diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/0-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/0-spatInSituPlotPoints.png new file mode 100644 index 000000000..601991aed Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/0-spatInSituPlotPoints.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/1-spatPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/1-spatPlot2D.png new file mode 100644 index 000000000..26b277b99 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/1-spatPlot2D.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/10-HVFplot.png b/vignettes/images/nanostring_cosmx_lung_cancer/10-HVFplot.png new file mode 100644 index 000000000..b7ad782e1 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/10-HVFplot.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/10.1_gini_violin.png b/vignettes/images/nanostring_cosmx_lung_cancer/10.1_gini_violin.png deleted file mode 100644 index 32f06a26b..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/10.1_gini_violin.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/10.2_heatmap.png b/vignettes/images/nanostring_cosmx_lung_cancer/10.2_heatmap.png deleted file mode 100644 index 1a3a4e992..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/10.2_heatmap.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/10.3_gini_genes.png b/vignettes/images/nanostring_cosmx_lung_cancer/10.3_gini_genes.png deleted file mode 100644 index 1d3f627d5..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/10.3_gini_genes.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/11-screePlot.png b/vignettes/images/nanostring_cosmx_lung_cancer/11-screePlot.png new file mode 100644 index 000000000..4de0a3e77 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/11-screePlot.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/11_anno_umap.png b/vignettes/images/nanostring_cosmx_lung_cancer/11_anno_umap.png deleted file mode 100644 index 88b17bf8d..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/11_anno_umap.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/12-PCA.png b/vignettes/images/nanostring_cosmx_lung_cancer/12-PCA.png new file mode 100644 index 000000000..7df8604ff Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/12-PCA.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/12_spatdim_type.png b/vignettes/images/nanostring_cosmx_lung_cancer/12_spatdim_type.png deleted file mode 100644 index 1d28fe10c..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/12_spatdim_type.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/13-UMAP.png b/vignettes/images/nanostring_cosmx_lung_cancer/13-UMAP.png new file mode 100644 index 000000000..cad52f3f0 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/13-UMAP.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/13_insitu_type.png b/vignettes/images/nanostring_cosmx_lung_cancer/13_insitu_type.png deleted file mode 100644 index b85be6c39..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/13_insitu_type.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/14-dimFeatPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/14-dimFeatPlot2D.png new file mode 100644 index 000000000..4f01671b1 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/14-dimFeatPlot2D.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/14_ICF.png b/vignettes/images/nanostring_cosmx_lung_cancer/14_ICF.png deleted file mode 100644 index db1d13f18..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/14_ICF.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/15-UMAP.png b/vignettes/images/nanostring_cosmx_lung_cancer/15-UMAP.png new file mode 100644 index 000000000..d965ff763 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/15-UMAP.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/16-spatDimPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/16-spatDimPlot2D.png new file mode 100644 index 000000000..f018d6e7f Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/16-spatDimPlot2D.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/17-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/17-spatInSituPlotPoints.png new file mode 100644 index 000000000..86b72d066 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/17-spatInSituPlotPoints.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/18-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/18-spatInSituPlotPoints.png new file mode 100644 index 000000000..6f0974916 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/18-spatInSituPlotPoints.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/19-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/19-spatInSituPlotPoints.png new file mode 100644 index 000000000..5e547313f Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/19-spatInSituPlotPoints.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/1_inSituFeats.png b/vignettes/images/nanostring_cosmx_lung_cancer/1_inSituFeats.png deleted file mode 100644 index 1596968d2..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/1_inSituFeats.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/2-filterDistributions.png b/vignettes/images/nanostring_cosmx_lung_cancer/2-filterDistributions.png new file mode 100644 index 000000000..49572ddf2 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/2-filterDistributions.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/20-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/20-spatInSituPlotPoints.png new file mode 100644 index 000000000..735c95156 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/20-spatInSituPlotPoints.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/21-spatFeatPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/21-spatFeatPlot2D.png new file mode 100644 index 000000000..b39f28dfc Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/21-spatFeatPlot2D.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/22-violinPlot.png b/vignettes/images/nanostring_cosmx_lung_cancer/22-violinPlot.png new file mode 100644 index 000000000..ef4b8dc62 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/22-violinPlot.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/23-plotMetaDataHeatmap.png b/vignettes/images/nanostring_cosmx_lung_cancer/23-plotMetaDataHeatmap.png new file mode 100644 index 000000000..ea54d26f6 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/23-plotMetaDataHeatmap.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/24-dimFeatPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/24-dimFeatPlot2D.png new file mode 100644 index 000000000..c78b0af2c Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/24-dimFeatPlot2D.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/25-UMAP.png b/vignettes/images/nanostring_cosmx_lung_cancer/25-UMAP.png new file mode 100644 index 000000000..bcd6ef84d Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/25-UMAP.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/26-spatDimPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/26-spatDimPlot2D.png new file mode 100644 index 000000000..eed7eee2e Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/26-spatDimPlot2D.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/27-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/27-spatInSituPlotPoints.png new file mode 100644 index 000000000..3bbb11ab1 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/27-spatInSituPlotPoints.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/28-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/28-spatInSituPlotPoints.png new file mode 100644 index 000000000..c0f8440ed Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/28-spatInSituPlotPoints.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/2_spatCentroids.png b/vignettes/images/nanostring_cosmx_lung_cancer/2_spatCentroids.png deleted file mode 100644 index ac8c7efe3..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/2_spatCentroids.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/3-filterDistributions.png b/vignettes/images/nanostring_cosmx_lung_cancer/3-filterDistributions.png new file mode 100644 index 000000000..d97037dea Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/3-filterDistributions.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/3.1_totalexpr.png b/vignettes/images/nanostring_cosmx_lung_cancer/3.1_totalexpr.png deleted file mode 100644 index 5ae2bce5f..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/3.1_totalexpr.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/3.2_totalnegprbe.png b/vignettes/images/nanostring_cosmx_lung_cancer/3.2_totalnegprbe.png deleted file mode 100644 index f00a32730..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/3.2_totalnegprbe.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/4-spatInSituPlotDensity.png b/vignettes/images/nanostring_cosmx_lung_cancer/4-spatInSituPlotDensity.png new file mode 100644 index 000000000..1ff2176f8 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/4-spatInSituPlotDensity.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/4_inSituDens.png b/vignettes/images/nanostring_cosmx_lung_cancer/4_inSituDens.png deleted file mode 100644 index 104044fb0..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/4_inSituDens.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5-filterDistributions.png b/vignettes/images/nanostring_cosmx_lung_cancer/5-filterDistributions.png new file mode 100644 index 000000000..5dc4c8d38 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/5-filterDistributions.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5.1_rna_norm_total_hist.png b/vignettes/images/nanostring_cosmx_lung_cancer/5.1_rna_norm_total_hist.png deleted file mode 100644 index 9f2800ee8..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/5.1_rna_norm_total_hist.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5.2_neg_norm_total_hist.png b/vignettes/images/nanostring_cosmx_lung_cancer/5.2_neg_norm_total_hist.png deleted file mode 100644 index 466cd969c..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/5.2_neg_norm_total_hist.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5.3_color_centroids.png b/vignettes/images/nanostring_cosmx_lung_cancer/5.3_color_centroids.png deleted file mode 100644 index 57eb5d363..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/5.3_color_centroids.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5.4_rna_color_polys.png b/vignettes/images/nanostring_cosmx_lung_cancer/5.4_rna_color_polys.png deleted file mode 100644 index 3ebd98b93..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/5.4_rna_color_polys.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/5.5_neg_color_polys.png b/vignettes/images/nanostring_cosmx_lung_cancer/5.5_neg_color_polys.png deleted file mode 100644 index 1b2cf4f59..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/5.5_neg_color_polys.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6-filterDistributions.png b/vignettes/images/nanostring_cosmx_lung_cancer/6-filterDistributions.png new file mode 100644 index 000000000..d84a6d724 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/6-filterDistributions.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6.1_pearson_HVF.png b/vignettes/images/nanostring_cosmx_lung_cancer/6.1_pearson_HVF.png deleted file mode 100644 index 9a10e0735..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/6.1_pearson_HVF.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6.2_screeplot.png b/vignettes/images/nanostring_cosmx_lung_cancer/6.2_screeplot.png deleted file mode 100644 index 4a8c1775c..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/6.2_screeplot.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6.3_PCA.png b/vignettes/images/nanostring_cosmx_lung_cancer/6.3_PCA.png deleted file mode 100644 index 36b89acc0..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/6.3_PCA.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6.4_UMAP.png b/vignettes/images/nanostring_cosmx_lung_cancer/6.4_UMAP.png deleted file mode 100644 index 647be4115..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/6.4_UMAP.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/6.5_UMAP_feats.png b/vignettes/images/nanostring_cosmx_lung_cancer/6.5_UMAP_feats.png deleted file mode 100644 index 814ad53b1..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/6.5_UMAP_feats.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/7-spatPlot2D.png b/vignettes/images/nanostring_cosmx_lung_cancer/7-spatPlot2D.png new file mode 100644 index 000000000..a86f2cd05 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/7-spatPlot2D.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/7.1_UMAP_leiden.png b/vignettes/images/nanostring_cosmx_lung_cancer/7.1_UMAP_leiden.png deleted file mode 100644 index 9882f88d9..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/7.1_UMAP_leiden.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/7.2_spatdim_leiden.png b/vignettes/images/nanostring_cosmx_lung_cancer/7.2_spatdim_leiden.png deleted file mode 100644 index 56364bc66..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/7.2_spatdim_leiden.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/7.3_spatinsitu_leiden.png b/vignettes/images/nanostring_cosmx_lung_cancer/7.3_spatinsitu_leiden.png deleted file mode 100644 index e797d4b8c..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/7.3_spatinsitu_leiden.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/8-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/8-spatInSituPlotPoints.png new file mode 100644 index 000000000..7ea3dcdde Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/8-spatInSituPlotPoints.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/8.1_smallfov_points.png b/vignettes/images/nanostring_cosmx_lung_cancer/8.1_smallfov_points.png deleted file mode 100644 index 0b0f95bc9..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/8.1_smallfov_points.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/8.2_smallfov_poly.png b/vignettes/images/nanostring_cosmx_lung_cancer/8.2_smallfov_poly.png deleted file mode 100644 index 3f091e877..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/8.2_smallfov_poly.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/8.3_smallfov_leiden.png b/vignettes/images/nanostring_cosmx_lung_cancer/8.3_smallfov_leiden.png deleted file mode 100644 index 09bae069c..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/8.3_smallfov_leiden.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/9-spatInSituPlotPoints.png b/vignettes/images/nanostring_cosmx_lung_cancer/9-spatInSituPlotPoints.png new file mode 100644 index 000000000..018e9f335 Binary files /dev/null and b/vignettes/images/nanostring_cosmx_lung_cancer/9-spatInSituPlotPoints.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/9_binspect_genes.png b/vignettes/images/nanostring_cosmx_lung_cancer/9_binspect_genes.png deleted file mode 100644 index 2a53edf99..000000000 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/9_binspect_genes.png and /dev/null differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/mat_comparison.png b/vignettes/images/nanostring_cosmx_lung_cancer/mat_comparison.png index 05f266f92..f93c62b2c 100644 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/mat_comparison.png and b/vignettes/images/nanostring_cosmx_lung_cancer/mat_comparison.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/preview_negprb.png b/vignettes/images/nanostring_cosmx_lung_cancer/preview_negprb.png index 76d059202..e5678349e 100644 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/preview_negprb.png and b/vignettes/images/nanostring_cosmx_lung_cancer/preview_negprb.png differ diff --git a/vignettes/images/nanostring_cosmx_lung_cancer/values_diff.png b/vignettes/images/nanostring_cosmx_lung_cancer/values_diff.png index 09dcb340b..180963aeb 100644 Binary files a/vignettes/images/nanostring_cosmx_lung_cancer/values_diff.png and b/vignettes/images/nanostring_cosmx_lung_cancer/values_diff.png differ diff --git a/vignettes/nanostring_cosmx_lung_cancer.Rmd b/vignettes/nanostring_cosmx_lung_cancer.Rmd index 6b4c016cf..85a51c894 100644 --- a/vignettes/nanostring_cosmx_lung_cancer.Rmd +++ b/vignettes/nanostring_cosmx_lung_cancer.Rmd @@ -34,18 +34,15 @@ if(!genv_exists){ # Setup - ```{r, eval=FALSE} library(Giotto) # Custom color palettes from rcartocolor -# pal10 = rcartocolor::carto_pal(n = 10, name = "Pastel") -pal10 = c("#66C5CC","#F6CF71","#F89C74","#DCB0F2","#87C55F", - "#9EB9F3","#FE88B1","#C9DB74","#8BE0A4","#B3B3B3") +pal10 <- c("#66C5CC","#F6CF71","#F89C74","#DCB0F2","#87C55F", + "#9EB9F3","#FE88B1","#C9DB74","#8BE0A4","#B3B3B3") -# viv10 = rcartocolor::carto_pal(n = 10, name = "Vivid") -viv10 = c("#E58606","#5D69B1","#52BCA3","#99C945","#CC61B0", - "#24796C","#DAA51B","#2F8AC4","#764E9F","#A5AA99") +viv10 <- c("#E58606","#5D69B1","#52BCA3","#99C945","#CC61B0", + "#24796C","#DAA51B","#2F8AC4","#764E9F","#A5AA99") # set working directory results_folder <- "/path/to/results/" @@ -65,7 +62,7 @@ instructions <- createGiottoInstructions(save_dir = results_folder, ``` -## CosMx Project loading function +# Create the Giotto object using the convenience function Convenience function for loading in the CosMx data. It loads subcellular transcript information and polygons and generates a `giotto` object with `giottoPoints` objects for both "rna" and "neg_probe" nested in the gobject `feat_info` slot, and a `giottoPolygon` object for the "cell" spatial unit in the `spatial_info` slot. @@ -76,7 +73,7 @@ Additionally, a comparison of the count matrix produced through the convenience ```{r, eval=FALSE} ## provide path to nanostring folder -data_path <- "/path/to/data/Lung12-Flat_files_and_images" +data_path <- "/path/to/data/" ## create giotto cosmx object fov_join <- createGiottoCosMxObject(cosmx_dir = data_path, @@ -89,7 +86,7 @@ showGiottoSpatialInfo(fov_join) ``` -# Data exploration and loading +# Manual creation of the Giotto object ## Subcellular detections (points info) @@ -108,7 +105,7 @@ showGiottoSpatialInfo(fov_join) ```{r, eval=FALSE} # load transcript coordinates -tx_coord_all <- data.table::fread(paste0(data_path, "Lung12_tx_file.csv")) +tx_coord_all <- data.table::fread(file.path(data_path, "Lung12_tx_file.csv")) colnames(tx_coord_all) @@ -169,8 +166,7 @@ plot(neg_points, ```{r, eval=FALSE} # load field of vision (fov) positions -fov_offset_file <- data.table::fread(paste0(data_path, - "Lung12_fov_positions_file.csv")) +fov_offset_file <- data.table::fread(file.path(data_path, "Lung12_fov_positions_file.csv")) ``` @@ -187,7 +183,7 @@ gobjects_list <- list() id_set <- c("02", "03", "04") ``` -# Create a Giotto Object for each FOV +## Create a Giotto Object for each FOV ```{r, eval=FALSE} for(fov_i in 1:length(id_set)) { @@ -235,7 +231,7 @@ for(fov_i in 1:length(id_set)) { name = "composite") fovsubset <- addGiottoImage(gobject = fovsubset, - largeImages = list(composite)) + images = list(composite)) fovsubset <- convertGiottoLargeImageToMG(giottoLargeImage = composite, @@ -248,7 +244,7 @@ for(fov_i in 1:length(id_set)) { ``` -# Join FOV Giotto Objects +## Join FOV Giotto Objects ```{r, eval=FALSE} @@ -293,11 +289,10 @@ spatInSituPlotPoints(fov_join, polygon_feat_type = "cell", polygon_color = "white", polygon_line_size = 0.03, - save_param = list(base_height = 3, - save_name = "1_inSituFeats")) + save_param = list(base_height = 3)) ``` -![](images/nanostring_cosmx_lung_cancer/1_inSituFeats.png) +![](images/nanostring_cosmx_lung_cancer/0-spatInSituPlotPoints.png) ## Visualize Cell Centroids @@ -311,11 +306,10 @@ spatPlot2D(gobject = fov_join, point_size = 0.01, point_alpha = 0.5, coord_fix_ratio = 1, - save_param = list(base_height = 2, - save_name = "2_spatCentroids")) + save_param = list(base_height = 2)) ``` -![](images/nanostring_cosmx_lung_cancer/2_spatCentroids.png) +![](images/nanostring_cosmx_lung_cancer/1-spatPlot2D.png) # Aggregate subcellular features @@ -354,25 +348,22 @@ filterDistributions(fov_join, method = "sum", feat_type = "rna", nr_bins = 100, - save_param = list(base_height = 3, - save_name = "3.1_totalexpr")) + save_param = list(base_height = 3)) +``` + +![](images/nanostring_cosmx_lung_cancer/2-filterDistributions.png) +```{r, eval=FALSE} filterDistributions(fov_join, plot_type = "hist", detection = "cells", method = "sum", feat_type = "neg_probe", nr_bins = 25, - save_param = list(base_height = 3, - save_name = "3.2_totalnegprbe")) + save_param = list(base_height = 3)) ``` - -**RNA** -![](images/nanostring_cosmx_lung_cancer/3.1_totalexpr.png) - -**Negative Probes** -![](images/nanostring_cosmx_lung_cancer/3.2_totalnegprbe.png) +![](images/nanostring_cosmx_lung_cancer/3-filterDistributions.png) ## 2D Density Plots @@ -383,11 +374,10 @@ spatInSituPlotDensity(gobject = fov_join, feats = c("MMP2", "VEGFA", "IGF1R", "MKI67", "EPCAM", "KRT8"), cow_n_col = 2, - save_param = list(base_height = 4, - save_name = "4_inSituDens")) + save_param = list(base_height = 4)) ``` -![](images/nanostring_cosmx_lung_cancer/4_inSituDens.png) +![](images/nanostring_cosmx_lung_cancer/4-spatInSituPlotDensity.png) ## Extract Data from Giotto Object @@ -471,9 +461,8 @@ pl_g <- pl_g + theme(panel.grid.major = element_blank(), combplot <- cowplot::plot_grid(pl_n, pl_g, nrow = 2, labels = "AUTO") -combplot -ggsave(paste0(results_folder, "mat_comparison.png")) +ggsave(file.path(results_folder, "mat_comparison.png"), combplot) ``` ![](images/nanostring_cosmx_lung_cancer/mat_comparison.png) @@ -494,9 +483,8 @@ pl <- ggplot() pl <- pl + geom_bar(data = vartestDT, aes(x = diff)) pl <- pl + theme_bw() pl <- pl + labs(x = "difference nanostring - Giotto") -pl -ggsave(paste0(results_folder,"values_diff.png")) +ggsave(file.path(results_folder,"values_diff.png"), pl) testDT[order(x)] ``` @@ -509,9 +497,7 @@ testDT[, .N, by = "method"] testDT[, method, by = combo][, sum(duplicated(combo))] ``` - -Overall, the nanostring matrix has **416099 - 415952 = 147** more non-zero values than giotto's matrix for FOV2. Within the **411050** shared entries that were called by both methods (common i and j indices), there appears to be no major bias in terms of counts/values assigned. Moreover, the vast majority of these shared entries have the same values (difference of 0). - +Overall, the nanostring matrix has **416099 - 415952 = 147** more non-zero values than giotto's matrix for FOV2. Within the **411053** shared entries that were called by both methods (common i and j indices), there appears to be no major bias in terms of counts/values assigned. Moreover, the vast majority of these shared entries have the same values (difference of 0). # Filtering and normalization @@ -587,27 +573,22 @@ filterDistributions(fov_join, expression_values = "normalized", method = "sum", nr_bins = 100, - save_param = list(base_height = 3, - save_name = "5.1_rna_norm_total_hist")) + save_param = list(base_height = 3)) +``` +![](images/nanostring_cosmx_lung_cancer/5-filterDistributions.png) + +```{r, eval=FALSE} filterDistributions(fov_join, detection = "cell", feat_type = "neg_probe", expression_values = "normalized", method = "sum", nr_bins = 20, - save_param = list(base_height = 3, - save_name = "5.2_neg_norm_total_hist")) + save_param = list(base_height = 3)) ``` - -**RNA** - -![](images/nanostring_cosmx_lung_cancer/5.1_rna_norm_total_hist.png) - -**Negative Probe** - -![](images/nanostring_cosmx_lung_cancer/5.2_neg_norm_total_hist.png) +![](images/nanostring_cosmx_lung_cancer/6-filterDistributions.png) ## Plot spatially as centroids @@ -619,11 +600,10 @@ spatPlot2D(gobject = fov_join, image_name = image_names, point_size = 0.9, point_alpha = 0.75, - save_param = list(base_height = 2, - save_name = "5.3_color_centroids")) + save_param = list(base_height = 2)) ``` -![](images/nanostring_cosmx_lung_cancer/5.3_color_centroids.png) +![](images/nanostring_cosmx_lung_cancer/7-spatPlot2D.png) ## Plot spatially as color-scaled polygons @@ -634,9 +614,12 @@ spatInSituPlotPoints(fov_join, polygon_line_size = 0.05, polygon_fill = "total_expr", polygon_fill_as_factor = FALSE, - save_param = list(base_height = 2, - save_name = "5.4_rna_color_polys")) + save_param = list(base_height = 2)) +``` + +![](images/nanostring_cosmx_lung_cancer/8-spatInSituPlotPoints.png) +```{r, eval=FALSE} spatInSituPlotPoints(fov_join, feat_type = "neg_probe", show_polygon = TRUE, @@ -644,18 +627,10 @@ spatInSituPlotPoints(fov_join, polygon_line_size = 0.05, polygon_fill = "total_expr", polygon_fill_as_factor = FALSE, - save_param = list(base_height = 2, - save_name = "5.5_neg_color_polys")) + save_param = list(base_height = 2)) ``` - -**RNA** - -![](images/nanostring_cosmx_lung_cancer/5.4_rna_color_polys.png) - -**Negative Probe** - -![](images/nanostring_cosmx_lung_cancer/5.5_neg_color_polys.png) +![](images/nanostring_cosmx_lung_cancer/9-spatInSituPlotPoints.png) # Dimension Reduction @@ -669,15 +644,16 @@ PCA generation will also be based on the "pearson" matrix. Scaling and centering fov_join <- calculateHVF(fov_join, method = "var_p_resid", expression_values = "pearson", - save_param = list(base_height = 5, - save_name = "6.1_pearson_HVF")) + save_plot = TRUE) +# If you get an Error related to future.apply, please modify the maximum size +# of global variables by running: options(future.globals.maxSize = 1e10) # print HVFs gene_metadata <- fDataDT(fov_join) gene_metadata[hvf == "yes", feat_ID] ``` -![](images/nanostring_cosmx_lung_cancer/6.1_pearson_HVF.png) +![](images/nanostring_cosmx_lung_cancer/10-HVFplot.png) ```{r, eval=FALSE} fov_join <- runPCA(fov_join, @@ -687,19 +663,20 @@ fov_join <- runPCA(fov_join, # screeplot uses the generated PCA. No need to specify expr values screePlot(fov_join, - ncp = 20, - save_param = list(save_name = "6.2_screeplot")) + ncp = 20) +``` + +![](images/nanostring_cosmx_lung_cancer/11-screePlot.png) +```{r, eval=FALSE} plotPCA(fov_join, cell_color = "nr_feats", # (from log norm statistics) color_as_factor = FALSE, point_size = 0.1, - point_shape = "no_border", - save_param = list(save_name = "6.3_PCA")) + point_shape = "no_border") ``` -![](images/nanostring_cosmx_lung_cancer/6.2_screeplot.png) -![](images/nanostring_cosmx_lung_cancer/6.3_PCA.png) +![](images/nanostring_cosmx_lung_cancer/12-PCA.png) ## Run UMAP @@ -709,11 +686,10 @@ fov_join <- runUMAP(fov_join, dimensions_to_use = 1:10, n_threads = 4) -plotUMAP(gobject = fov_join, - save_param = list(save_name = "6.4_UMAP")) +plotUMAP(gobject = fov_join) ``` -![](images/nanostring_cosmx_lung_cancer/6.4_UMAP.png) +![](images/nanostring_cosmx_lung_cancer/13-UMAP.png) ## Plot features on expression space @@ -726,11 +702,10 @@ dimFeatPlot2D(gobject = fov_join, point_shape = "no_border", point_size = 0.01, cow_n_col = 3, - save_param = list(base_height = 5, - save_name = "6.5_UMAP_feats")) + save_param = list(base_height = 5)) ``` -![](images/nanostring_cosmx_lung_cancer/6.5_UMAP_feats.png) +![](images/nanostring_cosmx_lung_cancer/14-dimFeatPlot2D.png) # Cluster @@ -750,11 +725,10 @@ plotUMAP(gobject = fov_join, cell_color = "leiden_clus", cell_color_code = pal10, show_NN_network = TRUE, - point_size = 2, - save_param = list(save_name = "7.1_UMAP_leiden")) + point_size = 2) ``` -![](images/nanostring_cosmx_lung_cancer/7.1_UMAP_leiden.png) +![](images/nanostring_cosmx_lung_cancer/15-UMAP.png) ## Visualize clustering on expression and spatial space @@ -765,11 +739,10 @@ spatDimPlot2D(gobject = fov_join, image_name = image_names, cell_color = "leiden_clus", cell_color_code = pal10, - spat_point_size = 1, - save_param = list(save_name = "7.2_spatdim_leiden")) + spat_point_size = 1) ``` -![](images/nanostring_cosmx_lung_cancer/7.2_spatdim_leiden.png) +![](images/nanostring_cosmx_lung_cancer/16-spatDimPlot2D.png) ## Map clustering spatially @@ -785,11 +758,10 @@ spatInSituPlotPoints(fov_join, polygon_fill = "leiden_clus", polygon_fill_as_factor = TRUE, polygon_fill_code = pal10, - save_param = list(base_height = 5, - save_name = "7.3_spatinsitu_leiden")) + save_param = list(base_height = 5)) ``` -![](images/nanostring_cosmx_lung_cancer/7.3_spatinsitu_leiden.png) +![](images/nanostring_cosmx_lung_cancer/17-spatInSituPlotPoints.png) # Small Subset Visualization @@ -812,10 +784,13 @@ spatInSituPlotPoints(smallfov, show_polygon = TRUE, polygon_color = "white", show_image = TRUE, - largeImage_name = "fov002-composite", - show_legend = FALSE, - save_param = list(save_name = "8.1_smallfov_points")) + image_name = "fov002-composite", + show_legend = FALSE) +``` +![](images/nanostring_cosmx_lung_cancer/18-spatInSituPlotPoints.png) + +```{r, eval=FALSE} # plot only the polygon outlines spatInSituPlotPoints(smallfov, polygon_line_size = 0.1, @@ -823,10 +798,13 @@ spatInSituPlotPoints(smallfov, polygon_color = "white", show_polygon = TRUE, show_image = TRUE, - largeImage_name = "fov002-composite", - show_legend = FALSE, - save_param = list(save_name = "8.2_smallfov_poly")) + image_name = "fov002-composite", + show_legend = FALSE) +``` + +![](images/nanostring_cosmx_lung_cancer/19-spatInSituPlotPoints.png) +```{r, eval=FALSE} # plot polygons colorlabeled with leiden clusters spatInSituPlotPoints(smallfov, polygon_line_size = 0.1, @@ -835,15 +813,11 @@ spatInSituPlotPoints(smallfov, polygon_fill_as_factor = TRUE, polygon_fill_code = pal10, show_image = TRUE, - largeImage_name = "fov002-composite", - show_legend = FALSE, - save_param = list(save_name = "8.3_smallfov_leiden")) + image_name = "fov002-composite", + show_legend = FALSE) ``` - -![](images/nanostring_cosmx_lung_cancer/8.1_smallfov_points.png) -![](images/nanostring_cosmx_lung_cancer/8.2_smallfov_poly.png) -![](images/nanostring_cosmx_lung_cancer/8.3_smallfov_leiden.png) +![](images/nanostring_cosmx_lung_cancer/20-spatInSituPlotPoints.png) # Spatial Expression Patterns @@ -861,15 +835,14 @@ km_spatialfeats <- binSpect(fov_join) # visualize spatial expression of selected genes obtained from binSpect spatFeatPlot2D(fov_join, expression_values = "normalized", - feats = km_spatialgenes$feats[1:10], + feats = km_spatialfeats$feats[1:10], point_shape = "no_border", point_border_stroke = 0.01, point_size = 0.01, - cow_n_col = 2, - save_param = list(save_name = "9_binspect_genes")) + cow_n_col = 2) ``` -![](images/nanostring_cosmx_lung_cancer/9_binspect_genes.png) +![](images/nanostring_cosmx_lung_cancer/21-spatFeatPlot2D.png) # Identify cluster differential expression genes @@ -893,11 +866,10 @@ topgenes_gini <- unique(markers_gini[, head(.SD, 2), by = "cluster"]$feats) violinPlot(fov_join, feats = topgenes_gini, cluster_column = "leiden_clus", - strip_position = "right", - save_param = list(save_name = "10.1_gini_violin")) + strip_position = "right") ``` -![](images/nanostring_cosmx_lung_cancer/10.1_gini_violin.png) +![](images/nanostring_cosmx_lung_cancer/22-violinPlot.png) ## Heatmap @@ -909,11 +881,10 @@ plotMetaDataHeatmap(fov_join, metadata_cols = "leiden_clus", selected_feats = topgenes_gini, custom_cluster_order = cluster_order, - save_param = list(base_height = 5, - save_name = "10.2_heatmap")) + save_param = list(base_height = 5)) ``` -![](images/nanostring_cosmx_lung_cancer/10.2_heatmap.png) +![](images/nanostring_cosmx_lung_cancer/23-plotMetaDataHeatmap.png) ## Plot gini genes on UMAP @@ -929,11 +900,10 @@ dimFeatPlot2D(fov_join, point_shape = "no_border", point_size = 0.001, cow_n_col = 4, - save_param = list(base_height = 8, - save_name = "10.3_gini_genes")) + save_param = list(base_height = 8)) ``` -![](images/nanostring_cosmx_lung_cancer/10.3_gini_genes.png) +![](images/nanostring_cosmx_lung_cancer/24-dimFeatPlot2D.png) ## Cell Type Annotation @@ -943,7 +913,7 @@ clusters_cell_types <- c("Normal Epithelial 1", "Cancer", "Stromal", "B-lineage" "Macrophage", "B-lineage", "Cancer", "Normal Epithelial 2", "Stromal", "B-lineage") -names(clusters_cell_types) = 1:10 +names(clusters_cell_types) <- 1:10 fov_join <- annotateGiotto(gobject = fov_join, annotation_vector = clusters_cell_types, @@ -953,11 +923,10 @@ fov_join <- annotateGiotto(gobject = fov_join, plotUMAP(fov_join, cell_color = "cell_types", cell_color_code = viv10, - point_size = 1.5, - save_param = list(save_name = "11_anno_umap")) + point_size = 1.5) ``` -![](images/nanostring_cosmx_lung_cancer/11_anno_umap.png) +![](images/nanostring_cosmx_lung_cancer/25-UMAP.png) ## Visualize @@ -967,11 +936,10 @@ spatDimPlot2D(gobject = fov_join, image_name = image_names, cell_color = "cell_types", cell_color_code = viv10, - spat_point_size = 1, - save_param = list(save_name = "12_spatdim_type")) + spat_point_size = 1) ``` -![](images/nanostring_cosmx_lung_cancer/12_spatdim_type.png) +![](images/nanostring_cosmx_lung_cancer/26-spatDimPlot2D.png) ```{r, eval=FALSE} spatInSituPlotPoints(fov_join, @@ -982,11 +950,10 @@ spatInSituPlotPoints(fov_join, polygon_fill = "cell_types", polygon_fill_as_factor = TRUE, polygon_fill_code = viv10, - save_param = list(base_height = 2, - save_name = "13_insitu_type")) + save_param = list(base_height = 2)) ``` -![](images/nanostring_cosmx_lung_cancer/13_insitu_type.png) +![](images/nanostring_cosmx_lung_cancer/27-spatInSituPlotPoints.png) # Interaction Changed Genes @@ -1013,11 +980,10 @@ spatInSituPlotPoints(fov_join, polygon_fill = "cell_types", polygon_fill_as_factor = TRUE, polygon_fill_code = pal10, - save_param = list(base_height = 6, - save_name = "14_ICF")) + save_param = list(base_height = 6)) ``` -![](images/nanostring_cosmx_lung_cancer/14_ICF.png) +![](images/nanostring_cosmx_lung_cancer/28-spatInSituPlotPoints.png) # Saving the giotto object @@ -1031,18 +997,20 @@ saveGiotto(gobject = fov_join, dir = "/directory/to/save/to/") ``` +# Session Info + ```{r, eval=FALSE} sessionInfo() ``` ```{r, eval=FALSE} -R version 4.3.2 (2023-10-31) -Platform: x86_64-apple-darwin20 (64-bit) -Running under: macOS Sonoma 14.3.1 +R version 4.4.1 (2024-06-14) +Platform: x86_64-apple-darwin20 +Running under: macOS Sonoma 14.6.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib -LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 +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 @@ -1054,42 +1022,44 @@ attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: -[1] ggplot2_3.4.4 Giotto_4.0.2 GiottoClass_0.1.3 +[1] ggplot2_3.5.1 Giotto_4.1.3 GiottoClass_0.4.0 loaded via a namespace (and not attached): - [1] tidyselect_1.2.0 viridisLite_0.4.2 dplyr_1.1.4 - [4] farver_2.1.1 GiottoVisuals_0.1.4 bitops_1.0-7 - [7] fastmap_1.1.1 SingleCellExperiment_1.24.0 RCurl_1.98-1.14 - [10] digest_0.6.34 rsvd_1.0.5 lifecycle_1.0.4 - [13] terra_1.7-71 dbscan_1.1-12 magrittr_2.0.3 - [16] compiler_4.3.2 rlang_1.1.3 tools_4.3.2 - [19] igraph_2.0.1.1 utf8_1.2.4 yaml_2.3.8 - [22] data.table_1.15.0 knitr_1.45 S4Arrays_1.2.0 - [25] labeling_0.4.3 reticulate_1.35.0 DelayedArray_0.28.0 - [28] RColorBrewer_1.1-3 abind_1.4-5 BiocParallel_1.36.0 - [31] withr_3.0.0 BiocGenerics_0.48.1 grid_4.3.2 - [34] stats4_4.3.2 fansi_1.0.6 beachmat_2.18.0 - [37] future_1.33.1 colorspace_2.1-0 progressr_0.14.0 - [40] globals_0.16.2 MASS_7.3-60.0.1 scales_1.3.0 - [43] gtools_3.9.5 SummarizedExperiment_1.32.0 cli_3.6.2 - [46] rmarkdown_2.25 crayon_1.5.2 ragg_1.2.7 - [49] generics_0.1.3 future.apply_1.11.1 rstudioapi_0.15.0 - [52] rjson_0.2.21 zlibbioc_1.48.0 parallel_4.3.2 - [55] XVector_0.42.0 matrixStats_1.2.0 vctrs_0.6.5 - [58] Matrix_1.6-5 jsonlite_1.8.8 BiocSingular_1.18.0 - [61] IRanges_2.36.0 S4Vectors_0.40.2 ggrepel_0.9.5 - [64] irlba_2.3.5.1 scattermore_1.2 listenv_0.9.1 - [67] systemfonts_1.0.5 magick_2.8.2 GiottoUtils_0.1.5 - [70] parallelly_1.36.0 glue_1.7.0 codetools_0.2-19 - [73] cowplot_1.1.3 uwot_0.1.16 RcppAnnoy_0.0.22 - [76] gtable_0.3.4 deldir_2.0-2 GenomeInfoDb_1.38.6 - [79] GenomicRanges_1.54.1 ScaledMatrix_1.10.0 munsell_0.5.0 - [82] tibble_3.2.1 pillar_1.9.0 htmltools_0.5.7 - [85] GenomeInfoDbData_1.2.11 R6_2.5.1 textshaping_0.3.7 - [88] evaluate_0.23 lattice_0.22-5 Biobase_2.62.0 - [91] png_0.1-8 backports_1.4.1 SpatialExperiment_1.12.0 - [94] Rcpp_1.0.12 SparseArray_1.2.4 checkmate_2.3.1 - [97] colorRamp2_0.1.0 xfun_0.42 MatrixGenerics_1.14.0 -[100] pkgconfig_2.0.3 + [1] colorRamp2_0.1.0 deldir_2.0-4 rlang_1.1.4 + [4] magrittr_2.0.3 RcppAnnoy_0.0.22 GiottoUtils_0.1.12 + [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_2.8.4 XVector_0.44.0 + [19] labeling_0.4.3 utf8_1.2.4 rmarkdown_2.28 + [22] UCSC.utils_1.0.0 ragg_1.3.2 purrr_1.0.2 + [25] xfun_0.47 beachmat_2.20.0 zlibbioc_1.50.0 + [28] GenomeInfoDb_1.40.1 jsonlite_1.8.8 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_1.4-5 + [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_0.24.0 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] munsell_0.5.1 scales_1.3.0 gtools_3.9.5 + [73] globals_0.16.3 glue_1.7.0 lazyeval_0.2.2 + [76] tools_4.4.1 GiottoVisuals_0.2.5 data.table_1.16.0 + [79] ScaledMatrix_1.12.0 cowplot_1.1.3 grid_4.4.1 + [82] tidyr_1.3.1 colorspace_2.1-1 SingleCellExperiment_1.26.0 + [85] GenomeInfoDbData_1.2.12 BiocSingular_1.20.0 rsvd_1.0.5 + [88] cli_3.6.3 textshaping_0.4.0 fansi_1.0.6 + [91] S4Arrays_1.4.1 viridisLite_0.4.2 dplyr_1.1.4 + [94] uwot_0.2.2 gtable_0.3.5 R.methodsS3_1.8.2 + [97] digest_0.6.37 progressr_0.14.0 BiocGenerics_0.50.0 +[100] SparseArray_1.4.8 ggrepel_0.9.6 rjson_0.2.22 +[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 +[109] MASS_7.3-60.2 ``` -