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update multiomics tutorial
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@josschavezf
josschavezf committed Sep 30, 2024
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140 changes: 74 additions & 66 deletions vignettes/visium_cytassist_human_glioblastoma.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,23 @@ The [Human glioblastoma (FFPE) dataset](https://www.10xgenomics.com/resources/da

More information about this dataset can be found [here](https://www.10xgenomics.com/resources/datasets/gene-and-protein-expression-library-of-human-glioblastoma-cytassist-ffpe-2-standard).

# Download dataset

```{r, eval=FALSE}
dir.create("data")
download.file(url = "https://cf.10xgenomics.com/samples/spatial-exp/2.1.0/CytAssist_FFPE_Protein_Expression_Human_Glioblastoma/CytAssist_FFPE_Protein_Expression_Human_Glioblastoma_raw_feature_bc_matrix.tar.gz",
destfile = "data/CytAssist_FFPE_Protein_Expression_Human_Glioblastoma_raw_feature_bc_matrix.tar.gz")
download.file(url = "https://cf.10xgenomics.com/samples/spatial-exp/2.1.0/CytAssist_FFPE_Protein_Expression_Human_Glioblastoma/CytAssist_FFPE_Protein_Expression_Human_Glioblastoma_spatial.tar.gz",
destfile = "data/CytAssist_FFPE_Protein_Expression_Human_Glioblastoma_spatial.tar.gz")
untar("data/CytAssist_FFPE_Protein_Expression_Human_Glioblastoma_raw_feature_bc_matrix.tar.gz",
exdir = "data")
untar("data/CytAssist_FFPE_Protein_Expression_Human_Glioblastoma_spatial.tar.gz",
exdir = "data")
```

# Start Giotto

```{r, eval=FALSE}
Expand Down Expand Up @@ -107,7 +124,7 @@ spatPlot2D(gobject = visium,
point_alpha = 0.7)
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/0-spatPlot2D.png")
```

Expand Down Expand Up @@ -135,7 +152,7 @@ spatPlot2D(gobject = visium,
color_as_factor = FALSE)
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/1-spatPlot2D.png")
```

Expand Down Expand Up @@ -169,7 +186,7 @@ spatPlot2D(gobject = visium,
color_as_factor = FALSE)
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/2-spatPlot2D.png")
```

Expand All @@ -189,7 +206,7 @@ visium <- runPCA(gobject = visium)
screePlot(visium, ncp = 30)
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/3-screePlot.png")
```

Expand All @@ -198,7 +215,7 @@ knitr::include_graphics("images/visium_cytassist_human_glioblastoma/3-screePlot.
plotPCA(gobject = visium)
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/4-PCA.png")
```

Expand All @@ -214,7 +231,7 @@ screePlot(visium,
ncp = 30)
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/5-screePlot.png")
```

Expand All @@ -225,7 +242,7 @@ plotPCA(gobject = visium,
feat_type = "protein")
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/6-PCA.png")
```

Expand Down Expand Up @@ -273,7 +290,7 @@ plotUMAP(gobject = visium,
point_size = 2)
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/7-UMAP.png")
```

Expand All @@ -292,7 +309,7 @@ plotUMAP(gobject = visium,
point_size = 2)
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/8-UMAP.png")
```

Expand All @@ -306,7 +323,7 @@ spatPlot2D(gobject = visium,
point_size = 2)
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/9-spatPlot2D.png")
```

Expand All @@ -320,7 +337,7 @@ spatPlot2D(gobject = visium,
point_size = 2)
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/10-spatPlot2D.png")
```

Expand Down Expand Up @@ -348,23 +365,15 @@ visium <- createNearestNetwork(gobject = visium,
# Run WNN
visium <- runWNN(visium,
spat_unit = "cell",
modality_1 = "rna",
modality_2 = "protein",
pca_name_modality_1 = "pca",
pca_name_modality_2 = "protein.pca",
feat_types = c("rna", "protein"),
reduction_methods = c("pca", "pca"),
reduction_names = c("pca", "protein.pca"),
k = 20,
integrated_feat_type = NULL,
matrix_result_name = NULL,
w_name_modality_1 = NULL,
w_name_modality_2 = NULL,
verbose = TRUE)
# Run Integrated umap
visium <- runIntegratedUMAP(visium,
modality1 = "rna",
modality2 = "protein",
spread = 5,
min_dist = 0.5,
feat_types = c("rna", "protein"),
force = FALSE)
# Calculate integrated clusters
Expand All @@ -374,7 +383,7 @@ visium <- doLeidenCluster(gobject = visium,
nn_network_to_use = "kNN",
network_name = "integrated_kNN",
name = "integrated_leiden_clus",
resolution = 1)
resolution = 0.5)
# Visualize integrated umap
plotUMAP(gobject = visium,
Expand All @@ -388,7 +397,7 @@ plotUMAP(gobject = visium,
axis_text = 10 )
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/11-UMAP.png")
```

Expand All @@ -403,7 +412,7 @@ spatPlot2D(visium,
title = "Integrated Leiden clustering")
```

```{r, echo=FALSE, out.width="60%"}
```{r, echo=FALSE, out.width="60%", fig.align='center'}
knitr::include_graphics("images/visium_cytassist_human_glioblastoma/12-spatPlot2D.png")
```

Expand All @@ -414,9 +423,9 @@ sessionInfo()
```

```{r, eval=FALSE}
R version 4.4.0 (2024-04-24)
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.5
Running under: macOS 15.0
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
Expand All @@ -432,45 +441,44 @@ attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Giotto_4.1.0 GiottoClass_0.3.4
[1] Giotto_4.1.3 GiottoClass_0.4.0
loaded via a namespace (and not attached):
[1] colorRamp2_0.1.0 deldir_2.0-4 rlang_1.1.4
[4] magrittr_2.0.3 RcppAnnoy_0.0.22 GiottoUtils_0.1.10
[7] matrixStats_1.3.0 compiler_4.4.0 png_0.1-8
[10] systemfonts_1.1.0 vctrs_0.6.5 reshape2_1.4.4
[13] stringr_1.5.1 pkgconfig_2.0.3 SpatialExperiment_1.14.0
[16] crayon_1.5.3 fastmap_1.2.0 backports_1.5.0
[19] magick_2.8.4 XVector_0.44.0 labeling_0.4.3
[22] utf8_1.2.4 rmarkdown_2.27 UCSC.utils_1.0.0
[25] ragg_1.3.2 purrr_1.0.2 xfun_0.46
[28] beachmat_2.20.0 zlibbioc_1.50.0 GenomeInfoDb_1.40.1
[31] jsonlite_1.8.8 DelayedArray_0.30.1 BiocParallel_1.38.0
[34] terra_1.7-78 irlba_2.3.5.1 parallel_4.4.0
[37] R6_2.5.1 stringi_1.8.4 RColorBrewer_1.1-3
[40] reticulate_1.38.0 parallelly_1.38.0 GenomicRanges_1.56.1
[43] scattermore_1.2 Rcpp_1.0.13 SummarizedExperiment_1.34.0
[46] knitr_1.48 future.apply_1.11.2 R.utils_2.12.3
[49] IRanges_2.38.1 Matrix_1.7-0 igraph_2.0.3
[52] tidyselect_1.2.1 rstudioapi_0.16.0 abind_1.4-5
[55] yaml_2.3.10 codetools_0.2-20 listenv_0.9.1
[58] lattice_0.22-6 tibble_3.2.1 plyr_1.8.9
[61] Biobase_2.64.0 withr_3.0.0 evaluate_0.24.0
[64] future_1.34.0 pillar_1.9.0 MatrixGenerics_1.16.0
[67] checkmate_2.3.2 stats4_4.4.0 plotly_4.10.4
[70] generics_0.1.3 dbscan_1.2-0 sp_2.1-4
[73] S4Vectors_0.42.1 ggplot2_3.5.1 munsell_0.5.1
[76] scales_1.3.0 globals_0.16.3 gtools_3.9.5
[79] glue_1.7.0 lazyeval_0.2.2 tools_4.4.0
[82] GiottoVisuals_0.2.4 data.table_1.15.4 ScaledMatrix_1.12.0
[85] cowplot_1.1.3 grid_4.4.0 tidyr_1.3.1
[88] colorspace_2.1-1 SingleCellExperiment_1.26.0 GenomeInfoDbData_1.2.12
[91] BiocSingular_1.20.0 rsvd_1.0.5 cli_3.6.3
[94] textshaping_0.4.0 fansi_1.0.6 S4Arrays_1.4.1
[97] viridisLite_0.4.2 dplyr_1.1.4 uwot_0.2.2
[100] gtable_0.3.5 R.methodsS3_1.8.2 digest_0.6.36
[103] BiocGenerics_0.50.0 SparseArray_1.4.8 ggrepel_0.9.5
[106] rjson_0.2.21 htmlwidgets_1.6.4 farver_2.1.2
[109] htmltools_0.5.8.1 R.oo_1.26.0 lifecycle_1.0.4
[112] httr_1.4.7
[4] magrittr_2.0.3 RcppAnnoy_0.0.22 GiottoUtils_0.1.12
[7] matrixStats_1.4.1 compiler_4.4.1 png_0.1-8
[10] systemfonts_1.1.0 vctrs_0.6.5 pkgconfig_2.0.3
[13] SpatialExperiment_1.14.0 crayon_1.5.3 fastmap_1.2.0
[16] backports_1.5.0 magick_2.8.5 XVector_0.44.0
[19] labeling_0.4.3 utf8_1.2.4 rmarkdown_2.28
[22] UCSC.utils_1.0.0 ragg_1.3.3 purrr_1.0.2
[25] xfun_0.47 beachmat_2.20.0 zlibbioc_1.50.0
[28] GenomeInfoDb_1.40.1 jsonlite_1.8.9 DelayedArray_0.30.1
[31] BiocParallel_1.38.0 terra_1.7-78 irlba_2.3.5.1
[34] parallel_4.4.1 R6_2.5.1 RColorBrewer_1.1-3
[37] reticulate_1.39.0 parallelly_1.38.0 GenomicRanges_1.56.1
[40] scattermore_1.2 Rcpp_1.0.13 SummarizedExperiment_1.34.0
[43] knitr_1.48 future.apply_1.11.2 R.utils_2.12.3
[46] IRanges_2.38.1 Matrix_1.7-0 igraph_2.0.3
[49] tidyselect_1.2.1 rstudioapi_0.16.0 abind_1.4-8
[52] yaml_2.3.10 codetools_0.2-20 listenv_0.9.1
[55] lattice_0.22-6 tibble_3.2.1 Biobase_2.64.0
[58] withr_3.0.1 evaluate_1.0.0 future_1.34.0
[61] pillar_1.9.0 MatrixGenerics_1.16.0 checkmate_2.3.2
[64] stats4_4.4.1 plotly_4.10.4 generics_0.1.3
[67] dbscan_1.2-0 sp_2.1-4 S4Vectors_0.42.1
[70] ggplot2_3.5.1 munsell_0.5.1 scales_1.3.0
[73] gtools_3.9.5 globals_0.16.3 glue_1.7.0
[76] lazyeval_0.2.2 tools_4.4.1 GiottoVisuals_0.2.5
[79] data.table_1.16.0 ScaledMatrix_1.12.0 cowplot_1.1.3
[82] grid_4.4.1 tidyr_1.3.1 colorspace_2.1-1
[85] SingleCellExperiment_1.26.0 GenomeInfoDbData_1.2.12 BiocSingular_1.20.0
[88] rsvd_1.0.5 cli_3.6.3 textshaping_0.4.0
[91] fansi_1.0.6 S4Arrays_1.4.1 viridisLite_0.4.2
[94] dplyr_1.1.4 uwot_0.2.2 gtable_0.3.5
[97] R.methodsS3_1.8.2 digest_0.6.37 BiocGenerics_0.50.0
[100] SparseArray_1.4.8 ggrepel_0.9.6 rjson_0.2.23
[103] htmlwidgets_1.6.4 farver_2.1.2 htmltools_0.5.8.1
[106] R.oo_1.26.0 lifecycle_1.0.4 httr_1.4.7
```

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