing Scater UMAP for sample 'pbmc_4k'. +#> Thu Feb 13 10:33:39 2025 ... Computing Scater UMAP for sample 'pbmc_4k'. plotDimRed(sce, "UMAP") @@ -427,15 +427,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runVAM.html b/docs/reference/runVAM.html index 110a0e6b9..4f61e4934 100644 --- a/docs/reference/runVAM.html +++ b/docs/reference/runVAM.html @@ -1,5 +1,5 @@ -Run VAM to score gene sets in single cell data — runVAM • singleCellTKRun VAM to score gene sets in single cell data — runVAM • singleCellTK - +
    @@ -30,7 +30,7 @@
    - +
    @@ -230,21 +230,23 @@

    Run VAM to score gene sets in single cell data

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    geneSetCollectionName
    +
    geneSetCollectionName

    Character. The name of the gene set collection to use. Default "H".

    -
    useAssay
    +
    useAssay

    Character. The name of the assay to use. This assay should contain log normalized counts. Default "logcounts".

    -
    resultNamePrefix
    +
    resultNamePrefix

    Character. Prefix to the name the VAM results which will be stored in the reducedDim slot of inSCE. The names of the output matrices will be resultNamePrefix_Distance and @@ -252,12 +254,12 @@

    Arguments

    "VAM_geneSetCollectionName_" will be used. Default NULL.

    -
    center
    +
    center

    Boolean. If TRUE, values will be mean centered when computing the Mahalanobis statistic. Default FALSE.

    -
    gamma
    +
    gamma

    Boolean. If TRUE, a gamma distribution will be fit to the non-zero squared Mahalanobis distances computed from a row-permuted version of the gene expression matrix. The estimated gamma distribution will @@ -269,9 +271,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object with VAM metrics stored +

    A SingleCellExperiment object with VAM metrics stored in reducedDim as VAM_NameOfTheGeneset_Distance and VAM_NameOfTheGeneset_CDF.

    @@ -301,7 +301,7 @@

    Examples

    sce <- runVAM(inSCE = sce, geneSetCollectionName = "GeneSetCollection", useAssay = "logcounts") -#> Fri May 3 07:19:47 2024 ... Running VAM +#> Thu Feb 13 10:33:45 2025 ... Running VAM #> gene.weights not specified, defaulting all weights to 1 #> Computing VAM distances for 2 gene sets, 195 cells and 200 genes. #> Min set size: 10, median size: 10 @@ -319,15 +319,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/runZINBWaVE.html b/docs/reference/runZINBWaVE.html index e5d3f2643..829c6aaef 100644 --- a/docs/reference/runZINBWaVE.html +++ b/docs/reference/runZINBWaVE.html @@ -1,5 +1,5 @@ -Apply ZINBWaVE Batch effect correction method to SingleCellExperiment object — runZINBWaVE • singleCellTKApply ZINBWaVE Batch effect correction method to SingleCellExperiment object — runZINBWaVE • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -231,59 +231,59 @@

    Apply ZINBWaVE Batch effect correction method to SingleCellExperiment object

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    useAssay
    +
    useAssay

    A single character indicating the name of the assay requiring batch correction. Note that ZINBWaVE works for counts (integer) input rather than logcounts that other methods prefer. Default "counts".

    -
    batch
    +
    batch

    A single character indicating a field in colData that annotates the batches. Default "batch".

    -
    nHVG
    +
    nHVG

    An integer. Number of highly variable genes to use when fitting the model. Default 1000L.

    -
    nComponents
    +
    nComponents

    An integer. The number of principle components or dimensionality to generate in the resulting matrix. Default 50L.

    -
    epsilon
    +
    epsilon

    An integer. Algorithmic parameter. Empirically, a high epsilon is often required to obtained a good low-level representation. Default 1000L.

    -
    nIter
    +
    nIter

    An integer, The max number of iterations to perform. Default 10L.

    -
    reducedDimName
    +
    reducedDimName

    A single character. The name for the corrected low-dimensional representation. Will be saved to reducedDim(inSCE). Default "zinbwave".

    -
    BPPARAM
    +
    BPPARAM

    A BiocParallelParam object specifying whether should be parallelized. Default BiocParallel::SerialParam().

    Value

    - - -

    The input SingleCellExperiment object with +

    The input SingleCellExperiment object with reducedDim(inSCE, reducedDimName) updated.

    @@ -294,9 +294,9 @@

    References

    Examples

    data('sceBatches', package = 'singleCellTK')
-if (FALSE) {
+if (FALSE) { # \dontrun{
     sceCorr <- runZINBWaVE(sceBatches, nIter = 5)
-}
+} # }
    @@ -311,15 +311,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/sampleSummaryStats.html b/docs/reference/sampleSummaryStats.html index 85955b6d3..4f5552052 100644 --- a/docs/reference/sampleSummaryStats.html +++ b/docs/reference/sampleSummaryStats.html @@ -1,11 +1,11 @@ -Generate table of SCTK QC outputs. — sampleSummaryStats • singleCellTKGenerate table of SCTK QC outputs. — sampleSummaryStats • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -223,36 +223,36 @@

    Generate table of SCTK QC outputs.

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved assay data and/or colData data. Required.

    -
    sample
    +
    sample

    Character vector. Indicates which sample each cell belongs to.

    -
    useAssay
    +
    useAssay

    A string specifying which assay in the SCE to use. Default 'counts'.

    -
    simple
    +
    simple

    Boolean. Indicates whether to generate a table of only basic QC stats (ex. library size), or to generate a summary table of all QC stats stored in the inSCE.

    -
    statsName
    +
    statsName

    Character. The name of the slot that will store the QC stat table. Default "qc_table".

    Value

    - - -

    A SingleCellExperiment object with a summary table for QC statistics +

    A SingleCellExperiment object with a summary table for QC statistics in the `sample_summary` slot of metadata.

    @@ -282,15 +282,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/scaterCPM.html b/docs/reference/scaterCPM.html index 533927626..009151f90 100644 --- a/docs/reference/scaterCPM.html +++ b/docs/reference/scaterCPM.html @@ -1,12 +1,10 @@ -scaterCPM -Uses CPM from scater library to compute counts-per-million. — scaterCPM • singleCellTKscaterCPM Uses CPM from scater library to compute counts-per-million. — scaterCPM • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    scaterCPM -Uses CPM from scater library to compute counts-per-million.

    +

    scaterCPM Uses CPM from scater library to compute counts-per-million.

    Source: R/scater_CPM.R
    @@ -218,23 +215,23 @@

    scaterCPM

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    assayName
    +
    assayName

    New assay name for cpm data.

    -
    useAssay
    +
    useAssay

    Input assay

    Value

    - - -

    inSCE Updated SingleCellExperiment object

    +

    inSCE Updated SingleCellExperiment object

    Author

    @@ -259,15 +256,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/scaterPCA.html b/docs/reference/scaterPCA.html index 0bbe38a03..391833ea1 100644 --- a/docs/reference/scaterPCA.html +++ b/docs/reference/scaterPCA.html @@ -1,11 +1,11 @@ -Perform scater PCA on a SingleCellExperiment Object — scaterPCA • singleCellTKPerform scater PCA on a SingleCellExperiment Object — scaterPCA • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -228,64 +228,64 @@

    Perform scater PCA on a SingleCellExperiment Object

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Assay to use for PCA computation. If useAltExp is specified, useAssay has to exist in assays(altExp(inSCE, useAltExp)). Default "logcounts"

    -
    useFeatureSubset
    +
    useFeatureSubset

    Subset of feature to use for dimension reduction. A character string indicating a rowData variable that stores the logical vector of HVG selection, or a vector that can subset the rows of inSCE. Default "hvg2000".

    -
    scale
    +
    scale

    Logical scalar, whether to standardize the expression values. Default TRUE.

    -
    reducedDimName
    +
    reducedDimName

    Name to use for the reduced output assay. Default "PCA".

    -
    nComponents
    +
    nComponents

    Number of principal components to obtain from the PCA computation. Default 50.

    -
    ntop
    +
    ntop

    Automatically detect this number of variable features to use for dimension reduction. Ignored when using useReducedDim or using useFeatureSubset. Default 2000.

    -
    useAltExp
    +
    useAltExp

    The subset to use for PCA computation, usually for the selected.variable features. Default NULL.

    -
    seed
    +
    seed

    Integer, random seed for reproducibility of PCA results. Default NULL.

    -
    BPPARAM
    +
    BPPARAM

    A BiocParallelParam object specifying whether the PCA should be parallelized.

    Value

    - - -

    A SingleCellExperiment object with PCA computation +

    A SingleCellExperiment object with PCA computation updated in reducedDim(inSCE, reducedDimName).

    @@ -302,15 +302,15 @@

    Examples

    sce <- runModelGeneVar(sce, useAssay = "logcounts") sce <- setTopHVG(sce, method = "modelGeneVar", hvgNumber = 100, featureSubsetName = "hvf") -#> Fri May 3 07:19:49 2024 ... Feature subset variable 'hvf' created. +#> Thu Feb 13 10:33:47 2025 ... Feature subset variable 'hvf' created. sce <- scaterPCA(sce, useAssay = "logcounts", scale = TRUE, useFeatureSubset = "hvf", nComponents = 5) -#> Fri May 3 07:19:49 2024 ... Computing Scater PCA. +#> Thu Feb 13 10:33:47 2025 ... Computing Scater PCA. # Alternatively, let the scater PCA function select the top variable genes sce <- scaterPCA(sce, useAssay = "logcounts", scale = TRUE, useFeatureSubset = NULL, ntop = 100, nComponents = 5) -#> Fri May 3 07:19:49 2024 ... Computing Scater PCA. +#> Thu Feb 13 10:33:47 2025 ... Computing Scater PCA.
    @@ -325,15 +325,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/scaterlogNormCounts.html b/docs/reference/scaterlogNormCounts.html index d894b43ce..8e4e8dc64 100644 --- a/docs/reference/scaterlogNormCounts.html +++ b/docs/reference/scaterlogNormCounts.html @@ -1,12 +1,10 @@ -scaterlogNormCounts -Uses logNormCounts to log normalize input data — scaterlogNormCounts • singleCellTKscaterlogNormCounts Uses logNormCounts to log normalize input data — scaterlogNormCounts • singleCellTK - +
    @@ -28,7 +26,7 @@
    - +
    -

    scaterlogNormCounts -Uses logNormCounts to log normalize input data

    +

    scaterlogNormCounts Uses logNormCounts to log normalize input data

    Source: R/scater_logNormCounts.R
    @@ -222,23 +219,23 @@

    scaterlogNormCounts

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object

    -
    assayName
    +
    assayName

    New assay name for log normalized data

    -
    useAssay
    +
    useAssay

    Input assay

    Value

    - - -

    inSCE Updated SingleCellExperiment object that contains the new log normalized data

    +

    inSCE Updated SingleCellExperiment object that contains the new log normalized data

    Author

    @@ -263,15 +260,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/sce.html b/docs/reference/sce.html index 4d5d280df..c4e5f21d6 100644 --- a/docs/reference/sce.html +++ b/docs/reference/sce.html @@ -1,7 +1,5 @@ -Example Single Cell RNA-Seq data in SingleCellExperiment Object, -subset of 10x public dataset — sce • singleCellTKExample Single Cell RNA-Seq data in SingleCellExperiment Object, subset of 10x public dataset — sce • singleCellTK - +
    @@ -33,7 +31,7 @@
    - +
    -

    Example Single Cell RNA-Seq data in SingleCellExperiment Object, -subset of 10x public dataset

    +

    Example Single Cell RNA-Seq data in SingleCellExperiment Object, subset of 10x public dataset

    Source: R/data.R
    @@ -232,9 +229,7 @@

    Format

    Value

    - - -

    Example Single Cell RNA-Seq data in SingleCellExperiment Object, +

    Example Single Cell RNA-Seq data in SingleCellExperiment Object, subset of 10x public dataset

    @@ -255,15 +250,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/sceBatches.html b/docs/reference/sceBatches.html index ed2275239..0378025f3 100644 --- a/docs/reference/sceBatches.html +++ b/docs/reference/sceBatches.html @@ -1,7 +1,5 @@ -Example Single Cell RNA-Seq data in SingleCellExperiment object, with -different batches annotated — sceBatches • singleCellTKExample Single Cell RNA-Seq data in SingleCellExperiment object, with different batches annotated — sceBatches • singleCellTK - +
    @@ -32,7 +30,7 @@
    - +
    -

    Example Single Cell RNA-Seq data in SingleCellExperiment object, with -different batches annotated

    +

    Example Single Cell RNA-Seq data in SingleCellExperiment object, with different batches annotated

    Source: R/data.R
    @@ -230,9 +227,7 @@

    Format

    Value

    - - -

    Example Single Cell RNA-Seq data in SingleCellExperiment object, with +

    Example Single Cell RNA-Seq data in SingleCellExperiment object, with different batches annotated

    @@ -248,15 +243,15 @@

    Value

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/sctkListGeneSetCollections.html b/docs/reference/sctkListGeneSetCollections.html index a38309c42..b974fe218 100644 --- a/docs/reference/sctkListGeneSetCollections.html +++ b/docs/reference/sctkListGeneSetCollections.html @@ -1,10 +1,10 @@ -Lists imported GeneSetCollections — sctkListGeneSetCollections • singleCellTKLists imported GeneSetCollections — sctkListGeneSetCollections • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -215,15 +215,15 @@

    Lists imported GeneSetCollections

    Arguments

    -
    inSCE
    + + +
    inSCE

    A SingleCellExperiment object.

    Value

    - - -

    Character vector.

    +

    Character vector.

    See also

    @@ -269,15 +269,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/sctkPythonInstallConda.html b/docs/reference/sctkPythonInstallConda.html index 657055d73..e9cb68a49 100644 --- a/docs/reference/sctkPythonInstallConda.html +++ b/docs/reference/sctkPythonInstallConda.html @@ -1,12 +1,12 @@ -Installs Python packages into a Conda environment — sctkPythonInstallConda • singleCellTKInstalls Python packages into a Conda environment — sctkPythonInstallConda • singleCellTK - +
    @@ -28,7 +28,7 @@
    - +
    @@ -230,49 +230,49 @@

    Installs Python packages into a Conda environment

    Arguments

    -
    envname
    + + +
    envname

    Character. Name of the conda environment to create.

    -
    conda
    +
    conda

    Character. Path to conda executable. Usue "auto" to find conda using the PATH and other conventional install locations. Default 'auto'.

    -
    packages
    +
    packages

    Character Vector. List of packages to install from Conda.

    -
    pipPackages
    +
    pipPackages

    Character Vector. List of packages to install into the Conda environment using 'pip'.

    -
    selectConda
    +
    selectConda

    Boolean. Run selectSCTKConda after installing all packages to select the Conda environment. Default TRUE.

    -
    forge
    +
    forge

    Boolean. Include the Conda Forge repository.

    -
    pipIgnoreInstalled
    +
    pipIgnoreInstalled

    Boolean. Ignore installed versions when using pip. This is TRUE by default so that specific package versions can be installed even if they are downgrades. The FALSE option is useful for situations where you don't want a pip install to attempt an overwrite of a conda binary package (e.g. SciPy on Windows which is very difficult to install via pip due to compilation requirements).

    -
    pythonVersion
    +
    pythonVersion

    Passed to python_version variable in conda_install. Default NULL.

    -
    ...
    +
    ...

    Other parameters to pass to conda_install.

    Value

    - - -

    None. Installation of Conda environment.

    +

    None. Installation of Conda environment.

    See also

    @@ -286,9 +286,9 @@

    See also

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 sctkPythonInstallConda(envname = "sctk-reticulate")
-}
+} # }
    @@ -303,15 +303,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/sctkPythonInstallVirtualEnv.html b/docs/reference/sctkPythonInstallVirtualEnv.html index 81a163ac6..69cd1face 100644 --- a/docs/reference/sctkPythonInstallVirtualEnv.html +++ b/docs/reference/sctkPythonInstallVirtualEnv.html @@ -1,11 +1,11 @@ -Installs Python packages into a virtual environment — sctkPythonInstallVirtualEnv • singleCellTKInstalls Python packages into a virtual environment — sctkPythonInstallVirtualEnv • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -223,27 +223,27 @@

    Installs Python packages into a virtual environment

    Arguments

    -
    envname
    + + +
    envname

    Character. Name of the virtual environment to create.

    -
    packages
    +
    packages

    Character Vector. List of packages to install.

    -
    selectEnvironment
    +
    selectEnvironment

    Boolean. Run selectSCTKVirtualEnvironment after installing all packages to select the virtual environment. Default TRUE.

    -
    python
    +
    python

    The path to a Python interpreter, to be used with the created virtual environment. When NULL, the Python interpreter associated with the current session will be used. Default NULL.

    Value

    - - -

    None. Installation of virtual environment.

    +

    None. Installation of virtual environment.

    See also

    @@ -256,9 +256,9 @@

    See also

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 sctkPythonInstallVirtualEnv(envname = "sctk-reticulate")
-}
+} # }
    @@ -273,15 +273,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/selectSCTKConda.html b/docs/reference/selectSCTKConda.html index 6f9bccef0..3304dcad1 100644 --- a/docs/reference/selectSCTKConda.html +++ b/docs/reference/selectSCTKConda.html @@ -1,9 +1,9 @@ -Selects a Conda environment — selectSCTKConda • singleCellTKSelects a Conda environment — selectSCTKConda • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,15 +213,15 @@

    Selects a Conda environment

    Arguments

    -
    envname
    + + +
    envname

    Character. Name of the conda environment to activate.

    Value

    - - -

    None. Selects Conda environment.

    +

    None. Selects Conda environment.

    See also

    @@ -235,10 +235,10 @@

    See also

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 sctkPythonInstallConda(envname = "sctk-reticulate", selectConda = FALSE)
 selectSCTKConda(envname = "sctk-reticulate")
-}
+} # }
    @@ -253,15 +253,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/selectSCTKVirtualEnvironment.html b/docs/reference/selectSCTKVirtualEnvironment.html index 9138935e3..f6acc9117 100644 --- a/docs/reference/selectSCTKVirtualEnvironment.html +++ b/docs/reference/selectSCTKVirtualEnvironment.html @@ -1,9 +1,9 @@ -Selects a virtual environment — selectSCTKVirtualEnvironment • singleCellTKSelects a virtual environment — selectSCTKVirtualEnvironment • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,15 +213,15 @@

    Selects a virtual environment

    Arguments

    -
    envname
    + + +
    envname

    Character. Name of the virtual environment to activate.

    Value

    - - -

    None. Selects virtual environment.

    +

    None. Selects virtual environment.

    See also

    @@ -232,10 +232,10 @@

    See also

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 sctkPythonInstallVirtualEnv(envname = "sctk-reticulate", selectEnvironment = FALSE)
 selectSCTKVirtualEnvironment(envname = "sctk-reticulate")
-}
+} # }
    @@ -250,15 +250,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/setRowNames.html b/docs/reference/setRowNames.html index 91068ce2f..4be17bb40 100644 --- a/docs/reference/setRowNames.html +++ b/docs/reference/setRowNames.html @@ -1,5 +1,5 @@ -Set rownames of SCE with a character vector or a rowData column — setRowNames • singleCellTKSet rownames of SCE with a character vector or a rowData column — setRowNames • singleCellTK - +
    @@ -31,7 +31,7 @@
    - +
    @@ -225,26 +225,26 @@

    Set rownames of SCE with a character vector or a rowData column

    Arguments

    -
    x
    + + +
    x

    Input object where the rownames will be modified.

    -
    rowNames
    +
    rowNames

    Character vector of the rownames. If x is an SingleCellExperiment object, a single character specifying a column in rowData(x).

    -
    dedup
    +
    dedup

    Logical. Whether to deduplicate the specified rowNames. Default TRUE

    Value

    - - -

    The input SCE object with rownames updated.

    +

    The input SCE object with rownames updated.

    @@ -270,15 +270,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/setSCTKDisplayRow-1.png b/docs/reference/setSCTKDisplayRow-1.png index f8f33922e..e4a725163 100644 Binary files a/docs/reference/setSCTKDisplayRow-1.png and b/docs/reference/setSCTKDisplayRow-1.png differ diff --git a/docs/reference/setSCTKDisplayRow.html b/docs/reference/setSCTKDisplayRow.html index 16a81f457..4db45f7d4 100644 --- a/docs/reference/setSCTKDisplayRow.html +++ b/docs/reference/setSCTKDisplayRow.html @@ -1,9 +1,9 @@ -Indicates which rowData to use for visualization — setSCTKDisplayRow • singleCellTKIndicates which rowData to use for visualization — setSCTKDisplayRow • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,20 +213,20 @@

    Indicates which rowData to use for visualization

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

    -
    featureDisplayRow
    +
    featureDisplayRow

    Indicates which column name of rowData to be used for plots.

    Value

    - - -

    A SingleCellExperiment object with the specific column name of rowData +

    A SingleCellExperiment object with the specific column name of rowData to be used for plotting stored in metadata.

    @@ -251,15 +251,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/singleCellTK.html b/docs/reference/singleCellTK.html index c1f14bb5a..f9ce84467 100644 --- a/docs/reference/singleCellTK.html +++ b/docs/reference/singleCellTK.html @@ -1,9 +1,9 @@ -Run the single cell analysis app — singleCellTK • singleCellTKRun the single cell analysis app — singleCellTK • singleCellTK - +
    @@ -25,7 +25,7 @@
    - +
    @@ -213,37 +213,37 @@

    Run the single cell analysis app

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    includeVersion
    +
    includeVersion

    Include the version number in the SCTK header. The default is TRUE.

    -
    theme
    +
    theme

    The bootswatch theme to use for the singleCellTK UI. The default is 'flatly'.

    Value

    - - -

    The shiny app will open

    +

    The shiny app will open

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 #Upload data through the app
 singleCellTK()
 
 # Load the app with a SingleCellExperiment object
 data("mouseBrainSubsetSCE")
 singleCellTK(mouseBrainSubsetSCE)
-}
+} # }
    @@ -258,15 +258,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/subDiffEx.html b/docs/reference/subDiffEx.html index 06003420b..3c80446bc 100644 --- a/docs/reference/subDiffEx.html +++ b/docs/reference/subDiffEx.html @@ -1,15 +1,11 @@ -Passes the output of generateSimulatedData() to differential expression -tests, picking either t-tests or ANOVA for data with only two conditions or -multiple conditions, respectively. — subDiffEx • singleCellTKPasses the output of generateSimulatedData() to differential expression tests, picking either t-tests or ANOVA for data with only two conditions or multiple conditions, respectively. — subDiffEx • singleCellTK - +
    @@ -31,7 +27,7 @@
    - +
    -

    Passes the output of generateSimulatedData() to differential expression -tests, picking either t-tests or ANOVA for data with only two conditions or -multiple conditions, respectively.

    +

    Passes the output of generateSimulatedData() to differential expression tests, picking either t-tests or ANOVA for data with only two conditions or multiple conditions, respectively.

    Source: R/DownsampleMatrix.R
    @@ -227,49 +221,45 @@

    Passes the output of generateSimulatedData() to differential expression

    Arguments

    -
    tempData
    + + +
    tempData

    Matrix. The output of generateSimulatedData(), where the first row contains condition labels.

    -
    countMatrix
    +
    countMatrix

    Matrix. A simulated counts matrix, sans labels.

    -
    class.labels
    +
    class.labels

    Factor. The condition labels for the simulated cells. Will be coerced into 1's and 0's.

    -
    test.type
    +
    test.type

    Type of test to perform. The default is t.equalvar.

    -
    condition
    +
    condition

    Factor. The condition labels for the simulated cells.

    Value

    - - -

    subDiffEx(): A vector of fdr-adjusted p-values for all genes. +

    subDiffEx(): A vector of fdr-adjusted p-values for all genes. Nonviable results (such as for genes with 0 counts in a simulated dataset) are coerced to 1.

    - -

    subDiffExttest(): A vector of fdr-adjusted p-values for all genes. Nonviable results (such as for genes with 0 counts in a simulated dataset) are coerced to 1.

    - -

    subDiffExANOVA(): A vector of fdr-adjusted p-values for all genes. Nonviable results (such as for genes with 0 counts in a simulated dataset) are coerced to 1.

    Functions

    - +

    • subDiffEx():

    • subDiffExttest(): Runs t-tests on all genes in a simulated dataset with 2 conditions, and adjusts for FDR.

      • @@ -328,15 +318,15 @@

      Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/subsetSCECols.html b/docs/reference/subsetSCECols.html index b29e5b0ea..8accb2f49 100644 --- a/docs/reference/subsetSCECols.html +++ b/docs/reference/subsetSCECols.html @@ -1,5 +1,5 @@ -Subset a SingleCellExperiment object by columns — subsetSCECols • singleCellTKSubset a SingleCellExperiment object by columns — subsetSCECols • singleCellTK - +
    @@ -29,7 +29,7 @@
    - +
    @@ -221,24 +221,26 @@

    Subset a SingleCellExperiment object by columns

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    index
    +
    index

    Integer vector. Vector of indicies indicating which columns to keep. If NULL, this will not be used for subsetting. Default NULL.

    -
    bool
    +
    bool

    Boolean vector. Vector of TRUE or FALSE indicating which columns should be kept. Needs to be the same length as the number of columns in inSCE. If NULL, this will not be used for subsetting. Default NULL.

    -
    colData
    +
    colData

    Character. An expression that will identify a subset of columns using variables found in the colData of inSCE. For example, if x is a numeric vector in colData, @@ -253,9 +255,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object that has +

    A SingleCellExperiment object that has been subsetted by colData.

    @@ -281,15 +281,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/subsetSCERows.html b/docs/reference/subsetSCERows.html index 055897159..7c5914ff8 100644 --- a/docs/reference/subsetSCERows.html +++ b/docs/reference/subsetSCERows.html @@ -1,5 +1,5 @@ -Subset a SingleCellExperiment object by rows — subsetSCERows • singleCellTKSubset a SingleCellExperiment object by rows — subsetSCERows • singleCellTK - +
    @@ -32,7 +32,7 @@
    - +
    @@ -235,24 +235,26 @@

    Subset a SingleCellExperiment object by rows

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    index
    +
    index

    Integer vector. Vector of indicies indicating which rows to keep. If NULL, this will not be used for subsetting. Default NULL.

    -
    bool
    +
    bool

    Boolean vector. Vector of TRUE or FALSE indicating which rows should be kept. Needs to be the same length as the number of rows in inSCE. If NULL, this will not be used for subsetting. Default NULL.

    -
    rowData
    +
    rowData

    Character. An expression that will identify a subset of rows using variables found in the rowData of inSCE. For example, if x is a numeric vector in rowData, then "x < 5" will @@ -264,19 +266,19 @@

    Arguments

    subsetting. Default NULL.

    -
    returnAsAltExp
    +
    returnAsAltExp

    Boolean. If TRUE, the subsetted SingleCellExperiment object will be returned in the altExp slot of inSCE. If FALSE, the subsetted SingleCellExperiment object will be directly returned.

    -
    altExpName
    +
    altExpName

    Character. Name of the alternative experiment object to add if returnAsAltExp = TRUE. Default subset.

    -
    prependAltExpName
    +
    prependAltExpName

    Boolean. If TRUE, altExpName will be added to the beginning of the assay names in the altExp object. This is only utilized if returnAsAltExp = TRUE. Default TRUE.

    @@ -284,9 +286,7 @@

    Arguments

    Value

    - - -

    A SingleCellExperiment object that has +

    A SingleCellExperiment object that has been subsetted by rowData.

    @@ -316,15 +316,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/summarizeSCE.html b/docs/reference/summarizeSCE.html index 9591b3673..fc70ae384 100644 --- a/docs/reference/summarizeSCE.html +++ b/docs/reference/summarizeSCE.html @@ -1,10 +1,10 @@ -Summarize an assay in a SingleCellExperiment — summarizeSCE • singleCellTKSummarize an assay in a SingleCellExperiment — summarizeSCE • singleCellTK - +
    @@ -26,7 +26,7 @@
    - +
    @@ -215,16 +215,18 @@

    Summarize an assay in a SingleCellExperiment

    Arguments

    -
    inSCE
    + + +
    inSCE

    Input SingleCellExperiment object.

    -
    useAssay
    +
    useAssay

    Indicate which assay to summarize. If NULL, then the first assay in inSCE will be used. Default NULL.

    -
    sampleVariableName
    +
    sampleVariableName

    Variable name in colData denoting which sample each cell belongs to. If NULL, all cells will be assumed to come from the same sample. Default "sample".

    @@ -232,9 +234,7 @@

    Arguments

    Value

    - - -

    A data.frame object of summary metrics.

    +

    A data.frame object of summary metrics.

    @@ -259,15 +259,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/reference/trimCounts.html b/docs/reference/trimCounts.html index 59eadaaf8..7a0daeab9 100644 --- a/docs/reference/trimCounts.html +++ b/docs/reference/trimCounts.html @@ -1,11 +1,11 @@ -Trim Counts — trimCounts • singleCellTKTrim Counts — trimCounts • singleCellTK - +
    @@ -27,7 +27,7 @@
    - +
    @@ -217,20 +217,20 @@

    Trim Counts

    Arguments

    -
    counts
    + + +
    counts

    matrix

    -
    trimValue
    +
    trimValue

    where trimValue[1] for upper threshold and trimValue[2] as lower threshold. Default is c(10,-10)

    Value

    - - -

    trimmed counts matrix

    +

    trimmed counts matrix

    @@ -252,15 +252,15 @@

    Examples

    -

    Site built with pkgdown 2.0.7.

    +

    Site built with pkgdown 2.1.1.

    - - + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 23612d5e6..67210f586 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,927 +1,306 @@ - - - - /404.html - - - /LICENSE-text.html - - - /articles/01_import_and_qc_tutorial.html - - - /articles/02_a_la_carte_workflow.html - - - /articles/2d_embedding.html - - - /articles/batch_correction.html - - - /articles/celda_curated_workflow.html - - - /articles/cell_type_labeling.html - - - /articles/clustering.html - - - /articles/cmd_qc.html - - - /articles/cnsl_cellqc.html - - - /articles/cnsl_dropletqc.html - - - /articles/delete_data.html - - - /articles/differential_expression.html - - - /articles/dimensionality_reduction.html - - - /articles/enrichR.html - - - /articles/export_data.html - - - /articles/feature_selection.html - - - /articles/filtering.html - - - /articles/find_marker.html - - - /articles/heatmap.html - - - /articles/import_annotation.html - - - /articles/import_data.html - - - 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/reference/detectCellOutlier.html - - - /reference/diffAbundanceFET.html - - - /reference/discreteColorPalette.html - - - /reference/distinctColors.html - - - /reference/downSampleCells.html - - - /reference/downSampleDepth.html - - - /reference/expData-ANY-character-method.html - - - /reference/expData-set-ANY-character-CharacterOrNullOrMissing-logical-method.html - - - /reference/expData-set.html - - - /reference/expData.html - - - /reference/expDataNames-ANY-method.html - - - /reference/expDataNames.html - - - /reference/expDeleteDataTag.html - - - /reference/expSetDataTag.html - - - /reference/expTaggedData.html - - - /reference/exportSCE.html - - - /reference/exportSCEToSeurat.html - - - /reference/exportSCEtoAnnData.html - - - /reference/exportSCEtoFlatFile.html - - - /reference/featureIndex.html - - - /reference/featureNameDedup.html - - - /reference/filterSCData.html - - - /reference/findMarkerDiffExp.html - - - /reference/findMarkerTopTable.html - - - 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+/reference/sctkListGeneSetCollections.html +/reference/sctkPythonInstallConda.html +/reference/sctkPythonInstallVirtualEnv.html +/reference/selectSCTKConda.html +/reference/selectSCTKVirtualEnvironment.html +/reference/setRowNames.html +/reference/setSCTKDisplayRow.html +/reference/setSampleSummaryStatsTable-set.html +/reference/simpleLog.html +/reference/singleCellTK.html +/reference/subDiffEx.html +/reference/subsetSCECols.html +/reference/subsetSCERows.html +/reference/summarizeSCE.html +/reference/thresholdGenes.html +/reference/trimCounts.html +/reference/visPlot.html + diff --git a/vignettes/articles/heatmap.Rmd b/vignettes/articles/heatmap.Rmd index fe018f2e8..62f85569b 100644 --- a/vignettes/articles/heatmap.Rmd +++ b/vignettes/articles/heatmap.Rmd @@ -313,14 +313,11 @@ colAnnotattionColor <- list( ```{R split, eval=TRUE, cache=TRUE} # Create a new label in the rowData using the cluster markers - +library(dplyr) data.frame(rowData(sce2)) %>% left_join(topMarkers, by = c("feature_name" = "Gene")) %>% rename("cluster_markers" = "scranSNN_PCA") -> new_row_data - -rownames(new_row_data)<-new_row_data$feature_name - -rowData(sce2)<-new_row_data +rowData(sce2)$cluster_markers <-new_row_data$cluster_markers plotSCEHeatmap(inSCE = sce2, useAssay = "logcounts", featureIndex = topMarkers$Gene, colDataName = c("type"), aggregateCol = "scranSNN_PCA", rowGap = grid::unit(2, 'mm'),rowLabel = TRUE, rowDataName = "cluster_markers", rowSplitBy = "cluster_markers")