├── .Rbuildignore ├── .github ├── .gitignore ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── new-feature-request-enhancement.md └── workflows │ └── R-CMD-check.yaml ├── .gitignore ├── CRAN-SUBMISSION ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── Color_Palettes.R ├── Data.R ├── Deprecated.R ├── Generics.R ├── Internal_Utilities.R ├── LIGER_Internal_Utilities.R ├── LIGER_Plotting.R ├── LIGER_Utilities.R ├── Object_Conversion.R ├── Object_Utilities.R ├── Plotting_Nebulosa.R ├── Plotting_QC_Seq_10X.R ├── Plotting_QC_Seurat.R ├── Plotting_Seurat.R ├── Plotting_Seurat_Iterative.R ├── Plotting_Statistics.R ├── Plotting_Utilities.R ├── QC_Utilities_Seurat.R ├── Read_&_Write_Data.R ├── Reexports.R ├── Statistics.R ├── Utilities.R ├── sysdata.rda └── zzz.R ├── README.md ├── _pkgdown.yml ├── cran-comments.md ├── data-raw ├── Create_Ensembl_ID_Mito_Ribo_Hemo_Lists_scCuztomize.R ├── Create_Ensembl_IEG_Gene_Lists_scCustomize.R └── Create_msigdb_Gene_Lists_scCustomize.R ├── data ├── ensembl_hemo_id.rda ├── ensembl_ieg_list.rda ├── ensembl_mito_id.rda ├── ensembl_ribo_id.rda ├── ieg_gene_list.rda ├── msigdb_qc_ensembl_list.rda └── msigdb_qc_gene_list.rda ├── docs ├── 404.html ├── LICENSE.html ├── articles │ ├── Cell_Bender_Functions.html │ ├── Cell_Bender_Functions_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ └── unnamed-chunk-22-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Color_Palettes.html │ ├── Color_Palettes_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-10-2.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-11-2.png │ │ │ ├── unnamed-chunk-11-3.png │ │ │ ├── unnamed-chunk-11-4.png │ │ │ ├── unnamed-chunk-11-5.png │ │ │ ├── unnamed-chunk-11-6.png │ │ │ ├── unnamed-chunk-11-7.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-12-2.png │ │ │ ├── unnamed-chunk-12-3.png │ │ │ ├── unnamed-chunk-12-4.png │ │ │ ├── unnamed-chunk-12-5.png │ │ │ ├── unnamed-chunk-12-6.png │ │ │ ├── unnamed-chunk-12-7.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-13-2.png │ │ │ ├── unnamed-chunk-13-3.png │ │ │ ├── unnamed-chunk-13-4.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-14-2.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-15-2.png │ │ │ ├── unnamed-chunk-15-3.png │ │ │ ├── unnamed-chunk-15-4.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-16-2.png │ │ │ ├── unnamed-chunk-16-3.png │ │ │ ├── unnamed-chunk-16-4.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-5-2.png │ │ │ ├── unnamed-chunk-5-3.png │ │ │ ├── unnamed-chunk-5-4.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-6-2.png │ │ │ ├── unnamed-chunk-6-3.png │ │ │ ├── unnamed-chunk-6-4.png │ │ │ ├── unnamed-chunk-6-5.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-7-2.png │ │ │ ├── unnamed-chunk-7-3.png │ │ │ ├── unnamed-chunk-7-4.png │ │ │ ├── unnamed-chunk-7-5.png │ │ │ ├── unnamed-chunk-7-6.png │ │ │ ├── unnamed-chunk-7-7.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ ├── unnamed-chunk-8-2.png │ │ │ ├── unnamed-chunk-8-3.png │ │ │ ├── unnamed-chunk-8-4.png │ │ │ └── unnamed-chunk-9-1.png │ ├── FAQ.html │ ├── Gene_Expression_Plotting.html │ ├── Gene_Expression_Plotting_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-27-1.png │ │ │ ├── unnamed-chunk-28-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-30-1.png │ │ │ ├── unnamed-chunk-31-1.png │ │ │ ├── unnamed-chunk-32-1.png │ │ │ ├── unnamed-chunk-33-1.png │ │ │ ├── unnamed-chunk-34-1.png │ │ │ ├── unnamed-chunk-35-1.png │ │ │ ├── unnamed-chunk-36-1.png │ │ │ ├── unnamed-chunk-37-1.png │ │ │ ├── unnamed-chunk-38-1.png │ │ │ ├── unnamed-chunk-39-1.png │ │ │ ├── unnamed-chunk-40-1.png │ │ │ ├── unnamed-chunk-41-1.png │ │ │ ├── unnamed-chunk-43-1.png │ │ │ ├── unnamed-chunk-44-1.png │ │ │ ├── unnamed-chunk-45-1.png │ │ │ ├── unnamed-chunk-46-1.png │ │ │ ├── unnamed-chunk-47-1.png │ │ │ ├── unnamed-chunk-48-1.png │ │ │ ├── unnamed-chunk-49-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-50-1.png │ │ │ ├── unnamed-chunk-51-1.png │ │ │ ├── unnamed-chunk-52-1.png │ │ │ ├── unnamed-chunk-53-1.png │ │ │ ├── unnamed-chunk-54-1.png │ │ │ ├── unnamed-chunk-55-1.png │ │ │ ├── unnamed-chunk-56-1.png │ │ │ ├── unnamed-chunk-57-1.png │ │ │ ├── unnamed-chunk-58-1.png │ │ │ ├── unnamed-chunk-59-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-60-1.png │ │ │ ├── unnamed-chunk-61-1.png │ │ │ ├── unnamed-chunk-62-1.png │ │ │ ├── unnamed-chunk-63-1.png │ │ │ ├── unnamed-chunk-64-1.png │ │ │ ├── unnamed-chunk-65-1.png │ │ │ ├── unnamed-chunk-66-1.png │ │ │ ├── unnamed-chunk-67-1.png │ │ │ ├── unnamed-chunk-68-1.png │ │ │ ├── unnamed-chunk-69-1.png │ │ │ ├── unnamed-chunk-70-1.png │ │ │ ├── unnamed-chunk-71-1.png │ │ │ ├── unnamed-chunk-72-1.png │ │ │ ├── unnamed-chunk-73-1.png │ │ │ ├── unnamed-chunk-74-1.png │ │ │ ├── unnamed-chunk-75-1.png │ │ │ ├── unnamed-chunk-76-1.png │ │ │ ├── unnamed-chunk-77-1.png │ │ │ ├── unnamed-chunk-78-1.png │ │ │ ├── unnamed-chunk-79-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ ├── unnamed-chunk-80-1.png │ │ │ ├── unnamed-chunk-81-1.png │ │ │ ├── unnamed-chunk-82-1.png │ │ │ ├── unnamed-chunk-84-1.png │ │ │ ├── unnamed-chunk-85-1.png │ │ │ ├── unnamed-chunk-86-1.png │ │ │ ├── unnamed-chunk-87-1.png │ │ │ ├── unnamed-chunk-88-1.png │ │ │ ├── unnamed-chunk-89-1.png │ │ │ ├── unnamed-chunk-91-1.png │ │ │ ├── unnamed-chunk-92-1.png │ │ │ ├── unnamed-chunk-93-1.png │ │ │ ├── unnamed-chunk-95-1.png │ │ │ ├── unnamed-chunk-97-1.png │ │ │ ├── unnamed-chunk-98-1.png │ │ │ └── unnamed-chunk-99-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Helpers_and_Utilities.html │ ├── Helpers_and_Utilities_files │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Installation.html │ ├── Iterative_Plotting.html │ ├── LIGER_Functions.html │ ├── LIGER_Functions_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── Markers_and_Cluster_Annotation.html │ ├── Markers_and_Cluster_Annotation_files │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Misc_Functions.html │ ├── Object_Conversion.html │ ├── Object_Conversion_files │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Object_QC_Functions.html │ ├── Object_QC_Functions_files │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── QC_Plots.html │ ├── QC_Plots_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-31-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Read_and_Write_Functions.html │ ├── Sequencing_QC_Plots.html │ ├── Sequencing_QC_Plots_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Spatial_Plotting.html │ ├── Spatial_Plotting_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-3-1.png │ │ │ └── unnamed-chunk-4-1.png │ ├── Statistics.html │ ├── Statistics_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-27-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── Update_Gene_Symbols.html │ ├── Update_Gene_Symbols_files │ │ ├── kePrint-0.0.1 │ │ │ └── kePrint.js │ │ └── lightable-0.0.1 │ │ │ └── lightable.css │ ├── articles │ │ ├── Cell_Bender_Functions.html │ │ ├── Color_Palettes.html │ │ ├── FAQ.html │ │ ├── Gene_Expression_Plotting.html │ │ ├── Helpers_and_Utilities.html │ │ ├── Installation.html │ │ ├── Iterative_Plotting.html │ │ ├── LIGER_Functions.html │ │ ├── Markers_and_Cluster_Annotation.html │ │ ├── Misc_Functions.html │ │ ├── Object_Conversion.html │ │ ├── Object_QC_Functions.html │ │ ├── QC_Plots.html │ │ ├── Read_and_Write_Functions.html │ │ ├── Sequencing_QC_Plots.html │ │ ├── Spatial_Plotting.html │ │ ├── Statistics.html │ │ └── Update_Gene_Symbols.html │ └── index.html ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── news │ └── index.html ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── Add_Alt_Feature_ID.html │ ├── Add_CellBender_Diff.html │ ├── Add_Cell_Complexity.Seurat.html │ ├── Add_Cell_Complexity.html │ ├── Add_Cell_Complexity.liger.html │ ├── Add_Cell_Complexity_LIGER.html │ ├── Add_Cell_Complexity_Seurat.html │ ├── Add_Cell_QC_Metrics.Seurat.html │ ├── Add_Cell_QC_Metrics.html │ ├── Add_Cell_QC_Metrics.liger.html │ ├── Add_Hemo.Seurat.html │ ├── Add_Hemo.html │ ├── Add_Hemo.liger.html │ ├── Add_Mito_Ribo.Seurat.html │ ├── Add_Mito_Ribo.html │ ├── Add_Mito_Ribo.liger.html │ ├── Add_Mito_Ribo_LIGER.html │ ├── Add_Mito_Ribo_Seurat.html │ ├── Add_Pct_Diff.html │ ├── Add_Sample_Meta.html │ ├── Add_Top_Gene_Pct.Seurat.html │ ├── Add_Top_Gene_Pct.html │ ├── Add_Top_Gene_Pct.liger.html │ ├── Add_Top_Gene_Pct_Seurat.html │ ├── Barcode_Plot.html │ ├── Blank_Theme-1.png │ ├── Blank_Theme.html │ ├── Case_Check.html │ ├── CellBender_Diff_Plot.html │ ├── CellBender_Feature_Diff.html │ ├── Cell_Highlight_Plot-1.png │ ├── Cell_Highlight_Plot.html │ ├── Cells.html │ ├── Cells_by_Identities_LIGER.html │ ├── Cells_per_Sample.html │ ├── Change_Delim_All.html │ ├── Change_Delim_Prefix.html │ ├── Change_Delim_Suffix.html │ ├── CheckMatrix_scCustom.html │ ├── Cluster_Highlight_Plot-1.png │ ├── Cluster_Highlight_Plot.html │ ├── Cluster_Stats_All_Samples.html │ ├── Clustered_DotPlot-1.png │ ├── Clustered_DotPlot-2.png │ ├── Clustered_DotPlot-3.png │ ├── Clustered_DotPlot.html │ ├── ColorBlind_Pal-1.png │ ├── ColorBlind_Pal.html │ ├── Convert_Assay.html │ ├── Copy_From_GCP.html │ ├── Copy_To_GCP.html │ ├── Create_10X_H5.html │ ├── Create_CellBender_Merged_Seurat.html │ ├── Create_Cluster_Annotation_File.html │ ├── Dark2_Pal-1.png │ ├── Dark2_Pal.html │ ├── DimPlot_All_Samples-1.png │ ├── DimPlot_All_Samples.html │ ├── DimPlot_LIGER.html │ ├── DimPlot_scCustom-1.png │ ├── DimPlot_scCustom.html │ ├── DiscretePalette_scCustomize-1.png │ ├── DiscretePalette_scCustomize.html │ ├── DotPlot_scCustom-1.png │ ├── DotPlot_scCustom.html │ ├── Embeddings.html │ ├── Extract_Modality.html │ ├── Extract_Sample_Meta.html │ ├── Extract_Top_Markers.html │ ├── Factor_Cor_Plot.html │ ├── FeaturePlot_DualAssay.html │ ├── FeaturePlot_scCustom-1.png │ ├── FeaturePlot_scCustom.html │ ├── FeatureScatter_scCustom-1.png │ ├── FeatureScatter_scCustom.html │ ├── Feature_Present.html │ ├── Features.html │ ├── Fetch_Meta.Seurat.html │ ├── Fetch_Meta.html │ ├── Fetch_Meta.liger.html │ ├── Find_Factor_Cor.html │ ├── Gene_Present.html │ ├── Hue_Pal-1.png │ ├── Hue_Pal.html │ ├── Idents.html │ ├── Iterate_Barcode_Rank_Plot.html │ ├── Iterate_Cluster_Highlight_Plot.html │ ├── Iterate_DimPlot_bySample.html │ ├── Iterate_FeaturePlot_scCustom.html │ ├── Iterate_Meta_Highlight_Plot.html │ ├── Iterate_PC_Loading_Plots.html │ ├── Iterate_Plot_Density_Custom.html │ ├── Iterate_Plot_Density_Joint.html │ ├── Iterate_VlnPlot_scCustom.html │ ├── JCO_Four-1.png │ ├── JCO_Four.html │ ├── LIGER_Features.html │ ├── Liger_to_Seurat.html │ ├── MAD_Stats.html │ ├── Median_Stats.html │ ├── Merge_Seurat_List.html │ ├── Merge_Sparse_Data_All.html │ ├── Merge_Sparse_Multimodal_All.html │ ├── Meta_Highlight_Plot-1.png │ ├── Meta_Highlight_Plot.html │ ├── Meta_Numeric.html │ ├── Meta_Present.html │ ├── Meta_Present_LIGER.html │ ├── Meta_Remove_Seurat.html │ ├── Move_Legend-1.png │ ├── Move_Legend.html │ ├── NavyAndOrange-1.png │ ├── NavyAndOrange.html │ ├── PC_Plotting-1.png │ ├── PC_Plotting.html │ ├── PalettePlot-1.png │ ├── PalettePlot.html │ ├── Percent_Expressing.html │ ├── Plot_Cells_per_Sample.html │ ├── Plot_Density_Custom-1.png │ ├── Plot_Density_Custom.html │ ├── Plot_Density_Joint_Only-1.png │ ├── Plot_Density_Joint_Only.html │ ├── Plot_Median_Genes-1.png │ ├── Plot_Median_Genes.html │ ├── Plot_Median_Mito.html │ ├── Plot_Median_Other.html │ ├── Plot_Median_UMIs-1.png │ ├── Plot_Median_UMIs.html │ ├── Proportion_Plot-1.png │ ├── Proportion_Plot.html │ ├── Pull_Cluster_Annotation.html │ ├── Pull_Directory_List.html │ ├── QC_Histogram.html │ ├── QC_Plot_GenevsFeature.html │ ├── QC_Plot_UMIvsFeature.html │ ├── QC_Plot_UMIvsGene-1.png │ ├── QC_Plot_UMIvsGene.html │ ├── QC_Plots_Combined_Vln.html │ ├── QC_Plots_Complexity-1.png │ ├── QC_Plots_Complexity.html │ ├── QC_Plots_Feature.html │ ├── QC_Plots_Genes-1.png │ ├── QC_Plots_Genes.html │ ├── QC_Plots_Mito.html │ ├── QC_Plots_UMIs-1.png │ ├── QC_Plots_UMIs.html │ ├── Random_Cells_Downsample.html │ ├── Read10X_GEO.html │ ├── Read10X_Multi_Directory.html │ ├── Read10X_h5_GEO.html │ ├── Read10X_h5_Multi_Directory.html │ ├── Read_CellBender_h5_Mat.html │ ├── Read_CellBender_h5_Multi_Directory.html │ ├── Read_CellBender_h5_Multi_File.html │ ├── Read_GEO_Delim.html │ ├── Read_Metrics_10X.html │ ├── Read_Metrics_CellBender.html │ ├── Reduction_Loading_Present.html │ ├── Rename_Clusters.Seurat.html │ ├── Rename_Clusters.html │ ├── Rename_Clusters.liger.html │ ├── Replace_Suffix.html │ ├── Rplot001.png │ ├── Rplot002.png │ ├── Rplot003.png │ ├── Seq_QC_Plot_Alignment_Combined.html │ ├── Seq_QC_Plot_Antisense.html │ ├── Seq_QC_Plot_Basic_Combined.html │ ├── Seq_QC_Plot_Exonic.html │ ├── Seq_QC_Plot_Genes.html │ ├── Seq_QC_Plot_Genome.html │ ├── Seq_QC_Plot_Intergenic.html │ ├── Seq_QC_Plot_Intronic.html │ ├── Seq_QC_Plot_Number_Cells.html │ ├── Seq_QC_Plot_Reads_in_Cells.html │ ├── Seq_QC_Plot_Reads_per_Cell.html │ ├── Seq_QC_Plot_Saturation.html │ ├── Seq_QC_Plot_Total_Genes.html │ ├── Seq_QC_Plot_Transcriptome.html │ ├── Seq_QC_Plot_UMIs.html │ ├── Setup_scRNAseq_Project.html │ ├── Single_Color_Palette-1.png │ ├── Single_Color_Palette.html │ ├── SpatialDimPlot_scCustom.html │ ├── Split_FeatureScatter-1.png │ ├── Split_FeatureScatter.html │ ├── Split_Layers.html │ ├── Split_Vector.html │ ├── Stacked_VlnPlot-1.png │ ├── Stacked_VlnPlot.html │ ├── Store_Misc_Info_Seurat.html │ ├── Store_Palette_Seurat.html │ ├── Subset_LIGER.html │ ├── Top_Genes_Factor.html │ ├── UnRotate_X-1.png │ ├── UnRotate_X.html │ ├── Updated_HGNC_Symbols.html │ ├── Updated_MGI_Symbols.html │ ├── VariableFeaturePlot_scCustom-1.png │ ├── VariableFeaturePlot_scCustom.html │ ├── Variable_Features_ALL_LIGER.html │ ├── VlnPlot_scCustom-1.png │ ├── VlnPlot_scCustom.html │ ├── WhichCells.html │ ├── as.LIGER.Seurat.html │ ├── as.LIGER.html │ ├── as.LIGER.list.html │ ├── as.Seurat.html │ ├── as.anndata.Seurat.html │ ├── as.anndata.html │ ├── as.anndata.liger.html │ ├── deprecated.html │ ├── ensembl_hemo_id.html │ ├── ensembl_ieg_list.html │ ├── ensembl_mito_id.html │ ├── ensembl_ribo_id.html │ ├── figures │ │ ├── assets │ │ │ ├── Barcode_Rank_Plot_Example.jpg │ │ │ ├── Iterate_named_plots.png │ │ │ ├── Read10X_GEO.png │ │ │ ├── annotation_info.png │ │ │ ├── delim_default.png │ │ │ ├── geo_merged.png │ │ │ ├── multimodal.png │ │ │ └── renamed.png │ │ ├── lifecycle-archived.svg │ │ ├── lifecycle-defunct.svg │ │ ├── lifecycle-deprecated.svg │ │ ├── lifecycle-experimental.svg │ │ ├── lifecycle-maturing.svg │ │ ├── lifecycle-questioning.svg │ │ ├── lifecycle-stable.svg │ │ ├── lifecycle-superseded.svg │ │ └── scCustomize_Logo.svg │ ├── ieg_gene_list.html │ ├── index.html │ ├── msigdb_qc_ensembl_list.html │ ├── msigdb_qc_gene_list.html │ ├── plotFactors_scCustom.html │ ├── reexports.html │ ├── scCustomize-package.html │ ├── scCustomize.html │ ├── scCustomize_Palette-1.png │ ├── scCustomize_Palette.html │ ├── seq_zeros.html │ ├── theme_ggprism_mod-1.png │ ├── theme_ggprism_mod.html │ ├── viridis_dark_high.html │ ├── viridis_inferno_dark_high.html │ ├── viridis_inferno_light_high.html │ ├── viridis_light_high.html │ ├── viridis_magma_dark_high.html │ ├── viridis_magma_light_high.html │ ├── viridis_plasma_light_high.html │ └── viridis_shortcut.html └── sitemap.xml ├── index.md ├── inst └── pkgdown.yml ├── man ├── Add_Alt_Feature_ID.Rd ├── Add_CellBender_Diff.Rd ├── Add_Cell_Complexity.Rd ├── Add_Cell_QC_Metrics.Rd ├── Add_Hemo.Rd ├── Add_Mito_Ribo.Rd ├── Add_Pct_Diff.Rd ├── Add_Sample_Meta.Rd ├── Add_Top_Gene_Pct.Rd ├── Barcode_Plot.Rd ├── Blank_Theme.Rd ├── Case_Check.Rd ├── CellBender_Diff_Plot.Rd ├── CellBender_Feature_Diff.Rd ├── Cell_Highlight_Plot.Rd ├── Cells.Rd ├── Cells_by_Identities_LIGER.Rd ├── Cells_per_Sample.Rd ├── Change_Delim_All.Rd ├── Change_Delim_Prefix.Rd ├── Change_Delim_Suffix.Rd ├── CheckMatrix_scCustom.Rd ├── Cluster_Highlight_Plot.Rd ├── Cluster_Stats_All_Samples.Rd ├── Clustered_DotPlot.Rd ├── ColorBlind_Pal.Rd ├── Convert_Assay.Rd ├── Copy_From_GCP.Rd ├── Copy_To_GCP.Rd ├── Create_10X_H5.Rd ├── Create_CellBender_Merged_Seurat.Rd ├── Create_Cluster_Annotation_File.Rd ├── Dark2_Pal.Rd ├── DimPlot_All_Samples.Rd ├── DimPlot_LIGER.Rd ├── DimPlot_scCustom.Rd ├── DiscretePalette_scCustomize.Rd ├── DotPlot_scCustom.Rd ├── Embeddings.Rd ├── Extract_Modality.Rd ├── Extract_Sample_Meta.Rd ├── Extract_Top_Markers.Rd ├── Factor_Cor_Plot.Rd ├── FeaturePlot_DualAssay.Rd ├── FeaturePlot_scCustom.Rd ├── FeatureScatter_scCustom.Rd ├── Feature_Present.Rd ├── Features.Rd ├── Fetch_Meta.Rd ├── Find_Factor_Cor.Rd ├── Hue_Pal.Rd ├── Idents.Rd ├── Iterate_Barcode_Rank_Plot.Rd ├── Iterate_Cluster_Highlight_Plot.Rd ├── Iterate_DimPlot_bySample.Rd ├── Iterate_FeaturePlot_scCustom.Rd ├── Iterate_Meta_Highlight_Plot.Rd ├── Iterate_PC_Loading_Plots.Rd ├── Iterate_Plot_Density_Custom.Rd ├── Iterate_Plot_Density_Joint.Rd ├── Iterate_VlnPlot_scCustom.Rd ├── JCO_Four.Rd ├── Liger_to_Seurat.Rd ├── MAD_Stats.Rd ├── Median_Stats.Rd ├── Merge_Seurat_List.Rd ├── Merge_Sparse_Data_All.Rd ├── Merge_Sparse_Multimodal_All.Rd ├── Meta_Highlight_Plot.Rd ├── Meta_Numeric.Rd ├── Meta_Present.Rd ├── Meta_Remove_Seurat.Rd ├── Move_Legend.Rd ├── NavyAndOrange.Rd ├── PC_Plotting.Rd ├── PalettePlot.Rd ├── Percent_Expressing.Rd ├── Plot_Cells_per_Sample.Rd ├── Plot_Density_Custom.Rd ├── Plot_Density_Joint_Only.Rd ├── Plot_Median_Genes.Rd ├── Plot_Median_Mito.Rd ├── Plot_Median_Other.Rd ├── Plot_Median_UMIs.Rd ├── Proportion_Plot.Rd ├── Pull_Cluster_Annotation.Rd ├── Pull_Directory_List.Rd ├── QC_Histogram.Rd ├── QC_Plot_GenevsFeature.Rd ├── QC_Plot_UMIvsFeature.Rd ├── QC_Plot_UMIvsGene.Rd ├── QC_Plots_Combined_Vln.Rd ├── QC_Plots_Complexity.Rd ├── QC_Plots_Feature.Rd ├── QC_Plots_Genes.Rd ├── QC_Plots_Mito.Rd ├── QC_Plots_UMIs.Rd ├── Random_Cells_Downsample.Rd ├── Read10X_GEO.Rd ├── Read10X_Multi_Directory.Rd ├── Read10X_h5_GEO.Rd ├── Read10X_h5_Multi_Directory.Rd ├── Read_CellBender_h5_Mat.Rd ├── Read_CellBender_h5_Multi_Directory.Rd ├── Read_CellBender_h5_Multi_File.Rd ├── Read_GEO_Delim.Rd ├── Read_Metrics_10X.Rd ├── Read_Metrics_CellBender.Rd ├── Reduction_Loading_Present.Rd ├── Rename_Clusters.Rd ├── Replace_Suffix.Rd ├── Seq_QC_Plot_Alignment_Combined.Rd ├── Seq_QC_Plot_Antisense.Rd ├── Seq_QC_Plot_Basic_Combined.Rd ├── Seq_QC_Plot_Exonic.Rd ├── Seq_QC_Plot_Genes.Rd ├── Seq_QC_Plot_Genome.Rd ├── Seq_QC_Plot_Intergenic.Rd ├── Seq_QC_Plot_Intronic.Rd ├── Seq_QC_Plot_Number_Cells.Rd ├── Seq_QC_Plot_Reads_in_Cells.Rd ├── Seq_QC_Plot_Reads_per_Cell.Rd ├── Seq_QC_Plot_Saturation.Rd ├── Seq_QC_Plot_Total_Genes.Rd ├── Seq_QC_Plot_Transcriptome.Rd ├── Seq_QC_Plot_UMIs.Rd ├── Setup_scRNAseq_Project.Rd ├── Single_Color_Palette.Rd ├── SpatialDimPlot_scCustom.Rd ├── Split_Layers.Rd ├── Split_Vector.Rd ├── Stacked_VlnPlot.Rd ├── Store_Misc_Info_Seurat.Rd ├── Store_Palette_Seurat.Rd ├── Subset_LIGER.Rd ├── Top_Genes_Factor.Rd ├── UnRotate_X.Rd ├── Updated_HGNC_Symbols.Rd ├── Updated_MGI_Symbols.Rd ├── VariableFeaturePlot_scCustom.Rd ├── Variable_Features_ALL_LIGER.Rd ├── VlnPlot_scCustom.Rd ├── WhichCells.Rd ├── as.LIGER.Rd ├── as.Seurat.Rd ├── as.anndata.Rd ├── deprecated.Rd ├── ensembl_hemo_id.Rd ├── ensembl_ieg_list.Rd ├── ensembl_mito_id.Rd ├── ensembl_ribo_id.Rd ├── figures │ ├── assets │ │ ├── Iterate_named_plots.png │ │ ├── Read10X_GEO.png │ │ ├── annotation_info.png │ │ ├── delim_default.png │ │ ├── geo_merged.png │ │ ├── multimodal.png │ │ └── renamed.png │ ├── lifecycle-archived.svg │ ├── lifecycle-defunct.svg │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-maturing.svg │ ├── lifecycle-questioning.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ └── scCustomize_Logo.svg ├── ieg_gene_list.Rd ├── msigdb_qc_ensembl_list.Rd ├── msigdb_qc_gene_list.Rd ├── plotFactors_scCustom.Rd ├── reexports.Rd ├── scCustomize-package.Rd ├── scCustomize_Palette.Rd ├── seq_zeros.Rd ├── theme_ggprism_mod.Rd └── viridis_shortcut.Rd ├── scCustomize.Rproj └── vignettes ├── .gitignore └── articles ├── Cell_Bender_Functions.Rmd ├── Color_Palettes.Rmd ├── FAQ.Rmd ├── Gene_Expression_Plotting.Rmd ├── Helpers_and_Utilities.Rmd ├── Installation.Rmd ├── Iterative_Plotting.Rmd ├── LIGER_Functions.Rmd ├── Markers_and_Cluster_Annotation.Rmd ├── Misc_Functions.Rmd ├── Object_Conversion.Rmd ├── Object_QC_Functions.Rmd ├── QC_Plots.Rmd ├── Read_and_Write_Functions.Rmd ├── Sequencing_QC_Plots.Rmd ├── Spatial_Plotting.Rmd ├── Statistics.Rmd └── Update_Gene_Symbols.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^.*\.Rproj$ 2 | ^\.Rproj\.user$ 3 | ^LICENSE\.md$ 4 | ^_pkgdown\.yml$ 5 | ^docs$ 6 | ^pkgdown$ 7 | ^vignettes$ 8 | ^index\.md$ 9 | .git 10 | ^inst$ 11 | ^\.github$ 12 | vignettes/*.orig$ 13 | ^vignettes$ 14 | ^index\.Rmd$ 15 | ^README\.Rmd$ 16 | ^cran-comments\.md$ 17 | ^CRAN-SUBMISSION$ 18 | ^data-raw$ 19 | -------------------------------------------------------------------------------- /.github/.gitignore: -------------------------------------------------------------------------------- 1 | *.html 2 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Bug report 3 | about: Report an Issue/Bug 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | ```r 22 | # insert reproducible example here 23 | ``` 24 | 25 | 26 |
27 | sessionInfo() output 28 | 29 | ```r 30 | PASTE HERE sessionInfo() output 31 | ``` 32 | 33 |
34 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/new-feature-request-enhancement.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: New Feature Request/Enhancement 3 | about: New Feature or Improvement to Existing Feature(s) 4 | title: '' 5 | labels: '' 6 | assignees: '' 7 | 8 | --- 9 | 10 | 11 | 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .Rproj.user 2 | .Rhistory 3 | .RData 4 | .Ruserdata 5 | scCustomize.Rproj 6 | .DS_Store 7 | vignettes/assets 8 | README.Rmd 9 | index.Rmd 10 | figure/ 11 | vignettes/articles/assets 12 | -------------------------------------------------------------------------------- /CRAN-SUBMISSION: -------------------------------------------------------------------------------- 1 | Version: 3.0.1 2 | Date: 2024-12-18 18:18:46 UTC 3 | SHA: 56e5fca4a67c56977dc8e02618af1461aab40b61 4 | -------------------------------------------------------------------------------- /R/Reexports.R: -------------------------------------------------------------------------------- 1 | #' @importFrom SeuratObject as.Seurat 2 | #' @export 3 | #' @note See \code{\link{as.Seurat.liger}} for scCustomize extension of this generic to converting Liger objects. 4 | #' 5 | #' 6 | SeuratObject::as.Seurat 7 | 8 | #' @importFrom SeuratObject WhichCells 9 | #' @export 10 | #' @note See \code{\link{WhichCells.liger}} for scCustomize extension of this generic to extract cell barcodes. 11 | #' 12 | #' 13 | SeuratObject::WhichCells 14 | 15 | #' @importFrom SeuratObject Cells 16 | #' @export 17 | #' @note See \code{\link{Cells.liger}} for scCustomize extension of this generic to extract cell barcodes. 18 | #' 19 | #' 20 | SeuratObject::Cells 21 | 22 | #' @importFrom SeuratObject Features 23 | #' @export 24 | #' @note See 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-------------------------------------------------------------------------------- 1 | pandoc: '3.2' 2 | pkgdown: 2.0.9 3 | pkgdown_sha: ~ 4 | articles: 5 | Cell_Bender_Functions: Cell_Bender_Functions.html 6 | Color_Palettes: Color_Palettes.html 7 | FAQ: FAQ.html 8 | Gene_Expression_Plotting: Gene_Expression_Plotting.html 9 | Helpers_and_Utilities: Helpers_and_Utilities.html 10 | Installation: Installation.html 11 | Iterative_Plotting: Iterative_Plotting.html 12 | LIGER_Functions: LIGER_Functions.html 13 | Markers_and_Cluster_Annotation: Markers_and_Cluster_Annotation.html 14 | Misc_Functions: Misc_Functions.html 15 | Object_Conversion: Object_Conversion.html 16 | Object_QC_Functions: Object_QC_Functions.html 17 | QC_Plots: QC_Plots.html 18 | Read_and_Write_Functions: Read_and_Write_Functions.html 19 | Sequencing_QC_Plots: Sequencing_QC_Plots.html 20 | Spatial_Plotting: Spatial_Plotting.html 21 | Statistics: Statistics.html 22 | Update_Gene_Symbols: Update_Gene_Symbols.html 23 | last_built: 2024-12-19T15:53Z 24 | urls: 25 | reference: https://samuel-marsh.github.io/scCustomize/reference 26 | article: https://samuel-marsh.github.io/scCustomize/articles 27 | 28 | -------------------------------------------------------------------------------- /man/Add_CellBender_Diff.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/QC_Utilities_Seurat.R 3 | \name{Add_CellBender_Diff} 4 | \alias{Add_CellBender_Diff} 5 | \title{Calculate and add differences post-cell bender analysis} 6 | \usage{ 7 | Add_CellBender_Diff(seurat_object, raw_assay_name, cell_bender_assay_name) 8 | } 9 | \arguments{ 10 | \item{seurat_object}{object name.} 11 | 12 | \item{raw_assay_name}{name of the assay containing the raw data.} 13 | 14 | \item{cell_bender_assay_name}{name of the assay containing the Cell Bender'ed data.} 15 | } 16 | \value{ 17 | Seurat object with 2 new columns in the meta.data slot. 18 | } 19 | \description{ 20 | Calculate the difference in features and UMIs per cell when both cell bender and raw assays are present. 21 | } 22 | \examples{ 23 | \dontrun{ 24 | object <- Add_CellBender_Diff(seurat_object = obj, raw_assay_name = "RAW", 25 | cell_bender_assay_name = "RNA") 26 | } 27 | 28 | } 29 | \concept{qc_util} 30 | -------------------------------------------------------------------------------- /man/Add_Pct_Diff.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Add_Pct_Diff} 4 | \alias{Add_Pct_Diff} 5 | \title{Add percentage difference to DE results} 6 | \usage{ 7 | Add_Pct_Diff( 8 | marker_dataframe, 9 | pct.1_name = "pct.1", 10 | pct.2_name = "pct.2", 11 | overwrite = FALSE 12 | ) 13 | } 14 | \arguments{ 15 | \item{marker_dataframe}{data.frame containing the results of \code{\link[Seurat]{FindMarkers}}, \code{\link[Seurat]{FindAllMarkers}}, or other DE test data.frame.} 16 | 17 | \item{pct.1_name}{the name of data.frame column corresponding to percent expressed in group 1. 18 | Default is Seurat default "pct.1".} 19 | 20 | \item{pct.2_name}{the name of data.frame column corresponding to percent expressed in group 2. 21 | Default is Seurat default "pct.2".} 22 | 23 | \item{overwrite}{logical. If the \code{marker_dataframe} already contains column named "pct_diff" whether to 24 | overwrite or return error message. Default is FALSE.} 25 | } 26 | \value{ 27 | Returns input \code{marker_dataframe} with additional "pct_diff" column. 28 | } 29 | \description{ 30 | Adds new column labeled "pct_diff" to the data.frame output of \code{\link[Seurat]{FindMarkers}}, \code{\link[Seurat]{FindAllMarkers}}, or other DE test data.frames. 31 | } 32 | \examples{ 33 | \dontrun{ 34 | marker_df <- FindAllMarkers(object = obj_name) 35 | marker_df <- Add_Pct_Diff(marker_dataframe = marker_df) 36 | # or piped with function 37 | marker_df <- FindAllMarkers(object = obj_name) \%>\% 38 | Add_Pct_Diff() 39 | } 40 | 41 | } 42 | \concept{marker_annotation_util} 43 | -------------------------------------------------------------------------------- /man/Barcode_Plot.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Plotting_QC_Seq_10X.R 3 | \name{Barcode_Plot} 4 | \alias{Barcode_Plot} 5 | \title{Create Barcode Rank Plot} 6 | \usage{ 7 | Barcode_Plot( 8 | br_out, 9 | pt.size = 6, 10 | plot_title = "Barcode Ranks", 11 | raster_dpi = c(1024, 1024), 12 | plateau = NULL 13 | ) 14 | } 15 | \arguments{ 16 | \item{br_out}{DFrame output from \code{\link[DropletUtils]{barcodeRanks}}.} 17 | 18 | \item{pt.size}{point size for plotting, default is 6.} 19 | 20 | \item{plot_title}{Title for plot, default is "Barcode Ranks".} 21 | 22 | \item{raster_dpi}{Pixel resolution for rasterized plots, passed to geom_scattermore(). 23 | Default is c(1024, 1024).} 24 | 25 | \item{plateau}{numerical value at which to add vertical line designating estimated 26 | empty droplet plateau (default is NULL).} 27 | } 28 | \value{ 29 | A ggplot object 30 | } 31 | \description{ 32 | Plot UMI vs. Barcode Rank with inflection and knee. Requires input from DropletUtils package. 33 | } 34 | \examples{ 35 | \dontrun{ 36 | mat <- Read10X_h5(filename = "raw_feature_bc_matrix.h5") 37 | 38 | br_results <- DropletUtils::barcodeRanks(mat) 39 | 40 | Barcode_Plot(br_out = br_results) 41 | } 42 | 43 | } 44 | \concept{seq_qc_plotting_basic} 45 | -------------------------------------------------------------------------------- /man/Blank_Theme.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Plotting_Utilities.R 3 | \name{Blank_Theme} 4 | \alias{Blank_Theme} 5 | \title{Blank Theme} 6 | \usage{ 7 | Blank_Theme(...) 8 | } 9 | \arguments{ 10 | \item{...}{extra arguments passed to \code{ggplot2::theme()}.} 11 | } 12 | \value{ 13 | Returns a list-like object of class \emph{theme}. 14 | } 15 | \description{ 16 | Shortcut for thematic modification to remove all axis labels and grid lines 17 | } 18 | \examples{ 19 | # Generate a plot and customize theme 20 | library(ggplot2) 21 | df <- data.frame(x = rnorm(n = 100, mean = 20, sd = 2), y = rbinom(n = 100, size = 100, prob = 0.2)) 22 | p <- ggplot(data = df, mapping = aes(x = x, y = y)) + geom_point(mapping = aes(color = 'red')) 23 | p + Blank_Theme() 24 | 25 | } 26 | \concept{themes} 27 | -------------------------------------------------------------------------------- /man/Case_Check.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Case_Check} 4 | \alias{Case_Check} 5 | \title{Check for alternate case features} 6 | \usage{ 7 | Case_Check( 8 | seurat_object, 9 | gene_list, 10 | case_check_msg = TRUE, 11 | return_features = TRUE, 12 | assay = NULL 13 | ) 14 | } 15 | \arguments{ 16 | \item{seurat_object}{Seurat object name.} 17 | 18 | \item{gene_list}{vector of genes to check.} 19 | 20 | \item{case_check_msg}{logical. Whether to print message to console if alternate case features are 21 | found in addition to inclusion in returned list. Default is TRUE.} 22 | 23 | \item{return_features}{logical. Whether to return vector of alternate case features. Default is TRUE.} 24 | 25 | \item{assay}{Name of assay to pull feature names from. If NULL will use the result of \code{DefaultAssay(seurat_object)}.} 26 | } 27 | \value{ 28 | If features found returns vector of found alternate case features and prints message depending on 29 | parameters specified. 30 | } 31 | \description{ 32 | Checks Seurat object for the presence of features with the same spelling but alternate case. 33 | } 34 | \examples{ 35 | \dontrun{ 36 | alt_features <- Case_Check(seurat_object = obj_name, gene_list = DEG_list) 37 | } 38 | 39 | } 40 | \concept{check_util} 41 | -------------------------------------------------------------------------------- /man/CellBender_Feature_Diff.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Statistics.R 3 | \name{CellBender_Feature_Diff} 4 | \alias{CellBender_Feature_Diff} 5 | \title{CellBender Feature Differences} 6 | \usage{ 7 | CellBender_Feature_Diff( 8 | seurat_object = NULL, 9 | raw_assay = NULL, 10 | cell_bender_assay = NULL, 11 | raw_mat = NULL, 12 | cell_bender_mat = NULL 13 | ) 14 | } 15 | \arguments{ 16 | \item{seurat_object}{Seurat object name.} 17 | 18 | \item{raw_assay}{Name of the assay containing the raw count data.} 19 | 20 | \item{cell_bender_assay}{Name of the assay containing the CellBender count data.} 21 | 22 | \item{raw_mat}{Name of raw count matrix in environment if not using Seurat object.} 23 | 24 | \item{cell_bender_mat}{Name of CellBender count matrix in environment if not using Seurat object.} 25 | } 26 | \value{ 27 | A data.frame containing summed raw counts, CellBender counts, count difference, and 28 | percent difference in counts. 29 | } 30 | \description{ 31 | Get quick values for raw counts, CellBender counts, count differences, and percent count differences 32 | per feature. 33 | } 34 | \examples{ 35 | \dontrun{ 36 | cb_stats <- CellBender_Feature_Diff(seurat_object - obj, raw_assay = "RAW", 37 | cell_bender_assay = "RNA") 38 | } 39 | 40 | } 41 | \concept{stats} 42 | -------------------------------------------------------------------------------- /man/Cells.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/LIGER_Utilities.R 3 | \name{Cells.liger} 4 | \alias{Cells.liger} 5 | \title{Extract Cells from LIGER Object} 6 | \usage{ 7 | \method{Cells}{liger}(x, by_dataset = FALSE, ...) 8 | } 9 | \arguments{ 10 | \item{x}{LIGER object name.} 11 | 12 | \item{by_dataset}{logical, whether to return list with vector of cell barcodes for each 13 | dataset in LIGER object or to return single vector of cell barcodes across all 14 | datasets in object (default is FALSE; return vector of cells).} 15 | 16 | \item{...}{Arguments passed to other methods} 17 | } 18 | \value{ 19 | vector or list depending on \code{by_dataset} parameter 20 | } 21 | \description{ 22 | Extract all cell barcodes from LIGER object 23 | } 24 | \examples{ 25 | \dontrun{ 26 | # return single vector of all cells 27 | all_features <- Cells(x = object, by_dataset = FALSE) 28 | 29 | # return list of vectors containing cells from each individual dataset in object 30 | dataset_features <- Cells(x = object, by_dataset = TRUE) 31 | } 32 | 33 | } 34 | \concept{liger_object_util} 35 | -------------------------------------------------------------------------------- /man/Cells_by_Identities_LIGER.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/LIGER_Utilities.R 3 | \name{Cells_by_Identities_LIGER} 4 | \alias{Cells_by_Identities_LIGER} 5 | \title{Extract Cells by identity} 6 | \usage{ 7 | Cells_by_Identities_LIGER(liger_object, group.by = NULL, by_dataset = FALSE) 8 | } 9 | \arguments{ 10 | \item{liger_object}{LIGER object name.} 11 | 12 | \item{group.by}{name of meta data column to use, default is current default clustering.} 13 | 14 | \item{by_dataset}{logical, whether to return list with entries for cell barcodes for each 15 | identity in \code{group.by} 16 | or to return list of lists (1 entry per dataset and each ident within the dataset) 17 | (default is FALSE; return list)} 18 | } 19 | \value{ 20 | list or list of lists depending on \code{by_dataset} parameter 21 | } 22 | \description{ 23 | Extract all cell barcodes by identity from LIGER object 24 | } 25 | \examples{ 26 | \dontrun{ 27 | # return single vector of all cells 28 | cells_by_idents <- Cells_by_Identities_LIGER(liger_object = object, by_dataset = FALSE) 29 | 30 | # return list of vectors containing cells from each individual dataset in object 31 | cells_by_idents_by_dataset <- Cells_by_Identities_LIGER(liger_object = object, by_dataset = TRUE) 32 | } 33 | 34 | } 35 | \concept{liger_object_util} 36 | -------------------------------------------------------------------------------- /man/Cells_per_Sample.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Statistics.R 3 | \name{Cells_per_Sample} 4 | \alias{Cells_per_Sample} 5 | \title{Cells per Sample} 6 | \usage{ 7 | Cells_per_Sample(seurat_object, sample_col = NULL) 8 | } 9 | \arguments{ 10 | \item{seurat_object}{Seurat object} 11 | 12 | \item{sample_col}{column name in meta.data that contains sample ID information. Default is NULL and 13 | will use "orig.ident column} 14 | } 15 | \value{ 16 | A data.frame 17 | } 18 | \description{ 19 | Get data.frame containing the number of cells per sample. 20 | } 21 | \examples{ 22 | library(Seurat) 23 | num_cells <- Cells_per_Sample(seurat_object = pbmc_small, sample_col = "orig.ident") 24 | 25 | } 26 | \concept{stats} 27 | -------------------------------------------------------------------------------- /man/Change_Delim_All.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Change_Delim_All} 4 | \alias{Change_Delim_All} 5 | \title{Change all delimiters in cell name} 6 | \usage{ 7 | Change_Delim_All(data, current_delim, new_delim) 8 | } 9 | \arguments{ 10 | \item{data}{Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.} 11 | 12 | \item{current_delim}{a single value of current delimiter.} 13 | 14 | \item{new_delim}{a single value of new delimiter desired.} 15 | } 16 | \value{ 17 | matrix or data.frame with new column names. 18 | } 19 | \description{ 20 | Change all instances of delimiter in cell names from list of data.frames/matrices or single data.frame/matrix 21 | } 22 | \examples{ 23 | \dontrun{ 24 | dge_matrix <- Change_Delim_All(data = dge_matrix, current_delim = ".", new_delim = "-") 25 | } 26 | 27 | } 28 | \concept{barcode_util} 29 | -------------------------------------------------------------------------------- /man/Change_Delim_Prefix.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Change_Delim_Prefix} 4 | \alias{Change_Delim_Prefix} 5 | \title{Change barcode prefix delimiter} 6 | \usage{ 7 | Change_Delim_Prefix(data, current_delim, new_delim) 8 | } 9 | \arguments{ 10 | \item{data}{Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.} 11 | 12 | \item{current_delim}{a single value of current delimiter.} 13 | 14 | \item{new_delim}{a single value of new delimiter desired.} 15 | } 16 | \value{ 17 | matrix or data.frame with new column names. 18 | } 19 | \description{ 20 | Change barcode prefix delimiter from list of data.frames/matrices or single data.frame/matrix 21 | } 22 | \examples{ 23 | \dontrun{ 24 | dge_matrix <- Change_Delim_Prefix(data = dge_matrix, current_delim = ".", new_delim = "-") 25 | } 26 | 27 | } 28 | \concept{barcode_util} 29 | -------------------------------------------------------------------------------- /man/Change_Delim_Suffix.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Change_Delim_Suffix} 4 | \alias{Change_Delim_Suffix} 5 | \title{Change barcode suffix delimiter} 6 | \usage{ 7 | Change_Delim_Suffix(data, current_delim, new_delim) 8 | } 9 | \arguments{ 10 | \item{data}{Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.} 11 | 12 | \item{current_delim}{a single value of current delimiter.} 13 | 14 | \item{new_delim}{a single value of new delimiter desired.} 15 | } 16 | \value{ 17 | matrix or data.frame with new column names. 18 | } 19 | \description{ 20 | Change barcode suffix delimiter from list of data.frames/matrices or single data.frame/matrix 21 | } 22 | \examples{ 23 | \dontrun{ 24 | dge_matrix <- Change_Delim_Suffix(data = dge_matrix, current_delim = ".", new_delim = "-") 25 | } 26 | 27 | } 28 | \concept{barcode_util} 29 | -------------------------------------------------------------------------------- /man/CheckMatrix_scCustom.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{CheckMatrix_scCustom} 4 | \alias{CheckMatrix_scCustom} 5 | \title{Check Matrix Validity} 6 | \usage{ 7 | CheckMatrix_scCustom( 8 | object, 9 | checks = c("infinite", "logical", "integer", "na") 10 | ) 11 | } 12 | \arguments{ 13 | \item{object}{A matrix} 14 | 15 | \item{checks}{Type of checks to perform, choose one or more from: 16 | \itemize{ 17 | \item \dQuote{\code{infinite}}: Emit a warning if any value is infinite 18 | \item \dQuote{\code{logical}}: Emit a warning if any value is a logical 19 | \item \dQuote{\code{integer}}: Emit a warning if any value is \emph{not} 20 | an integer 21 | \item \dQuote{\code{na}}: Emit a warning if any value is an \code{NA} 22 | or \code{NaN} 23 | }} 24 | } 25 | \value{ 26 | Emits warnings for each test and invisibly returns \code{NULL} 27 | } 28 | \description{ 29 | Native implementation of SeuratObjects CheckMatrix but with modified warning messages. 30 | } 31 | \examples{ 32 | \dontrun{ 33 | mat <- Read10X(...) 34 | CheckMatrix_scCustom(object = mat) 35 | } 36 | 37 | } 38 | \references{ 39 | Re-implementing \code{CheckMatrix} only for sparse matrices with modified warning messages. Original function from SeuratObject \url{https://github.com/satijalab/seurat-object/blob/9c0eda946e162d8595696e5280a6ecda6284db39/R/utils.R#L625-L650} (License: MIT). 40 | } 41 | \concept{check_util} 42 | -------------------------------------------------------------------------------- /man/Cluster_Stats_All_Samples.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Statistics.R 3 | \name{Cluster_Stats_All_Samples} 4 | \alias{Cluster_Stats_All_Samples} 5 | \title{Calculate Cluster Stats} 6 | \usage{ 7 | Cluster_Stats_All_Samples(seurat_object, group_by_var = "orig.ident") 8 | } 9 | \arguments{ 10 | \item{seurat_object}{Seurat object name.} 11 | 12 | \item{group_by_var}{meta data column to classify samples (default = "orig.ident").} 13 | } 14 | \value{ 15 | A data.frame with rows in order of frequency 16 | } 17 | \description{ 18 | Calculates both overall and per sample cell number and percentages per cluster based on orig.ident. 19 | } 20 | \examples{ 21 | \dontrun{ 22 | stats <- Cluster_Stats_All_Samples(seurat_object = object, group_by_var = "orig.ident") 23 | } 24 | 25 | } 26 | \concept{stats} 27 | -------------------------------------------------------------------------------- /man/ColorBlind_Pal.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Color_Palettes.R 3 | \name{ColorBlind_Pal} 4 | \alias{ColorBlind_Pal} 5 | \title{Color Universal Design Short Palette} 6 | \usage{ 7 | ColorBlind_Pal() 8 | } 9 | \value{ 10 | modified/reordered color palette (8 colors) based on ditto-seq 11 | } 12 | \description{ 13 | Shortcut ta a modified 8 color palette based on Color Universal Design (CUD) colorblindness friendly palette. 14 | } 15 | \examples{ 16 | cols <- ColorBlind_Pal() 17 | PalettePlot(pal = cols) 18 | 19 | } 20 | \references{ 21 | palette is slightly modified version of the Color Universal Design (CUD) colorblindness 22 | friendly palette \url{https://jfly.uni-koeln.de/color/}. 23 | } 24 | \concept{palettes} 25 | -------------------------------------------------------------------------------- /man/Convert_Assay.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Object_Conversion.R 3 | \name{Convert_Assay} 4 | \alias{Convert_Assay} 5 | \title{Convert between Seurat Assay types} 6 | \usage{ 7 | Convert_Assay(seurat_object, assay = NULL, convert_to) 8 | } 9 | \arguments{ 10 | \item{seurat_object}{Seurat object name.} 11 | 12 | \item{assay}{name(s) of assays to convert. Default is NULL and will check with users 13 | which assays they want to convert.} 14 | 15 | \item{convert_to}{value of what assay type to convert current assays to. 16 | #' \itemize{ 17 | \item Accepted values for V3/4 are: "Assay", "assay", "V3", or "v3". 18 | \item Accepted values for V5 are: "Assay5", "assay5", "V5", or "v5". 19 | }} 20 | } 21 | \description{ 22 | Will convert assays within a Seurat object between "Assay" and "Assay5" types. 23 | } 24 | \examples{ 25 | \dontrun{ 26 | # Convert to V3/4 assay 27 | obj <- Convert_Assay(seurat_object = obj, convert_to = "V3") 28 | 29 | # Convert to 5 assay 30 | obj <- Convert_Assay(seurat_object = obj, convert_to = "V5") 31 | } 32 | 33 | } 34 | \concept{object_conversion} 35 | -------------------------------------------------------------------------------- /man/Copy_From_GCP.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Copy_From_GCP} 4 | \alias{Copy_From_GCP} 5 | \title{Copy folder from GCP bucket from R Console} 6 | \usage{ 7 | Copy_From_GCP(folder_file_path, gcp_bucket_path) 8 | } 9 | \arguments{ 10 | \item{folder_file_path}{folder to be copied to GCP bucket.} 11 | 12 | \item{gcp_bucket_path}{GCP bucket path to copy to files.} 13 | } 14 | \value{ 15 | No return value. Performs system copy from GCP bucket. 16 | } 17 | \description{ 18 | Run command from R console without moving to terminal to copy folder from GCP bucket to local storage 19 | } 20 | \examples{ 21 | \dontrun{ 22 | Copy_From_GCP(folder_file_path = "plots/", gcp_bucket_path = "gs://bucket_name_and_folder_path") 23 | } 24 | 25 | } 26 | \concept{organization_util} 27 | -------------------------------------------------------------------------------- /man/Copy_To_GCP.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Copy_To_GCP} 4 | \alias{Copy_To_GCP} 5 | \title{Copy folder to GCP bucket from R Console} 6 | \usage{ 7 | Copy_To_GCP(folder_file_path, gcp_bucket_path) 8 | } 9 | \arguments{ 10 | \item{folder_file_path}{folder to be copied to GCP bucket.} 11 | 12 | \item{gcp_bucket_path}{GCP bucket path to copy to files.} 13 | } 14 | \value{ 15 | No return value. Performs system copy to GCP bucket. 16 | } 17 | \description{ 18 | Run command from R console without moving to terminal to copy folder to GCP bucket 19 | } 20 | \examples{ 21 | \dontrun{ 22 | Copy_To_GCP(folder_file_path = "plots/", gcp_bucket_path = "gs://bucket_name_and_folder_path") 23 | } 24 | 25 | } 26 | \concept{organization_util} 27 | -------------------------------------------------------------------------------- /man/Create_10X_H5.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Read_&_Write_Data.R 3 | \name{Create_10X_H5} 4 | \alias{Create_10X_H5} 5 | \title{Create H5 from 10X Outputs} 6 | \usage{ 7 | Create_10X_H5( 8 | raw_data_file_path, 9 | source_type = "10X", 10 | save_file_path, 11 | save_name 12 | ) 13 | } 14 | \arguments{ 15 | \item{raw_data_file_path}{file path to raw data file(s).} 16 | 17 | \item{source_type}{type of source data (Default is "10X"). Alternatively can provide "Matrix" or "data.frame".} 18 | 19 | \item{save_file_path}{file path to directory to save file.} 20 | 21 | \item{save_name}{name prefix for output H5 file.} 22 | } 23 | \value{ 24 | A HDF5 format file that will be recognized as 10X Cell Ranger formatted file by Seurat or LIGER. 25 | } 26 | \description{ 27 | Creates HDF5 formatted output analogous to the outputs created by Cell Ranger and can be read into 28 | Seurat, LIGER, or SCE class object. Requires DropletUtils package from Bioconductor. 29 | } 30 | \examples{ 31 | \dontrun{ 32 | Create_10X_H5(raw_data_file_path = "file_path", save_file_path = "file_path2", save_name = "NAME") 33 | } 34 | 35 | } 36 | \concept{read_&_write} 37 | -------------------------------------------------------------------------------- /man/Create_Cluster_Annotation_File.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Create_Cluster_Annotation_File} 4 | \alias{Create_Cluster_Annotation_File} 5 | \title{Create cluster annotation csv file} 6 | \usage{ 7 | Create_Cluster_Annotation_File( 8 | file_path = NULL, 9 | file_name = "cluster_annotation" 10 | ) 11 | } 12 | \arguments{ 13 | \item{file_path}{path to directory to save file. Default is current working directory.} 14 | 15 | \item{file_name}{name to use for annotation file. Function automatically adds file type ".csv" suffix. 16 | Default is "cluster_annotation".} 17 | } 18 | \value{ 19 | No value returned. Creates .csv file. 20 | } 21 | \description{ 22 | create annotation file 23 | } 24 | \examples{ 25 | \dontrun{ 26 | Create_Cluster_Annotation_File(file_path = "cluster_annotation_folder_name") 27 | } 28 | 29 | } 30 | \concept{marker_annotation_util} 31 | -------------------------------------------------------------------------------- /man/Dark2_Pal.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Color_Palettes.R 3 | \name{Dark2_Pal} 4 | \alias{Dark2_Pal} 5 | \title{Dark2 Palette} 6 | \usage{ 7 | Dark2_Pal() 8 | } 9 | \value{ 10 | "Dark2" color palette (8 colors) 11 | } 12 | \description{ 13 | Shortcut to Dark2 color palette from RColorBrewer (8 Colors) 14 | } 15 | \examples{ 16 | cols <- Dark2_Pal() 17 | PalettePlot(pal= cols) 18 | 19 | } 20 | \references{ 21 | Dark2 palette from RColorBrewer being called through paletteer. 22 | See RColorBrewer for more info on palettes 23 | \url{https://CRAN.R-project.org/package=RColorBrewer} 24 | } 25 | \concept{palettes} 26 | -------------------------------------------------------------------------------- /man/Embeddings.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/LIGER_Utilities.R 3 | \name{Embeddings.liger} 4 | \alias{Embeddings.liger} 5 | \title{Extract matrix of embeddings} 6 | \usage{ 7 | \method{Embeddings}{liger}(object, reduction = NULL, iNMF = FALSE, check_only = FALSE, ...) 8 | } 9 | \arguments{ 10 | \item{object}{LIGER object name.} 11 | 12 | \item{reduction}{name of dimensionality reduction to pull} 13 | 14 | \item{iNMF}{logical, whether to extract iNMF h.norm matrix instead of dimensionality reduction embeddings.} 15 | 16 | \item{check_only}{logical, return \code{TRUE} if valid reduction is present.} 17 | 18 | \item{...}{Arguments passed to other methods} 19 | } 20 | \value{ 21 | matrix 22 | } 23 | \description{ 24 | Extract matrix containing iNMF or dimensionality reduction embeddings. 25 | } 26 | \examples{ 27 | \dontrun{ 28 | # Extract embedding matrix for current dimensionality reduction 29 | UMAP_coord <- Embeddings(object = liger_object) 30 | 31 | # Extract iNMF h.norm matrix 32 | iNMF_mat <- Embeddings(object = liger_object, reduction = "iNMF") 33 | } 34 | 35 | } 36 | \concept{liger_object_util} 37 | -------------------------------------------------------------------------------- /man/Extract_Modality.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Extract_Modality} 4 | \alias{Extract_Modality} 5 | \title{Extract multi-modal data into list by modality} 6 | \usage{ 7 | Extract_Modality(matrix_list) 8 | } 9 | \arguments{ 10 | \item{matrix_list}{list of matrices to split by modality} 11 | } 12 | \value{ 13 | list of lists, with one sublist per data modality. Sub-list contain 1 matrix entry per sample 14 | } 15 | \description{ 16 | Reorganize multi-modal data after import with \code{Read10X()} or scCustomize read functions. 17 | Organizes sub-lists by data modality instead of by sample. 18 | } 19 | \examples{ 20 | \dontrun{ 21 | multi_mat <- Read10X(...) 22 | new_multi_mat <- Extract_Modality(matrix_list = multi_mat) 23 | } 24 | 25 | } 26 | \concept{read_merge_util} 27 | -------------------------------------------------------------------------------- /man/Features.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/LIGER_Utilities.R 3 | \name{Features.liger} 4 | \alias{Features.liger} 5 | \title{Extract Features from LIGER Object} 6 | \usage{ 7 | \method{Features}{liger}(x, by_dataset = FALSE, ...) 8 | } 9 | \arguments{ 10 | \item{x}{LIGER object name.} 11 | 12 | \item{by_dataset}{logical, whether to return list with vector of features for each dataset in 13 | LIGER object or to return single vector of unique features across all datasets in object 14 | (default is FALSE; return vector of unique features)} 15 | 16 | \item{...}{Arguments passed to other methods} 17 | } 18 | \value{ 19 | vector or list depending on \code{by_dataset} parameter 20 | } 21 | \description{ 22 | Extract all unique features from LIGER object 23 | } 24 | \examples{ 25 | \dontrun{ 26 | # return single vector of all unique features 27 | all_features <- Features(x = object, by_dataset = FALSE) 28 | 29 | # return list of vectors containing features from each individual dataset in object 30 | dataset_features <- Features(x = object, by_dataset = TRUE) 31 | } 32 | 33 | } 34 | \concept{liger_object_util} 35 | -------------------------------------------------------------------------------- /man/Fetch_Meta.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Generics.R, R/LIGER_Utilities.R, 3 | % R/Object_Utilities.R 4 | \name{Fetch_Meta} 5 | \alias{Fetch_Meta} 6 | \alias{Fetch_Meta.liger} 7 | \alias{Fetch_Meta.Seurat} 8 | \title{Get meta data from object} 9 | \usage{ 10 | Fetch_Meta(object, ...) 11 | 12 | \method{Fetch_Meta}{liger}(object, ...) 13 | 14 | \method{Fetch_Meta}{Seurat}(object, ...) 15 | } 16 | \arguments{ 17 | \item{object}{Object of class Seurat or liger.} 18 | 19 | \item{...}{Arguments passed to other methods} 20 | } 21 | \value{ 22 | A data.frame containing cell-level meta data 23 | } 24 | \description{ 25 | Quick function to properly pull meta.data from objects. 26 | } 27 | \examples{ 28 | library(Seurat) 29 | meta_data <- Fetch_Meta(object = pbmc_small) 30 | head(meta_data, 5) 31 | 32 | } 33 | \concept{get_set_util} 34 | \concept{liger_object_util} 35 | -------------------------------------------------------------------------------- /man/Find_Factor_Cor.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/LIGER_Utilities.R 3 | \name{Find_Factor_Cor} 4 | \alias{Find_Factor_Cor} 5 | \title{Find Factor Correlations} 6 | \usage{ 7 | Find_Factor_Cor(object, reduction = NULL) 8 | } 9 | \arguments{ 10 | \item{object}{LIGER/Seurat object name.} 11 | 12 | \item{reduction}{reduction name to pull loadings for. Only valid if supplying a Seurat object.} 13 | } 14 | \value{ 15 | correlation matrix 16 | } 17 | \description{ 18 | Calculate correlations between gene loadings for all factors in liger or Seurat object. 19 | } 20 | \examples{ 21 | \dontrun{ 22 | factor_correlations <- Find_Factor_Cor(object = object) 23 | } 24 | 25 | } 26 | \concept{liger_object_util} 27 | -------------------------------------------------------------------------------- /man/Hue_Pal.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Color_Palettes.R 3 | \name{Hue_Pal} 4 | \alias{Hue_Pal} 5 | \title{Hue_Pal} 6 | \usage{ 7 | Hue_Pal(num_colors) 8 | } 9 | \arguments{ 10 | \item{num_colors}{number of colors to return in palette.} 11 | } 12 | \value{ 13 | hue color palette (as many colors as desired) 14 | } 15 | \description{ 16 | Shortcut to hue_pal to return to ggplot2 defaults if user desires, from scales package. 17 | } 18 | \examples{ 19 | cols <- Hue_Pal(num_colors = 8) 20 | PalettePlot(pal= cols) 21 | 22 | } 23 | \concept{palettes} 24 | -------------------------------------------------------------------------------- /man/Idents.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/LIGER_Utilities.R 3 | \name{Idents.liger} 4 | \alias{Idents.liger} 5 | \alias{Idents<-.liger} 6 | \title{Extract or set default identities from object} 7 | \usage{ 8 | \method{Idents}{liger}(object, ...) 9 | 10 | \method{Idents}{liger}(object, ...) <- value 11 | } 12 | \arguments{ 13 | \item{object}{LIGER object name.} 14 | 15 | \item{...}{Arguments passed to other methods} 16 | 17 | \item{value}{name of column in cellMeta slot to set as new default cluster/ident} 18 | } 19 | \value{ 20 | factor 21 | 22 | object 23 | } 24 | \description{ 25 | Extract default identities from object in factor form. 26 | } 27 | \note{ 28 | Use of Idents<- is only for setting new default ident/cluster from column already present in cellMeta. 29 | To add new column with new cluster values to cellMeta and set as default see \code{\link{Rename_Clusters}}. 30 | } 31 | \examples{ 32 | \dontrun{ 33 | # Extract idents 34 | object_idents <- Idents(object = liger_object) 35 | } 36 | 37 | \dontrun{ 38 | # Set idents 39 | Idents(object = liger_object) <- "new_annotation" 40 | } 41 | 42 | } 43 | \concept{liger_object_util} 44 | -------------------------------------------------------------------------------- /man/Iterate_PC_Loading_Plots.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Plotting_Seurat_Iterative.R 3 | \name{Iterate_PC_Loading_Plots} 4 | \alias{Iterate_PC_Loading_Plots} 5 | \title{Iterate PC Loading Plots} 6 | \usage{ 7 | Iterate_PC_Loading_Plots( 8 | seurat_object, 9 | dims_plot = NULL, 10 | file_path = NULL, 11 | name_prefix = NULL, 12 | file_name = "PC_Loading_Plots", 13 | return_plots = FALSE 14 | ) 15 | } 16 | \arguments{ 17 | \item{seurat_object}{Seurat object name.} 18 | 19 | \item{dims_plot}{number of PCs to plot (integer). Default is all dims present in PCA.} 20 | 21 | \item{file_path}{directory file path to save file.} 22 | 23 | \item{name_prefix}{prefix for file name (optional).} 24 | 25 | \item{file_name}{suffix for file name. Default is "PC_Loading_Plots".} 26 | 27 | \item{return_plots}{Whether to return the plot list (Default is FALSE). Must assign to environment 28 | to save plot list.} 29 | } 30 | \value{ 31 | A list of plots outputted as pdf 32 | } 33 | \description{ 34 | Plot PC Heatmaps and Dim Loadings for exploratory analysis 35 | } 36 | \examples{ 37 | \dontrun{ 38 | Iterate_PC_Loading_Plots(seurat_object = seurat, dims_plot = 25, file_path = "plots/") 39 | } 40 | 41 | } 42 | \seealso{ 43 | \code{\link[Seurat]{PCHeatmap}} and \code{\link[Seurat]{VizDimLoadings}} 44 | } 45 | \concept{iterative_plotting} 46 | -------------------------------------------------------------------------------- /man/JCO_Four.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Color_Palettes.R 3 | \name{JCO_Four} 4 | \alias{JCO_Four} 5 | \title{Four Color Palette (JCO)} 6 | \usage{ 7 | JCO_Four() 8 | } 9 | \value{ 10 | 4 color palette from the JCO ggsci palette 11 | } 12 | \description{ 13 | Shortcut to a specific JCO 4 color palette from ggsci package. 14 | } 15 | \examples{ 16 | cols <- JCO_Four() 17 | PalettePlot(pal= cols) 18 | 19 | } 20 | \references{ 21 | Selection of colors from the JCO palette from ggsci being called through paletteer. 22 | See ggsci for more info on palettes 23 | \url{https://CRAN.R-project.org/package=ggsci} 24 | } 25 | \concept{palettes} 26 | -------------------------------------------------------------------------------- /man/MAD_Stats.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Statistics.R 3 | \name{MAD_Stats} 4 | \alias{MAD_Stats} 5 | \title{Median Absolute Deviation Statistics} 6 | \usage{ 7 | MAD_Stats( 8 | seurat_object, 9 | group_by_var = "orig.ident", 10 | default_var = TRUE, 11 | mad_var = NULL, 12 | mad_num = 2 13 | ) 14 | } 15 | \arguments{ 16 | \item{seurat_object}{Seurat object name.} 17 | 18 | \item{group_by_var}{Column in meta.data slot to group results by (default = "orig.ident").} 19 | 20 | \item{default_var}{logical. Whether to include the default meta.data variables of: "nCount_RNA", 21 | "nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI" 22 | in addition to variables supplied to \code{mad_var}.} 23 | 24 | \item{mad_var}{Column(s) in \verb{@meta.data} to calculate medians for in addition to defaults. 25 | Must be of \code{class()} integer or numeric.} 26 | 27 | \item{mad_num}{integer value to multiply the MAD in returned data.frame (default is 2). 28 | Often helpful when calculating a outlier range to base of of median + (X*MAD).} 29 | } 30 | \value{ 31 | A data.frame. 32 | } 33 | \description{ 34 | Get quick values for X x median absolute deviation for Genes, UMIs, \%mito per cell grouped by meta.data variable. 35 | } 36 | \examples{ 37 | \dontrun{ 38 | mad_stats <- MAD_Stats(seurat_object = obj, group_by_var = "orig.ident") 39 | } 40 | 41 | } 42 | \concept{stats} 43 | -------------------------------------------------------------------------------- /man/Median_Stats.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Statistics.R 3 | \name{Median_Stats} 4 | \alias{Median_Stats} 5 | \title{Median Statistics} 6 | \usage{ 7 | Median_Stats( 8 | seurat_object, 9 | group_by_var = "orig.ident", 10 | default_var = TRUE, 11 | median_var = NULL 12 | ) 13 | } 14 | \arguments{ 15 | \item{seurat_object}{Seurat object name.} 16 | 17 | \item{group_by_var}{Column in meta.data slot to group results by (default = "orig.ident").} 18 | 19 | \item{default_var}{logical. Whether to include the default meta.data variables of: "nCount_RNA", 20 | "nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI" 21 | in addition to variables supplied to \code{median_var}.} 22 | 23 | \item{median_var}{Column(s) in \verb{@meta.data} to calculate medians for in addition to defaults. 24 | Must be of \code{class()} integer or numeric.} 25 | } 26 | \value{ 27 | A data.frame. 28 | } 29 | \description{ 30 | Get quick values for median Genes, UMIs, \%mito per cell grouped by meta.data variable. 31 | } 32 | \examples{ 33 | \dontrun{ 34 | med_stats <- Median_Stats(seurat_object - obj, group_by_var = "orig.ident") 35 | } 36 | 37 | } 38 | \concept{stats} 39 | -------------------------------------------------------------------------------- /man/Merge_Seurat_List.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Object_Utilities.R 3 | \name{Merge_Seurat_List} 4 | \alias{Merge_Seurat_List} 5 | \title{Merge a list of Seurat Objects} 6 | \usage{ 7 | Merge_Seurat_List( 8 | list_seurat, 9 | add.cell.ids = NULL, 10 | merge.data = TRUE, 11 | project = "SeuratProject" 12 | ) 13 | } 14 | \arguments{ 15 | \item{list_seurat}{list composed of multiple Seurat Objects.} 16 | 17 | \item{add.cell.ids}{A character vector of equal length to the number of objects in \code{list_seurat}. 18 | Appends the corresponding values to the start of each objects' cell names. See \code{\link[SeuratObject]{merge}}.} 19 | 20 | \item{merge.data}{Merge the data slots instead of just merging the counts (which requires renormalization). 21 | This is recommended if the same normalization approach was applied to all objects. 22 | See \code{\link[SeuratObject]{merge}}.} 23 | 24 | \item{project}{Project name for the Seurat object. See \code{\link[SeuratObject]{merge}}.} 25 | } 26 | \value{ 27 | A Seurat Object 28 | } 29 | \description{ 30 | Enables easy merge of a list of Seurat Objects. See See \code{\link[SeuratObject]{merge}} for more information, 31 | } 32 | \examples{ 33 | \dontrun{ 34 | object_list <- list(obj1, obj2, obj3, ...) 35 | merged_object <- Merge_Seurat_List(list_seurat = object_list) 36 | } 37 | 38 | } 39 | \concept{misc_util} 40 | -------------------------------------------------------------------------------- /man/Merge_Sparse_Data_All.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Merge_Sparse_Data_All} 4 | \alias{Merge_Sparse_Data_All} 5 | \title{Merge a list of Sparse Matrices} 6 | \usage{ 7 | Merge_Sparse_Data_All( 8 | matrix_list, 9 | add_cell_ids = NULL, 10 | prefix = TRUE, 11 | cell_id_delimiter = "_" 12 | ) 13 | } 14 | \arguments{ 15 | \item{matrix_list}{list of matrices to merge.} 16 | 17 | \item{add_cell_ids}{a vector of sample ids to add as prefix to cell barcode during merge.} 18 | 19 | \item{prefix}{logical. Whether \code{add_cell_ids} should be added as prefix to current cell barcodes/names 20 | or as suffix to current cell barcodes/names. Default is TRUE, add as prefix.} 21 | 22 | \item{cell_id_delimiter}{The delimiter to use when adding cell id prefix/suffix. Default is "_".} 23 | } 24 | \value{ 25 | A sparse Matrix 26 | } 27 | \description{ 28 | Enables easy merge of a list of sparse matrices 29 | } 30 | \examples{ 31 | \dontrun{ 32 | data_list <- Read10X_GEO(...) 33 | merged <- Merge_Sparse_Data_All(matrix_list = data_list, add_cell_ids = names(data_list), 34 | prefix = TRUE, cell_id_delimiter = "_") 35 | } 36 | 37 | } 38 | \references{ 39 | Original function is part of LIGER package 40 | \url{https://github.com/welch-lab/liger/blob/master/R/mergeObject.R} (License: GPL-3). 41 | Function was modified for use in scCustomize (add progress bar, prefix vs. suffix, and delimiter options). 42 | } 43 | \concept{read_merge_util} 44 | -------------------------------------------------------------------------------- /man/Merge_Sparse_Multimodal_All.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Merge_Sparse_Multimodal_All} 4 | \alias{Merge_Sparse_Multimodal_All} 5 | \title{Merge a list of Sparse Matrices contain multi-modal data.} 6 | \usage{ 7 | Merge_Sparse_Multimodal_All( 8 | matrix_list, 9 | add_cell_ids = NULL, 10 | prefix = TRUE, 11 | cell_id_delimiter = "_" 12 | ) 13 | } 14 | \arguments{ 15 | \item{matrix_list}{list of matrices to merge.} 16 | 17 | \item{add_cell_ids}{a vector of sample ids to add as prefix to cell barcode during merge.} 18 | 19 | \item{prefix}{logical. Whether \code{add_cell_ids} should be added as prefix to current cell barcodes/names 20 | or as suffix to current cell barcodes/names. Default is TRUE, add as prefix.} 21 | 22 | \item{cell_id_delimiter}{The delimiter to use when adding cell id prefix/suffix. Default is "_".} 23 | } 24 | \value{ 25 | A list containing one sparse matrix for each modality 26 | } 27 | \description{ 28 | Enables easy merge of a list of sparse matrices for multi-modal data. 29 | } 30 | \examples{ 31 | \dontrun{ 32 | data_list <- Read10X_GEO(...) 33 | merged_list <- Merge_Sparse_Multimodal_All(matrix_list = data_list, add_cell_ids = names(data_list), 34 | prefix = TRUE, cell_id_delimiter = "_") 35 | } 36 | 37 | } 38 | \concept{read_merge_util} 39 | -------------------------------------------------------------------------------- /man/Meta_Numeric.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Meta_Numeric} 4 | \alias{Meta_Numeric} 5 | \title{Check if meta data columns are numeric} 6 | \usage{ 7 | Meta_Numeric(data) 8 | } 9 | \arguments{ 10 | \item{data}{a data.frame contain meta.data.} 11 | } 12 | \value{ 13 | vector of meta data columns that are numeric. 14 | } 15 | \description{ 16 | Check if any present meta data columns are numeric and returns vector of valid numeric columns. 17 | Issues warning message if any columns not in numeric form. 18 | } 19 | \examples{ 20 | \dontrun{ 21 | numeric_meta_columns <- Meta_Numeric(data = meta_data) 22 | } 23 | 24 | } 25 | \concept{check_util} 26 | -------------------------------------------------------------------------------- /man/Meta_Present.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Meta_Present} 4 | \alias{Meta_Present} 5 | \title{Check if meta data are present} 6 | \usage{ 7 | Meta_Present( 8 | object, 9 | meta_col_names, 10 | print_msg = TRUE, 11 | omit_warn = TRUE, 12 | return_none = FALSE 13 | ) 14 | } 15 | \arguments{ 16 | \item{object}{Seurat or Liger object name.} 17 | 18 | \item{meta_col_names}{vector of column names to check.} 19 | 20 | \item{print_msg}{logical. Whether message should be printed if all features are found. Default is TRUE.} 21 | 22 | \item{omit_warn}{logical. Whether to print message about features that are not found in current object. Default is TRUE.} 23 | 24 | \item{return_none}{logical. Whether list of found vs. bad features should still be returned if no 25 | \code{meta_col_names} are found. Default is FALSE.} 26 | } 27 | \value{ 28 | vector of meta data columns that are present 29 | } 30 | \description{ 31 | Check if meta data columns are present in object and return vector of found columns 32 | Return warning messages for meta data columns not found. 33 | } 34 | \examples{ 35 | \dontrun{ 36 | meta_variables <- Meta_Present(object = obj_name, meta_col_names = "percent_mito", print_msg = TRUE) 37 | } 38 | 39 | } 40 | \concept{check_util} 41 | -------------------------------------------------------------------------------- /man/Meta_Remove_Seurat.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Object_Utilities.R 3 | \name{Meta_Remove_Seurat} 4 | \alias{Meta_Remove_Seurat} 5 | \title{Remove meta data columns containing Seurat Defaults} 6 | \usage{ 7 | Meta_Remove_Seurat( 8 | meta_data, 9 | seurat_object, 10 | barcodes_to_rownames = FALSE, 11 | barcodes_colname = "barcodes" 12 | ) 13 | } 14 | \arguments{ 15 | \item{meta_data}{data.frame containing meta data.} 16 | 17 | \item{seurat_object}{object name.} 18 | 19 | \item{barcodes_to_rownames}{logical, are barcodes present as column and should they be moved to 20 | rownames (to be compatible with \code{Seurat::AddMetaData}). Default is FALSE.} 21 | 22 | \item{barcodes_colname}{name of barcodes column in meta_data. Required if \code{barcodes_to_rownames = TRUE}.} 23 | } 24 | \value{ 25 | data.frame with only new columns. 26 | } 27 | \description{ 28 | Remove any columns from new meta_data data.frame in preparation for adding back to Seurat Object 29 | } 30 | \examples{ 31 | \dontrun{ 32 | new_meta <- Meta_Remove_Seurat(meta_data = meta_data_df, seurat_object = object) 33 | object <- AddMetaData(object = object, metadata = new_meta) 34 | } 35 | 36 | } 37 | \concept{get_set_util} 38 | -------------------------------------------------------------------------------- /man/Move_Legend.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Plotting_Utilities.R 3 | \name{Move_Legend} 4 | \alias{Move_Legend} 5 | \title{Move Legend Position} 6 | \usage{ 7 | Move_Legend(position = "right", ...) 8 | } 9 | \arguments{ 10 | \item{position}{valid position to move legend. Default is "right".} 11 | 12 | \item{...}{extra arguments passed to \code{ggplot2::theme()}.} 13 | } 14 | \value{ 15 | Returns a list-like object of class \emph{theme}. 16 | } 17 | \description{ 18 | Shortcut for thematic modification to move legend position. 19 | } 20 | \examples{ 21 | # Generate a plot and customize theme 22 | library(ggplot2) 23 | df <- data.frame(x = rnorm(n = 100, mean = 20, sd = 2), y = rbinom(n = 100, size = 100, prob = 0.2)) 24 | p <- ggplot(data = df, mapping = aes(x = x, y = y)) + geom_point(mapping = aes(color = 'red')) 25 | p + Move_Legend("left") 26 | 27 | } 28 | \concept{themes} 29 | -------------------------------------------------------------------------------- /man/NavyAndOrange.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Color_Palettes.R 3 | \name{NavyAndOrange} 4 | \alias{NavyAndOrange} 5 | \title{Navy and Orange Dual Color Palette} 6 | \usage{ 7 | NavyAndOrange(flip_order = FALSE) 8 | } 9 | \arguments{ 10 | \item{flip_order}{Whether to flip the order of colors.} 11 | } 12 | \value{ 13 | Navy orange palette 14 | } 15 | \description{ 16 | Shortcut to navy orange color plot 17 | } 18 | \examples{ 19 | cols <- NavyAndOrange() 20 | PalettePlot(pal= cols) 21 | 22 | } 23 | \concept{palettes} 24 | -------------------------------------------------------------------------------- /man/PC_Plotting.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Plotting_Utilities.R 3 | \name{PC_Plotting} 4 | \alias{PC_Plotting} 5 | \title{PC Plots} 6 | \usage{ 7 | PC_Plotting(seurat_object, dim_number) 8 | } 9 | \arguments{ 10 | \item{seurat_object}{Seurat Object.} 11 | 12 | \item{dim_number}{A single dim to plot (integer).} 13 | } 14 | \value{ 15 | A plot of PC heatmap and gene loadings for single 16 | } 17 | \description{ 18 | Plot PC Heatmaps and Dim Loadings for exploratory analysis. Plots a single Heatmap and Gene Loading Plot. 19 | Used for PC_Loading_Plots function. 20 | } 21 | \examples{ 22 | library(Seurat) 23 | PC_Plotting(seurat_object = pbmc_small, dim_number = 1) 24 | 25 | } 26 | \seealso{ 27 | \code{\link[Seurat]{PCHeatmap}} and \code{\link[Seurat]{VizDimLoadings}} 28 | } 29 | \concept{seurat_plotting} 30 | -------------------------------------------------------------------------------- /man/PalettePlot.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Color_Palettes.R 3 | \name{PalettePlot} 4 | \alias{PalettePlot} 5 | \title{Plot color palette in viewer} 6 | \usage{ 7 | PalettePlot(pal = NULL, label_color_num = NULL) 8 | } 9 | \arguments{ 10 | \item{pal}{a vector of colors (either named colors of hex codes).} 11 | 12 | \item{label_color_num}{logical, whether or not to numerically label the colors in output plot. 13 | Default is TRUE is number of colors in \code{pal} is less than 75 and FALSE is greater than 75.} 14 | } 15 | \value{ 16 | Plot of all colors in supplied palette/vector 17 | } 18 | \description{ 19 | Plots given color vector/palette in viewer to evaluate palette before plotting on data. 20 | } 21 | \examples{ 22 | pal <- DiscretePalette_scCustomize(num_colors = 36, palette = "varibow") 23 | PalettePlot(pal = pal) 24 | 25 | } 26 | \references{ 27 | Adapted from colorway package \code{build_palette} internals (License: GPL-3). 28 | \url{https://github.com/hypercompetent/colorway}. 29 | } 30 | \concept{palettes} 31 | -------------------------------------------------------------------------------- /man/Plot_Density_Joint_Only.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Plotting_Nebulosa.R 3 | \name{Plot_Density_Joint_Only} 4 | \alias{Plot_Density_Joint_Only} 5 | \title{Nebulosa Joint Density Plot} 6 | \usage{ 7 | Plot_Density_Joint_Only( 8 | seurat_object, 9 | features, 10 | viridis_palette = "magma", 11 | custom_palette = NULL, 12 | pt.size = 1, 13 | aspect_ratio = NULL, 14 | reduction = NULL, 15 | ... 16 | ) 17 | } 18 | \arguments{ 19 | \item{seurat_object}{Seurat object name.} 20 | 21 | \item{features}{Features to plot.} 22 | 23 | \item{viridis_palette}{default viridis palette to use (must be one of: "viridis", "magma", "cividis", 24 | "inferno", "plasma"). Default is "magma".} 25 | 26 | \item{custom_palette}{non-default color palette to be used in place of default viridis options.} 27 | 28 | \item{pt.size}{Adjust point size for plotting.} 29 | 30 | \item{aspect_ratio}{Control the aspect ratio (y:x axes ratio length). Must be numeric value; 31 | Default is NULL.} 32 | 33 | \item{reduction}{Dimensionality Reduction to use (if NULL then defaults to Object default).} 34 | 35 | \item{...}{Extra parameters passed to \code{\link[Nebulosa]{plot_density}}.} 36 | } 37 | \value{ 38 | A ggplot object 39 | } 40 | \description{ 41 | Return only the joint density plot from Nebulosa plot_density function. Requires Nebulosa package from Bioconductor. 42 | } 43 | \examples{ 44 | \dontrun{ 45 | library(Seurat) 46 | Plot_Density_Joint_Only(seurat_object = pbmc_small, features = c("CD8A", "CD3E")) 47 | } 48 | 49 | } 50 | \concept{other_seurat_plotting} 51 | -------------------------------------------------------------------------------- /man/Pull_Cluster_Annotation.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Pull_Cluster_Annotation} 4 | \alias{Pull_Cluster_Annotation} 5 | \title{Pull cluster information from annotation csv file.} 6 | \usage{ 7 | Pull_Cluster_Annotation( 8 | annotation = NULL, 9 | cluster_name_col = "cluster", 10 | cell_type_col = "cell_type" 11 | ) 12 | } 13 | \arguments{ 14 | \item{annotation}{name of the data.frame/tibble or path to CSV file containing cluster annotation.} 15 | 16 | \item{cluster_name_col}{name of column containing cluster names/numbers (default is "cluster").} 17 | 18 | \item{cell_type_col}{name of column contain the cell type annotation (default is "cell_type").} 19 | } 20 | \value{ 21 | a list of named vectors for every cell type in the \code{cell_type_col} column of the annotation table and 22 | vectors new cluster names (for use with \code{Rename_Clusters} function or manual identity renaming). 23 | } 24 | \description{ 25 | shortcut filter and pull function compatible with annotation files created by \code{Create_Cluster_Annotation_File} 26 | by default but also any other csv file. 27 | } 28 | \examples{ 29 | \dontrun{ 30 | # If pulling from a data.frame/tibble 31 | cluster_annotation <- Pull_Cluster_Annotation(annotation = annotation_df, 32 | cluster_name_col = "cluster", cell_type_col = "cell_type") 33 | 34 | # If pulling from csv file 35 | cluster_annotation <- Pull_Cluster_Annotation(annotation = "file_path/file_name.csv", 36 | cluster_name_col = "cluster", cell_type_col = "cell_type") 37 | } 38 | 39 | } 40 | \concept{marker_annotation_util} 41 | -------------------------------------------------------------------------------- /man/Pull_Directory_List.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Read_&_Write_Data.R 3 | \name{Pull_Directory_List} 4 | \alias{Pull_Directory_List} 5 | \title{Pull Directory List} 6 | \usage{ 7 | Pull_Directory_List(base_path) 8 | } 9 | \arguments{ 10 | \item{base_path}{path to the parent directory which contains all of the subdirectories of interest.} 11 | } 12 | \value{ 13 | A vector of sub-directories within \code{base_path}. 14 | } 15 | \description{ 16 | Enables easy listing of all sub-directories for use as input library lists in Read10X multi functions. 17 | } 18 | \examples{ 19 | \dontrun{ 20 | data_dir <- 'path/to/data/directory' 21 | library_list <- Pull_Directory_List(base_path = data_dir) 22 | } 23 | 24 | } 25 | \concept{read_&_write} 26 | -------------------------------------------------------------------------------- /man/Read_CellBender_h5_Mat.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Read_&_Write_Data.R 3 | \name{Read_CellBender_h5_Mat} 4 | \alias{Read_CellBender_h5_Mat} 5 | \title{Load CellBender h5 matrices (corrected)} 6 | \usage{ 7 | Read_CellBender_h5_Mat( 8 | file_name, 9 | use.names = TRUE, 10 | unique.features = TRUE, 11 | h5_group_name = NULL, 12 | feature_slot_name = "features" 13 | ) 14 | } 15 | \arguments{ 16 | \item{file_name}{Path to h5 file.} 17 | 18 | \item{use.names}{Label row names with feature names rather than ID numbers (default TRUE).} 19 | 20 | \item{unique.features}{Make feature names unique (default TRUE).} 21 | 22 | \item{h5_group_name}{Name of the group within H5 file that contains count data. This is only 23 | required if H5 file contains multiple subgroups and non-default names. Default is \code{NULL}.} 24 | 25 | \item{feature_slot_name}{Name of the slot contain feature names/ids. Must be one of: 26 | "features"(Cell Ranger v3+) or "genes" (Cell Ranger v1/v2 or STARsolo). Default is "features".} 27 | } 28 | \value{ 29 | sparse matrix 30 | } 31 | \description{ 32 | Extract sparse matrix with corrected counts from CellBender h5 output file. 33 | } 34 | \examples{ 35 | \dontrun{ 36 | mat <- Read_CellBender_h5_Mat(file_name = "/SampleA_out_filtered.h5") 37 | } 38 | 39 | } 40 | \references{ 41 | Code used in function has been modified from \code{Seurat::Read10X_h5} function of 42 | Seurat package \url{https://github.com/satijalab/seurat} (License: GPL-3). 43 | } 44 | \concept{read_&_write} 45 | -------------------------------------------------------------------------------- /man/Read_Metrics_CellBender.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Read_&_Write_Data.R 3 | \name{Read_Metrics_CellBender} 4 | \alias{Read_Metrics_CellBender} 5 | \title{Read Overall Statistics from CellBender} 6 | \usage{ 7 | Read_Metrics_CellBender(base_path, lib_list = NULL, lib_names = NULL) 8 | } 9 | \arguments{ 10 | \item{base_path}{path to the parent directory which contains all of the sub-directories of interest or 11 | path to single metrics csv file.} 12 | 13 | \item{lib_list}{a list of sample names (matching directory names) to import. If \code{NULL} will read 14 | in all samples in parent directory.} 15 | 16 | \item{lib_names}{a set of sample names to use for each sample. If \code{NULL} will set names to the 17 | directory name of each sample.} 18 | } 19 | \value{ 20 | A data frame with sample metrics from CellBender. 21 | } 22 | \description{ 23 | Get data.frame with all metrics from the CellBender \code{remove-background} analysis. 24 | } 25 | \examples{ 26 | \dontrun{ 27 | CB_metrics <- Read_Metrics_CellBender(base_path = "/path/to/directories") 28 | } 29 | 30 | } 31 | \concept{read_&_write} 32 | -------------------------------------------------------------------------------- /man/Reduction_Loading_Present.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Reduction_Loading_Present} 4 | \alias{Reduction_Loading_Present} 5 | \title{Check if reduction loadings are present} 6 | \usage{ 7 | Reduction_Loading_Present( 8 | seurat_object, 9 | reduction_names, 10 | print_msg = TRUE, 11 | omit_warn = TRUE, 12 | return_none = FALSE 13 | ) 14 | } 15 | \arguments{ 16 | \item{seurat_object}{object name.} 17 | 18 | \item{reduction_names}{vector of genes to check.} 19 | 20 | \item{print_msg}{logical. Whether message should be printed if all features are found. Default is TRUE.} 21 | 22 | \item{omit_warn}{logical. Whether to print message about features that are not found in current object. 23 | Default is TRUE.} 24 | 25 | \item{return_none}{logical. Whether list of found vs. bad features should still be returned if no 26 | features are found. Default is FALSE.} 27 | } 28 | \value{ 29 | A list of length 3 containing 1) found features, 2) not found features. 30 | } 31 | \description{ 32 | Check if reduction loadings are present in object and return vector of found loading names. Return 33 | warning messages for genes not found. 34 | } 35 | \examples{ 36 | \dontrun{ 37 | reductions <- Reduction_Loading_Present(seurat_object = obj_name, reduction_name = "PC_1") 38 | found_reductions <- reductions[[1]] 39 | } 40 | 41 | } 42 | \concept{check_util} 43 | -------------------------------------------------------------------------------- /man/Replace_Suffix.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Replace_Suffix} 4 | \alias{Replace_Suffix} 5 | \title{Replace barcode suffixes} 6 | \usage{ 7 | Replace_Suffix(data, current_suffix, new_suffix) 8 | } 9 | \arguments{ 10 | \item{data}{Either matrix/data.frame or list of matrices/data.frames with the cell barcodes in the column names.} 11 | 12 | \item{current_suffix}{a single value or vector of values representing current barcode suffix. 13 | If suffix is the same for all matrices/data.frames in list only single value is required.} 14 | 15 | \item{new_suffix}{a single value or vector of values representing new barcode suffix to be added. 16 | If desired suffix is the same for all matrices/data.frames in list only single value is required. 17 | If no suffix is desired set \code{new_suffix = ""}.`} 18 | } 19 | \value{ 20 | matrix or data.frame with new column names. 21 | } 22 | \description{ 23 | Replace barcode suffixes in matrix, data.frame, or list of matrices/data.frames 24 | } 25 | \examples{ 26 | \dontrun{ 27 | dge_matrix <- Replace_Suffix(data = dge_matrix, current_suffix = "-1", new_suffix = "-2") 28 | } 29 | 30 | } 31 | \concept{barcode_util} 32 | -------------------------------------------------------------------------------- /man/Seq_QC_Plot_Genes.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Plotting_QC_Seq_10X.R 3 | \name{Seq_QC_Plot_Genes} 4 | \alias{Seq_QC_Plot_Genes} 5 | \title{QC Plots Sequencing metrics} 6 | \usage{ 7 | Seq_QC_Plot_Genes( 8 | metrics_dataframe, 9 | plot_by = "sample_id", 10 | colors_use = NULL, 11 | dot_size = 1, 12 | x_lab_rotate = FALSE, 13 | significance = FALSE, 14 | ... 15 | ) 16 | } 17 | \arguments{ 18 | \item{metrics_dataframe}{data.frame contain Cell Ranger QC Metrics (see \code{\link{Read_Metrics_10X}}).} 19 | 20 | \item{plot_by}{Grouping factor for the plot. Default is to plot as single group with single point per sample.} 21 | 22 | \item{colors_use}{colors to use for plot if plotting by group. Defaults to RColorBrewer Dark2 palette if 23 | less than 8 groups and \code{DiscretePalette_scCustomize(palette = "polychrome")} if more than 8.} 24 | 25 | \item{dot_size}{size of the dots plotted if \code{plot_by} is not \code{sample_id} Default is 1.} 26 | 27 | \item{x_lab_rotate}{logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.} 28 | 29 | \item{significance}{logical. Whether to calculate and plot p-value comparisons when plotting by 30 | grouping factor. Default is FALSE.} 31 | 32 | \item{...}{Other variables to pass to \code{ggpubr::stat_compare_means} when doing significance testing.} 33 | } 34 | \value{ 35 | A ggplot object 36 | } 37 | \description{ 38 | Plot the median genes per cell per sample 39 | } 40 | \examples{ 41 | \dontrun{ 42 | Seq_QC_Plot_Genes(metrics_dataframe = metrics) 43 | } 44 | 45 | } 46 | \concept{seq_qc_plotting_basic} 47 | -------------------------------------------------------------------------------- /man/Seq_QC_Plot_UMIs.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Plotting_QC_Seq_10X.R 3 | \name{Seq_QC_Plot_UMIs} 4 | \alias{Seq_QC_Plot_UMIs} 5 | \title{QC Plots Sequencing metrics} 6 | \usage{ 7 | Seq_QC_Plot_UMIs( 8 | metrics_dataframe, 9 | plot_by = "sample_id", 10 | colors_use = NULL, 11 | dot_size = 1, 12 | x_lab_rotate = FALSE, 13 | significance = FALSE, 14 | ... 15 | ) 16 | } 17 | \arguments{ 18 | \item{metrics_dataframe}{data.frame contain Cell Ranger QC Metrics (see \code{\link{Read_Metrics_10X}}).} 19 | 20 | \item{plot_by}{Grouping factor for the plot. Default is to plot as single group with single point per sample.} 21 | 22 | \item{colors_use}{colors to use for plot if plotting by group. Defaults to RColorBrewer Dark2 palette if 23 | less than 8 groups and \code{DiscretePalette_scCustomize(palette = "polychrome")} if more than 8.} 24 | 25 | \item{dot_size}{size of the dots plotted if \code{plot_by} is not \code{sample_id} Default is 1.} 26 | 27 | \item{x_lab_rotate}{logical. Whether to rotate the axes labels on the x-axis. Default is FALSE.} 28 | 29 | \item{significance}{logical. Whether to calculate and plot p-value comparisons when plotting by 30 | grouping factor. Default is FALSE.} 31 | 32 | \item{...}{Other variables to pass to \code{ggpubr::stat_compare_means} when doing significance testing.} 33 | } 34 | \value{ 35 | A ggplot object 36 | } 37 | \description{ 38 | Plot the median UMIs per cell per sample 39 | } 40 | \examples{ 41 | \dontrun{ 42 | Seq_QC_Plot_UMIs(metrics_dataframe = metrics) 43 | } 44 | 45 | } 46 | \concept{seq_qc_plotting_basic} 47 | -------------------------------------------------------------------------------- /man/Setup_scRNAseq_Project.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Setup_scRNAseq_Project} 4 | \alias{Setup_scRNAseq_Project} 5 | \title{Setup project directory structure} 6 | \usage{ 7 | Setup_scRNAseq_Project( 8 | custom_dir_file = NULL, 9 | cluster_annotation_path = NULL, 10 | cluster_annotation_file_name = "cluster_annotation.csv" 11 | ) 12 | } 13 | \arguments{ 14 | \item{custom_dir_file}{file to file containing desired directory structure. Default is NULL and 15 | will provide generic built-in directory structure.} 16 | 17 | \item{cluster_annotation_path}{path to place cluster annotation file using \code{\link{Create_Cluster_Annotation_File}}.} 18 | 19 | \item{cluster_annotation_file_name}{name to use for annotation file if created (optional).} 20 | } 21 | \value{ 22 | no return value. Creates system folders. 23 | } 24 | \description{ 25 | Create reproducible project directory organization when initiating a new analysis. 26 | } 27 | \examples{ 28 | \dontrun{ 29 | # If using built-in directory structure. 30 | Setup_scRNAseq_Project() 31 | } 32 | 33 | } 34 | \concept{organization_util} 35 | -------------------------------------------------------------------------------- /man/Single_Color_Palette.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Color_Palettes.R 3 | \name{Single_Color_Palette} 4 | \alias{Single_Color_Palette} 5 | \title{Single Color Palettes for Plotting} 6 | \usage{ 7 | Single_Color_Palette(pal_color, num_colors = NULL, seed_use = 123) 8 | } 9 | \arguments{ 10 | \item{pal_color}{color palette to select (Options are: 'reds', 'blues', 11 | 'greens', 'purples', 'oranges', 'grays').} 12 | 13 | \item{num_colors}{set number of colors (max = 7).} 14 | 15 | \item{seed_use}{set seed for reproducibility (default: 123).} 16 | } 17 | \value{ 18 | A vector of colors 19 | } 20 | \description{ 21 | Selects colors from modified versions of RColorBrewer single colors palettes 22 | } 23 | \examples{ 24 | pal <- Single_Color_Palette(pal_color = "reds", num_colors = 7) 25 | PalettePlot(pal= pal) 26 | 27 | } 28 | \references{ 29 | See RColorBrewer for more info on palettes 30 | \url{https://CRAN.R-project.org/package=RColorBrewer} 31 | } 32 | \concept{palettes} 33 | -------------------------------------------------------------------------------- /man/Split_Layers.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Object_Conversion.R 3 | \name{Split_Layers} 4 | \alias{Split_Layers} 5 | \title{Split Seurat object into layers} 6 | \usage{ 7 | Split_Layers(seurat_object, assay = "RNA", split.by) 8 | } 9 | \arguments{ 10 | \item{seurat_object}{Seurat object name.} 11 | 12 | \item{assay}{name(s) of assays to convert. Defaults to current active assay.} 13 | 14 | \item{split.by}{Variable in meta.data to use for splitting layers.} 15 | } 16 | \description{ 17 | Split Assay5 of Seurat object into layers by variable in meta.data 18 | } 19 | \examples{ 20 | \dontrun{ 21 | # Split object by "treatment" 22 | obj <- Split_Layers(object = obj, assay = "RNA", split.by = "treatment") 23 | } 24 | 25 | } 26 | \concept{object_conversion} 27 | -------------------------------------------------------------------------------- /man/Split_Vector.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{Split_Vector} 4 | \alias{Split_Vector} 5 | \title{Split vector into list} 6 | \usage{ 7 | Split_Vector(x, chunk_size = NULL, num_chunk = NULL, verbose = FALSE) 8 | } 9 | \arguments{ 10 | \item{x}{vector to split} 11 | 12 | \item{chunk_size}{size of chunks for vector to be split into, default is NULL. Only valid if 13 | \code{num_chunk} is NULL.} 14 | 15 | \item{num_chunk}{number of chunks to split the vector into, default is NULL. Only valid if 16 | \code{chunk_size} is NULL.} 17 | 18 | \item{verbose}{logical, print details of vector and split, default is FALSE.} 19 | } 20 | \value{ 21 | list with vector of X length 22 | } 23 | \description{ 24 | Splits vector into chunks of x sizes 25 | } 26 | \examples{ 27 | vector <- c("gene1", "gene2", "gene3", "gene4", "gene5", "gene6") 28 | 29 | vector_list <- Split_Vector(x = vector, chunk_size = 3) 30 | 31 | } 32 | \references{ 33 | Base code from stackoverflow post: 34 | \url{https://stackoverflow.com/a/3321659/15568251} 35 | } 36 | \concept{misc_util} 37 | -------------------------------------------------------------------------------- /man/Top_Genes_Factor.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/LIGER_Utilities.R 3 | \name{Top_Genes_Factor} 4 | \alias{Top_Genes_Factor} 5 | \title{Extract top loading genes for LIGER factor} 6 | \usage{ 7 | Top_Genes_Factor(liger_object, liger_factor, num_genes = 10) 8 | } 9 | \arguments{ 10 | \item{liger_object}{LIGER object name.} 11 | 12 | \item{liger_factor}{LIGER factor number to pull genes from.} 13 | 14 | \item{num_genes}{number of top loading genes to return as vector.} 15 | } 16 | \value{ 17 | A LIGER Object 18 | } 19 | \description{ 20 | Extract vector to the top loading genes for specified LIGER iNMF factor 21 | } 22 | \examples{ 23 | \dontrun{ 24 | top_genes_factor10 <- Top_Genes_Factor(liger_object = object, num_genes = 10) 25 | } 26 | 27 | } 28 | \concept{liger_object_util} 29 | -------------------------------------------------------------------------------- /man/UnRotate_X.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Plotting_Utilities.R 3 | \name{UnRotate_X} 4 | \alias{UnRotate_X} 5 | \title{Unrotate x axis on VlnPlot} 6 | \usage{ 7 | UnRotate_X(...) 8 | } 9 | \arguments{ 10 | \item{...}{extra arguments passed to \code{ggplot2::theme()}.} 11 | } 12 | \value{ 13 | Returns a list-like object of class \emph{theme}. 14 | } 15 | \description{ 16 | Shortcut for thematic modification to unrotate the x axis (e.g., for Seurat VlnPlot is rotated by default). 17 | } 18 | \examples{ 19 | library(Seurat) 20 | p <- VlnPlot(object = pbmc_small, features = "CD3E") 21 | p + UnRotate_X() 22 | 23 | } 24 | \concept{themes} 25 | -------------------------------------------------------------------------------- /man/WhichCells.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/LIGER_Utilities.R 3 | \name{WhichCells.liger} 4 | \alias{WhichCells.liger} 5 | \title{Extract Cells for particular identity} 6 | \usage{ 7 | \method{WhichCells}{liger}( 8 | object, 9 | idents = NULL, 10 | ident_col = NULL, 11 | by_dataset = FALSE, 12 | invert = FALSE, 13 | ... 14 | ) 15 | } 16 | \arguments{ 17 | \item{object}{LIGER object name.} 18 | 19 | \item{idents}{identities to extract cell barcodes.} 20 | 21 | \item{ident_col}{name of meta data column to use when subsetting cells by identity values. 22 | Default is NULL, which will use the objects default clustering as the \code{ident_col}.} 23 | 24 | \item{by_dataset}{logical, whether to return vector with cell barcodes for all \code{idents} in or 25 | to return list (1 entry per dataset with vector of cells) (default is FALSE; return vector).} 26 | 27 | \item{invert}{logical, invert the selection of cells (default is FALSE).} 28 | 29 | \item{...}{Arguments passed to other methods} 30 | } 31 | \value{ 32 | vector or list depending on \code{by_dataset} parameter 33 | } 34 | \description{ 35 | Extract all cell barcodes for a specific identity 36 | } 37 | \examples{ 38 | \dontrun{ 39 | # Extract cells from ident =1 in current default clustering 40 | ident1_cells <- WhichCells(object = liger_object, idents = 1) 41 | 42 | # Extract all cells from "stim" treatment from object 43 | stim_cells <- WhichCells(object = liger_object, idents = "stim", ident_col = "Treatment") 44 | } 45 | 46 | } 47 | \concept{liger_object_util} 48 | -------------------------------------------------------------------------------- /man/ensembl_hemo_id.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Data.R 3 | \docType{data} 4 | \name{ensembl_hemo_id} 5 | \alias{ensembl_hemo_id} 6 | \title{Ensembl Hemo IDs} 7 | \format{ 8 | A list of six vectors 9 | \describe{ 10 | \item{Mus_musculus_hemo_ensembl}{Ensembl IDs for mouse hemoglobin genes} 11 | \item{Homo_sapiens_hemo_ensembl}{Ensembl IDs for human hemoglobin genes} 12 | \item{Danio_rerio_hemo_ensembl}{Ensembl IDs for zebrafish hemoglobin genes} 13 | \item{Rattus_norvegicus_hemo_ensembl}{Ensembl IDs for rat hemoglobin genes} 14 | \item{Drosophila_melanogaster_hemo_ensembl}{Ensembl IDs for fly hemoglobin genes} 15 | \item{Macaca_mulatta_hemo_ensembl}{Ensembl IDs for macaque hemoglobin genes} 16 | \item{Gallus_gallus_ribo_ensembl}{Ensembl IDs for chicken hemoglobin genes} 17 | } 18 | } 19 | \source{ 20 | See data-raw directory for scripts used to create gene list. 21 | } 22 | \usage{ 23 | ensembl_hemo_id 24 | } 25 | \description{ 26 | A list of ensembl ids for hemoglobin genes (Ensembl version 112; 4/29/2024) 27 | } 28 | \concept{data} 29 | \keyword{datasets} 30 | -------------------------------------------------------------------------------- /man/ensembl_ieg_list.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Data.R 3 | \docType{data} 4 | \name{ensembl_ieg_list} 5 | \alias{ensembl_ieg_list} 6 | \title{Immediate Early Gene (IEG) gene lists} 7 | \format{ 8 | A list of seven vectors 9 | \describe{ 10 | \item{Mus_musculus_IEGs}{Ensembl IDs for IEGs from source publication (see below)} 11 | \item{Homo_sapiens_IEGs}{Ensembl IDs for homologous genes from mouse gene list} 12 | 13 | } 14 | } 15 | \source{ 16 | Mouse gene list is from: SI Table 4 from \doi{10.1016/j.neuron.2017.09.026}. Human 17 | gene list was compiled by first creating homologous gene list using biomaRt and then adding some manually curated 18 | homologs according to HGNC. See data-raw directory for scripts used to create gene list. 19 | } 20 | \usage{ 21 | ensembl_ieg_list 22 | } 23 | \description{ 24 | Ensembl IDs for immediate early genes (Ensembl version 112; 4/29/2024) 25 | } 26 | \concept{data} 27 | \keyword{datasets} 28 | -------------------------------------------------------------------------------- /man/ensembl_mito_id.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Data.R 3 | \docType{data} 4 | \name{ensembl_mito_id} 5 | \alias{ensembl_mito_id} 6 | \title{Ensembl Mito IDs} 7 | \format{ 8 | A list of six vectors 9 | \describe{ 10 | \item{Mus_musculus_mito_ensembl}{Ensembl IDs for mouse mitochondrial genes} 11 | \item{Homo_sapiens_mito_ensembl}{Ensembl IDs for human mitochondrial genes} 12 | \item{Danio_rerio_mito_ensembl}{Ensembl IDs for zebrafish mitochondrial genes} 13 | \item{Rattus_norvegicus_mito_ensembl}{Ensembl IDs for rat mitochondrial genes} 14 | \item{Drosophila_melanogaster_mito_ensembl}{Ensembl IDs for fly mitochondrial genes} 15 | \item{Macaca_mulatta_mito_ensembl}{Ensembl IDs for macaque mitochondrial genes} 16 | \item{Gallus_gallus_ribo_ensembl}{Ensembl IDs for chicken mitochondrial genes} 17 | } 18 | } 19 | \source{ 20 | See data-raw directory for scripts used to create gene list. 21 | } 22 | \usage{ 23 | ensembl_mito_id 24 | } 25 | \description{ 26 | A list of ensembl ids for mitochondrial genes (Ensembl version 112; 4/29/2024) 27 | } 28 | \concept{data} 29 | \keyword{datasets} 30 | -------------------------------------------------------------------------------- /man/ensembl_ribo_id.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Data.R 3 | \docType{data} 4 | \name{ensembl_ribo_id} 5 | \alias{ensembl_ribo_id} 6 | \title{Ensembl Ribo IDs} 7 | \format{ 8 | A list of eight vectors 9 | \describe{ 10 | \item{Mus_musculus_ribo_ensembl}{Ensembl IDs for mouse ribosomal genes} 11 | \item{Homo_sapiens_ribo_ensembl}{Ensembl IDs for human ribosomal genes} 12 | \item{Callithrix_jacchus_ribo_ensembl}{Ensembl IDs for marmoset ribosomal genes} 13 | \item{Danio_rerio_ribo_ensembl}{Ensembl IDs for zebrafish ribosomal genes} 14 | \item{Rattus_norvegicus_ribo_ensembl}{Ensembl IDs for rat ribosomal genes} 15 | \item{Drosophila_melanogaster_ribo_ensembl}{Ensembl IDs for fly ribosomal genes} 16 | \item{Macaca_mulatta_ribo_ensembl}{Ensembl IDs for macaque ribosomal genes} 17 | \item{Gallus_gallus_ribo_ensembl}{Ensembl IDs for chicken ribosomal genes} 18 | } 19 | } 20 | \source{ 21 | See data-raw directory for scripts used to create gene list. 22 | } 23 | \usage{ 24 | ensembl_ribo_id 25 | } 26 | \description{ 27 | A list of ensembl ids for ribosomal genes (Ensembl version 112; 4/29/2024) 28 | } 29 | \concept{data} 30 | \keyword{datasets} 31 | 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\item{Mus_musculus_IEGs}{Gene symbols for IEGs from source publication (see below)} 11 | \item{Homo_sapiens_IEGs}{Human gene symbols for homologous genes from mouse gene list} 12 | 13 | } 14 | } 15 | \source{ 16 | Mouse gene list is from: SI Table 4 from \doi{10.1016/j.neuron.2017.09.026}. Human 17 | gene list was compiled by first creating homologous gene list using biomaRt and then adding some manually curated 18 | homologs according to HGNC. See data-raw directory for scripts used to create gene list. 19 | } 20 | \usage{ 21 | ieg_gene_list 22 | } 23 | \description{ 24 | Gene symbols for immediate early genes 25 | } 26 | \concept{data} 27 | \keyword{datasets} 28 | -------------------------------------------------------------------------------- /man/scCustomize_Palette.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Color_Palettes.R 3 | \name{scCustomize_Palette} 4 | \alias{scCustomize_Palette} 5 | \title{Color Palette Selection for scCustomize} 6 | \usage{ 7 | scCustomize_Palette( 8 | num_groups, 9 | ggplot_default_colors = FALSE, 10 | color_seed = 123 11 | ) 12 | } 13 | \arguments{ 14 | \item{num_groups}{number of groups to be plotted. If \code{ggplot_default_colors = FALSE} then by default: 15 | \itemize{ 16 | \item If number of levels plotted equal to 2 then colors will be \code{NavyAndOrange()}. 17 | \item If number of levels plotted greater than 2 but less than or equal to 36 it will use "polychrome" from \code{DiscretePalette_scCustomize()}. 18 | \item If greater than 36 will use "varibow" with shuffle = TRUE from \code{DiscretePalette_scCustomize}. 19 | }} 20 | 21 | \item{ggplot_default_colors}{logical. Whether to use default ggplot hue palette or not.} 22 | 23 | \item{color_seed}{random seed to use for shuffling the "varibow" palette.} 24 | } 25 | \value{ 26 | vector of colors to use for plotting. 27 | } 28 | \description{ 29 | Function to return package default discrete palettes depending on number of groups plotted. 30 | } 31 | \examples{ 32 | cols <- scCustomize_Palette(num_groups = 24, ggplot_default_colors = FALSE) 33 | PalettePlot(pal= cols) 34 | 35 | } 36 | \concept{palettes} 37 | -------------------------------------------------------------------------------- /man/seq_zeros.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Utilities.R 3 | \name{seq_zeros} 4 | \alias{seq_zeros} 5 | \title{Create sequence with zeros} 6 | \usage{ 7 | seq_zeros(seq_length, num_zeros = NULL) 8 | } 9 | \arguments{ 10 | \item{seq_length}{a seqeunce or numbers of numbers to create sequence. 11 | Users can provide sequence (1:XX) or number of values to add in sequence (will 12 | be used as second number in \code{seq_len}; 1:XX).} 13 | 14 | \item{num_zeros}{number of zeros to prefix sequence, default is (e.g, 01, 02, 03, ...)} 15 | } 16 | \value{ 17 | vector of numbers in sequence 18 | } 19 | \description{ 20 | Create sequences of numbers like \code{seq()} or \code{seq_len()} but with zeros prefixed to 21 | keep numerical order 22 | } 23 | \examples{ 24 | # Using sequence 25 | new_seq <- seq_zeros(seq_length = 1:15, num_zeros = 1) 26 | new_seq 27 | 28 | # Using number 29 | new_seq <- seq_zeros(seq_length = 15, num_zeros = 1) 30 | new_seq 31 | 32 | # Sequence with 2 zeros 33 | new_seq <- seq_zeros(seq_length = 1:15, num_zeros = 2) 34 | new_seq 35 | 36 | } 37 | \references{ 38 | Base code from stackoverflow post: 39 | \url{https://stackoverflow.com/a/38825614} 40 | } 41 | \concept{misc_util} 42 | -------------------------------------------------------------------------------- /scCustomize.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | ProjectId: 36c01bc4-551d-46b8-b881-69c09777ce3d 3 | 4 | RestoreWorkspace: Default 5 | SaveWorkspace: Default 6 | AlwaysSaveHistory: Default 7 | 8 | EnableCodeIndexing: Yes 9 | UseSpacesForTab: Yes 10 | NumSpacesForTab: 2 11 | Encoding: UTF-8 12 | 13 | RnwWeave: Sweave 14 | LaTeX: pdfLaTeX 15 | 16 | AutoAppendNewline: Yes 17 | StripTrailingWhitespace: Yes 18 | 19 | BuildType: Package 20 | PackageUseDevtools: Yes 21 | PackageInstallArgs: --no-multiarch --with-keep.source 22 | PackageBuildArgs: --no-build-vignettes 23 | PackageCheckArgs: --ignore-vignettes 24 | -------------------------------------------------------------------------------- /vignettes/.gitignore: -------------------------------------------------------------------------------- 1 | Iterate_named_plots.png 2 | *.html 3 | *.R 4 | --------------------------------------------------------------------------------