├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── R ├── AUCell_basic.R ├── Anndata.R ├── CalcStats.R ├── Cellrank.R ├── ClusterDistrBar.R ├── Colors.R ├── DimPlot.R ├── DotPlot.R ├── FeaturePlot.R ├── Functions.R ├── GeneSetAnalysis.R ├── GeneSetAnalysisGO.R ├── GeneSetAnalysisReactome.R ├── GenesymbolConversion.R ├── Heatmap.R ├── Internal.R ├── Loom.R ├── Palantir.R ├── Pseudotime.R ├── Python.R ├── RunBasicSeurat.R ├── RunSlingshot.R ├── Scenic.R ├── SearchDatabase.R ├── Vlnplots.R ├── VolcanoPlot.R ├── WaterfallPlot.R ├── generics.R ├── import.R ├── runGSVA.R └── scVelo.R ├── README.md ├── SeuratExtend.Rproj ├── _pkgdown.yml ├── data-raw ├── PanglaoDB.R ├── colors_iwanthue.R ├── colors_pro.R └── pbmc.R ├── data ├── PanglaoDB_data.rda ├── hall50.rda ├── human_ensembl_genesymbol.rda ├── mouse_ensembl_genesymbol.rda ├── mouse_human_genesymbols.rda ├── pbmc.rda ├── presets_color_iwh.rda └── presets_color_pro.rda ├── docs ├── 404.html ├── LICENSE.html ├── articles │ ├── FAQ.html │ ├── GSEA.html │ ├── GSEA_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-28-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-8-1.png │ ├── News.html │ ├── News_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.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-18-1.png │ │ │ ├── unnamed-chunk-2-1.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 │ ├── SCENIC.html │ ├── SCENIC_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ └── unnamed-chunk-6-1.png │ ├── Trajectory.html │ ├── Trajectory_files │ │ └── figure-html │ │ │ ├── access-slingshot-output-1.png │ │ │ ├── calculate-pseudotime-1.png │ │ │ ├── gene-trend-curve-custom-1.png │ │ │ ├── gene-trend-curve-initial-1.png │ │ │ ├── gene-trend-curve-slingshot-1.png │ │ │ ├── gene-trend-heatmap-1.png │ │ │ ├── gene-trend-heatmap-slingshot-1.png │ │ │ ├── run-diffusion-map-1.png │ │ │ └── run-magic-1.png │ ├── Utilities.html │ ├── Utilities_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-12-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ └── unnamed-chunk-22-1.png │ ├── Visualization.html │ ├── Visualization_files │ │ ├── RGB_mixing.png │ │ ├── RYB_mixing.png │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── 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-17-2.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-19-2.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.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-3-1.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-4-1.png │ │ │ ├── unnamed-chunk-40-1.png │ │ │ ├── unnamed-chunk-41-1.png │ │ │ ├── unnamed-chunk-42-1.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-7-1.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-76-1.png │ │ │ ├── unnamed-chunk-77-1.png │ │ │ ├── unnamed-chunk-78-1.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-88-1.png │ │ │ ├── unnamed-chunk-89-1.png │ │ │ └── unnamed-chunk-9-1.png │ ├── figures │ │ ├── scvelo_quick_start_scvelo.png │ │ ├── scvelo_umap1.png │ │ ├── scvelo_umap2_specified_area.png │ │ ├── scvelo_umap3_ms.png │ │ ├── scvelo_umap3_ms_cellrank.png │ │ └── scvelo_umap4_load_adata.png │ ├── index.html │ ├── quick_start_files │ │ ├── figure-gfm │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-16-1.png │ │ │ ├── unnamed-chunk-2-1.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 │ │ └── figure-markdown_strict │ │ │ ├── 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-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.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-53-1.png │ │ │ ├── unnamed-chunk-54-1.png │ │ │ ├── unnamed-chunk-55-1.png │ │ │ ├── unnamed-chunk-56-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ └── single-cell-course │ │ ├── 1.basic-R.html │ │ ├── 1.basic-R_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-29-1.png │ │ │ └── unnamed-chunk-29-2.png │ │ ├── 2.Seurat.html │ │ ├── 2.Seurat_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-17-1.png │ │ │ ├── unnamed-chunk-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ └── unnamed-chunk-27-1.png │ │ ├── 3.Visualization.html │ │ ├── 3.Visualization_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-1-1.png │ │ │ ├── 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-18-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-21-1.png │ │ │ ├── unnamed-chunk-22-1.png │ │ │ ├── unnamed-chunk-23-1.png │ │ │ ├── unnamed-chunk-24-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-27-1.png │ │ │ ├── unnamed-chunk-29-1.png │ │ │ ├── unnamed-chunk-3-1.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-4-1.png │ │ │ ├── unnamed-chunk-40-1.png │ │ │ ├── unnamed-chunk-41-1.png │ │ │ ├── unnamed-chunk-42-1.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-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ └── unnamed-chunk-9-1.png │ │ ├── 4.GSEA.html │ │ ├── 4.GSEA_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-25-1.png │ │ │ ├── unnamed-chunk-26-1.png │ │ │ ├── unnamed-chunk-36-1.png │ │ │ ├── unnamed-chunk-37-1.png │ │ │ ├── unnamed-chunk-38-1.png │ │ │ ├── unnamed-chunk-39-1.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 │ │ ├── 5.Core-Enhancement.html │ │ ├── 5.Core-Enhancement_files │ │ └── figure-html │ │ │ ├── unnamed-chunk-10-1.png │ │ │ ├── unnamed-chunk-11-1.png │ │ │ ├── unnamed-chunk-13-1.png │ │ │ ├── unnamed-chunk-14-1.png │ │ │ ├── unnamed-chunk-15-1.png │ │ │ ├── unnamed-chunk-19-1.png │ │ │ ├── unnamed-chunk-2-1.png │ │ │ ├── unnamed-chunk-20-1.png │ │ │ ├── unnamed-chunk-3-1.png │ │ │ ├── unnamed-chunk-4-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ └── unnamed-chunk-8-1.png │ │ ├── 6.Advanced-2.html │ │ ├── 6.Advanced-2_files │ │ └── figure-html │ │ │ ├── visualize-magic-1.png │ │ │ └── visualize_results-1.png │ │ ├── 6.Advanced.html │ │ ├── 6.Advanced_files │ │ └── figure-html │ │ │ ├── gene_trends-1.png │ │ │ ├── gene_trends-2.png │ │ │ ├── ligand_activity-1.png │ │ │ ├── ligand_expression-1.png │ │ │ ├── palantir_dm-1.png │ │ │ ├── palantir_pseudotime-1.png │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ ├── unnamed-chunk-7-1.png │ │ │ ├── unnamed-chunk-8-1.png │ │ │ ├── visualize_cellchat-1.png │ │ │ └── visualize_cellchat-2.png │ │ ├── figures │ │ ├── scvelo_scvelo_basic.png │ │ └── scvelo_scvelo_custom.png │ │ ├── images │ │ ├── RGB_mixing.png │ │ ├── RYB_mixing.png │ │ ├── fastq_example.png │ │ ├── final_umap.png │ │ ├── gene_count_matrix.png │ │ ├── normalized_gene_expression.png │ │ ├── pca_output.png │ │ ├── rstudio_interface.png │ │ ├── sc_analysis_flowchart.png │ │ ├── scenic_gene_regulatory_networks.png │ │ ├── test_copykat_heatmap.jpeg │ │ ├── umap_coordinates.png │ │ ├── umap_example.png │ │ └── unsupervised_clustering.png │ │ └── results │ │ └── pbmc_umap_plot.png ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── deps │ ├── Roboto-0.4.9 │ │ ├── KFOmCnqEu92Fr1Mu4WxKOzY.woff2 │ │ ├── KFOmCnqEu92Fr1Mu4mxK.woff2 │ │ ├── KFOmCnqEu92Fr1Mu5mxKOzY.woff2 │ │ ├── KFOmCnqEu92Fr1Mu72xKOzY.woff2 │ │ ├── KFOmCnqEu92Fr1Mu7GxKOzY.woff2 │ │ ├── KFOmCnqEu92Fr1Mu7WxKOzY.woff2 │ │ ├── KFOmCnqEu92Fr1Mu7mxKOzY.woff2 │ │ └── font.css │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js │ ├── clipboard.js-2.0.11 │ │ └── clipboard.min.js │ ├── data-deps.txt │ ├── font-awesome-6.4.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── headroom-0.11.0 │ │ ├── headroom.min.js │ │ └── jQuery.headroom.min.js │ ├── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map │ └── search-1.0.0 │ │ ├── autocomplete.jquery.min.js │ │ ├── fuse.min.js │ │ └── mark.min.js ├── docsearch.css ├── docsearch.js ├── index.html ├── katex-auto.js ├── lightswitch.js ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml └── reference │ ├── BarOfCluster.html │ ├── BuildAUCRank.html │ ├── CalcScoreGeneral.html │ ├── CalcStats.html │ ├── Cellrank-Methods.html │ ├── ClusterDistrBar.html │ ├── ClusterDistrPlot.html │ ├── DimPlot2.html │ ├── DotPlot2.html │ ├── FeaturePlot3-grid.html │ ├── FeaturePlot3.html │ ├── FilterGOTerms.html │ ├── GSEAplot.html │ ├── GeneSetAnalysis.html │ ├── GeneTrendCurve-Methods.html │ ├── GeneTrendHeatmap-Methods.html │ ├── Heatmap.html │ ├── ImportPyscenicLoom.html │ ├── Palantir-Magic.html │ ├── Palantir-Methods.html │ ├── RenameGO.html │ ├── RunBasicSeurat.html │ ├── RunPalantirDiffusionMap.html │ ├── RunSlingshot.html │ ├── SearchDatabase.html │ ├── SearchPathways.html │ ├── StackedViolin.html │ ├── UniprotToGenesymbol.html │ ├── VlnPlot2.html │ ├── VolcanoPlot.html │ ├── WaterfallPlot.html │ ├── WaterfallPlot_v3.html │ ├── activate_python.html │ ├── adata.Load.html │ ├── color_iwh.html │ ├── color_pro.html │ ├── create_condaenv_seuratextend.html │ ├── feature_percent.html │ ├── gene-naming-conversions.html │ ├── index.html │ ├── install_SeuratExtendData.html │ ├── ryb2rgb.html │ ├── save_colors.html │ ├── scVelo-SeuratToLoom-and-RunBasic.html │ ├── scVelo.SeuratToAnndata.html │ ├── show_col2.html │ └── theme_umap_arrows.html ├── inst └── extdata │ ├── environment-linux.yml │ ├── environment-mac-silicon.yml │ ├── environment-mac.yml │ └── environment-windows.yml ├── man ├── BarOfCluster.Rd ├── BuildAUCRank.Rd ├── CalcScoreGeneral.Rd ├── CalcStats.Rd ├── Cellrank-Methods.Rd ├── ClusterDistrBar.Rd ├── ClusterDistrPlot.Rd ├── DimPlot2.Rd ├── DotPlot2.Rd ├── FeaturePlot3-grid.Rd ├── FeaturePlot3.Rd ├── FilterGOTerms.Rd ├── GSEAplot.Rd ├── GeneSetAnalysis.Rd ├── GeneTrendCurve-Methods.Rd ├── GeneTrendHeatmap-Methods.Rd ├── Heatmap.Rd ├── ImportPyscenicLoom.Rd ├── Palantir-Magic.Rd ├── Palantir-Methods.Rd ├── RenameGO.Rd ├── RunBasicSeurat.Rd ├── RunPalantirDiffusionMap.Rd ├── RunSlingshot.Rd ├── SearchDatabase.Rd ├── SearchPathways.Rd ├── StackedViolin.Rd ├── UniprotToGenesymbol.Rd ├── VlnPlot2.Rd ├── VolcanoPlot.Rd ├── WaterfallPlot.Rd ├── WaterfallPlot_v3.Rd ├── activate_python.Rd ├── adata.Load.Rd ├── color_iwh.Rd ├── color_pro.Rd ├── create_condaenv_seuratextend.Rd ├── feature_percent.Rd ├── gene-naming-conversions.Rd ├── install_SeuratExtendData.Rd ├── ryb2rgb.Rd ├── save_colors.Rd ├── scVelo-SeuratToLoom-and-RunBasic.Rd ├── scVelo.SeuratToAnndata.Rd ├── show_col2.Rd └── theme_umap_arrows.Rd └── vignettes ├── FAQ.Rmd ├── FAQ.md ├── GSEA.Rmd ├── GSEA.md ├── GSEA_files └── figure-gfm │ ├── unnamed-chunk-11-1.png │ ├── unnamed-chunk-28-1.png │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-4-1.png │ ├── unnamed-chunk-5-1.png │ └── unnamed-chunk-6-1.png ├── News.Rmd ├── News.md ├── News_files └── figure-gfm │ ├── unnamed-chunk-1-1.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-18-1.png │ ├── unnamed-chunk-2-1.png │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-4-1.png │ ├── unnamed-chunk-5-1.png │ └── unnamed-chunk-6-1.png ├── SCENIC.Rmd ├── SCENIC.md ├── SCENIC_files └── figure-markdown_strict │ ├── unnamed-chunk-11-1.png │ ├── unnamed-chunk-12-1.png │ ├── unnamed-chunk-13-1.png │ ├── unnamed-chunk-17-1.png │ ├── unnamed-chunk-18-1.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-4-1.png │ ├── unnamed-chunk-5-1.png │ └── unnamed-chunk-6-1.png ├── Trajectory.Rmd ├── Trajectory.md ├── Trajectory_files └── figure-gfm │ ├── access-slingshot-output-1.png │ ├── calculate-pseudotime-1.png │ ├── gene-trend-curve-custom-1.png │ ├── gene-trend-curve-initial-1.png │ ├── gene-trend-curve-slingshot-1.png │ ├── gene-trend-heatmap-1.png │ ├── gene-trend-heatmap-slingshot-1.png │ ├── run-diffusion-map-1.png │ └── run-magic-1.png ├── Utilities.Rmd ├── Utilities.md ├── Utilities_files └── figure-markdown_strict │ ├── 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-17-1.png │ ├── unnamed-chunk-22-1.png │ ├── unnamed-chunk-24-1.png │ ├── unnamed-chunk-48-1.png │ ├── unnamed-chunk-49-1.png │ ├── unnamed-chunk-52-1.png │ └── unnamed-chunk-59-1.png ├── Visualization.Rmd ├── Visualization.md ├── Visualization_files ├── RGB_mixing.png ├── RYB_mixing.png └── figure-gfm │ ├── unnamed-chunk-1-1.png │ ├── 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-18-1.png │ ├── unnamed-chunk-19-1.png │ ├── unnamed-chunk-19-2.png │ ├── unnamed-chunk-2-1.png │ ├── unnamed-chunk-20-1.png │ ├── unnamed-chunk-21-1.png 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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-7-1.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-76-1.png │ ├── unnamed-chunk-78-1.png │ ├── unnamed-chunk-8-1.png │ ├── unnamed-chunk-80-1.png │ ├── unnamed-chunk-82-1.png │ ├── unnamed-chunk-84-1.png │ ├── unnamed-chunk-85-1.png │ ├── unnamed-chunk-86-1.png │ ├── unnamed-chunk-88-1.png │ ├── unnamed-chunk-89-1.png │ └── unnamed-chunk-9-1.png ├── figures ├── scvelo_quick_start_scvelo.png ├── scvelo_umap1.png ├── scvelo_umap2_specified_area.png ├── scvelo_umap3_ms.png ├── scvelo_umap3_ms_cellrank.png └── scvelo_umap4_load_adata.png ├── quick_start.Rmd ├── quick_start.md └── quick_start_files └── figure-gfm ├── unnamed-chunk-1-1.png ├── unnamed-chunk-10-1.png ├── unnamed-chunk-11-1.png ├── unnamed-chunk-13-1.png ├── unnamed-chunk-14-1.png ├── unnamed-chunk-15-1.png ├── unnamed-chunk-16-1.png ├── unnamed-chunk-2-1.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 /.Rbuildignore: -------------------------------------------------------------------------------- 1 | ^.*\.Rproj$ 2 | ^\.Rproj\.user$ 3 | ^doc$ 4 | ^Meta$ 5 | ^_pkgdown\.yml$ 6 | ^docs$ 7 | ^pkgdown$ 8 | ^LICENSE\.md$ 9 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # History and config files 2 | .Rhistory 3 | .Rapp.history 4 | .Rbuildignore 5 | 6 | # Session Data files 7 | .RData 8 | 9 | # Example code in package build process 10 | *-Ex.R 11 | 12 | # Output files from R CMD build 13 | /*.tar.gz 14 | 15 | # Output files from R CMD check 16 | /*.Rcheck/ 17 | 18 | # RStudio files 19 | .Rproj.user/ 20 | .Rproj 21 | 22 | # produced vignettes 23 | vignettes/*.html 24 | vignettes/*.pdf 25 | 26 | # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 27 | .httr-oauth 28 | 29 | # knitr and R markdown default cache directories 30 | /*_cache/ 31 | /cache/ 32 | 33 | # Temporary files created by R markdown 34 | *.utf8.md 35 | *.knit.md 36 | 37 | # Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html 38 | rsconnect/ 39 | /Meta/ 40 | 41 | # Ignore .DS_Store files in all directories and subdirectories 42 | **/.DS_Store 43 | 44 | # Test script in data-raw 45 | data-raw/Test.R 46 | 47 | # Course build artifacts 48 | vignettes/single-cell-course 49 | 50 | # Temporary folder 51 | tmp/ 52 | data-raw/2024-4-5 color pro from i want hue 53 | -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 1 | Package: SeuratExtend 2 | Type: Package 3 | Title: SeuratExtend 4 | Version: 1.2.1 5 | Author: Yichao Hua 6 | Maintainer: Yichao Hua 7 | Description: SeuratExtend is an R package designed to improve and simplify the analysis of scRNA-seq data using the Seurat object. It provides an array of enhanced visualization tools, an integrated functional and pathway analysis pipeline, seamless integration with popular Python tools, and a suite of utility functions to aid in data manipulation and presentation. 8 | License: GPL (>= 3) 9 | Encoding: UTF-8 10 | LazyData: true 11 | RoxygenNote: 7.3.2 12 | VignetteBuilder: knitr 13 | Imports: 14 | Seurat, dplyr, remotes, rlist, mosaic, ggplot2, reshape2, purrr, magrittr, tidyr, scales, 15 | ggpubr, BiocManager, reticulate, glue, hdf5r 16 | Suggests: 17 | rgl, GSVA, GSVAdata, slingshot, AUCell, biomaRt, ontologyIndex, viridis, 18 | doMC, doRNG, doParallel, foreach, mgsa, GSEABase, egg, loomR, mgsa, 19 | knitr, rmarkdown, RColorBrewer 20 | Depends: 21 | R (>= 3.6), SeuratExtendData, SeuratObject 22 | Remotes: 23 | huayc09/SeuratExtendData 24 | Collate: 25 | 'AUCell_basic.R' 26 | 'Anndata.R' 27 | 'generics.R' 28 | 'CalcStats.R' 29 | 'Cellrank.R' 30 | 'ClusterDistrBar.R' 31 | 'Colors.R' 32 | 'DimPlot.R' 33 | 'DotPlot.R' 34 | 'FeaturePlot.R' 35 | 'Functions.R' 36 | 'GeneSetAnalysis.R' 37 | 'GeneSetAnalysisGO.R' 38 | 'GeneSetAnalysisReactome.R' 39 | 'GenesymbolConversion.R' 40 | 'Heatmap.R' 41 | 'Internal.R' 42 | 'Loom.R' 43 | 'Palantir.R' 44 | 'Pseudotime.R' 45 | 'Python.R' 46 | 'RunBasicSeurat.R' 47 | 'RunSlingshot.R' 48 | 'Scenic.R' 49 | 'SearchDatabase.R' 50 | 'Vlnplots.R' 51 | 'VolcanoPlot.R' 52 | 'WaterfallPlot.R' 53 | 'import.R' 54 | 'runGSVA.R' 55 | 'scVelo.R' 56 | -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- 1 | # Generated by roxygen2: do not edit by hand 2 | 3 | S3method(CalcStats,Seurat) 4 | S3method(CalcStats,default) 5 | S3method(VlnPlot2,Seurat) 6 | S3method(VlnPlot2,default) 7 | S3method(VolcanoPlot,Seurat) 8 | S3method(VolcanoPlot,default) 9 | S3method(WaterfallPlot,Seurat) 10 | S3method(WaterfallPlot,default) 11 | S3method(ggplot2::ggplot_add,theme_umap_arrows) 12 | export(BarOfCluster) 13 | export(BuildAUCRank) 14 | export(CalcScoreGeneral) 15 | export(CalcScoreGeneral_v3) 16 | export(CalcStats) 17 | export(Cellrank.Compute) 18 | export(Cellrank.Plot) 19 | export(ClusterDistrBar) 20 | export(ClusterDistrPlot) 21 | export(DimPlot2) 22 | export(DotPlot2) 23 | export(EnsemblToGenesymbol) 24 | export(FeaturePlot3) 25 | export(FeaturePlot3.grid) 26 | export(FilterGOTerms) 27 | export(FilterReactomeTerms) 28 | export(GSEAplot) 29 | export(GeneSetAnalysis) 30 | export(GeneSetAnalysisGO) 31 | export(GeneSetAnalysisReactome) 32 | export(GeneTrendCurve.Palantir) 33 | export(GeneTrendCurve.Slingshot) 34 | export(GeneTrendHeatmap.Palantir) 35 | export(GeneTrendHeatmap.Slingshot) 36 | export(GenesymbolToEnsembl) 37 | export(Heatmap) 38 | export(HumanToMouseGenesymbol) 39 | export(ImportPyscenicLoom) 40 | export(MouseToHumanGenesymbol) 41 | export(Palantir.Magic) 42 | export(Palantir.Pseudotime) 43 | export(Palantir.RunDM) 44 | export(RenameGO) 45 | export(RenameReactome) 46 | export(RunBasicSeurat) 47 | export(RunPalantirDiffusionMap) 48 | export(RunSlingshot) 49 | export(ScoreAndOrder) 50 | export(SearchDatabase) 51 | export(SearchPathways) 52 | export(Seu2Adata) 53 | export(Seu2Loom) 54 | export(StackedViolin) 55 | export(StackedViolin_v3) 56 | export(UniprotToGenesymbol) 57 | export(VlnPlot2) 58 | export(VolcanoPlot) 59 | export(WaterfallPlot) 60 | export(WaterfallPlot_v3) 61 | export(activate_python) 62 | export(adata.AddDR) 63 | export(adata.AddMetadata) 64 | export(adata.Load) 65 | export(adata.LoadLoom) 66 | export(adata.Save) 67 | export(color_iwh) 68 | export(color_pro) 69 | export(create_condaenv_seuratextend) 70 | export(feature_percent) 71 | export(install_SeuratExtendData) 72 | export(ryb2rgb) 73 | export(save_colors) 74 | export(scVelo.Plot) 75 | export(scVelo.RunBasic) 76 | export(scVelo.SeuratToAnndata) 77 | export(scVelo.SeuratToLoom) 78 | export(show_col2) 79 | export(theme_umap_arrows) 80 | import(ggplot2) 81 | importFrom(reshape2,melt) 82 | -------------------------------------------------------------------------------- /SeuratExtend.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: Sweave 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | 18 | BuildType: Package 19 | PackageUseDevtools: Yes 20 | PackageInstallArgs: --no-multiarch --with-keep.source 21 | -------------------------------------------------------------------------------- /_pkgdown.yml: -------------------------------------------------------------------------------- 1 | template: 2 | params: 3 | toc: true 4 | toc_float: true 5 | toc_depth: 3 6 | 7 | navbar: 8 | left: 9 | - text: "Reference" 10 | href: reference/index.html 11 | - text: "Vignettes" 12 | menu: 13 | - text: "What's New in v1.2.0" 14 | href: articles/News.html 15 | - text: "-----------------" 16 | - text: "Enhanced Visualization" 17 | href: articles/Visualization.html 18 | - text: "Geneset Enrichment Analysis (GSEA) " 19 | href: articles/GSEA.html 20 | - text: "Trajectory and Pseudotime Analysis " 21 | href: articles/Trajectory.html 22 | - text: "SCENIC for Gene Regulatory Networks Analysis " 23 | href: articles/SCENIC.html 24 | - text: "Utility Tools and Functions" 25 | href: articles/Utilities.html 26 | - text: "scRNA-seq Course" 27 | menu: 28 | - text: "1. Introduction to R" 29 | href: articles/single-cell-course/1.basic-R.html 30 | - text: "2. Basic Single-Cell Analysis Workflow" 31 | href: articles/single-cell-course/2.Seurat.html 32 | - text: "3. Advanced Visualization Techniques" 33 | href: articles/single-cell-course/3.Visualization.html 34 | - text: "4. Gene Set Enrichment Analysis" 35 | href: articles/single-cell-course/4.GSEA.html 36 | - text: "5. Core scRNA-seq Workflow Enhancements" 37 | href: articles/single-cell-course/5.Core-Enhancement.html 38 | - text: "6. Advanced Methods (Part 1)" 39 | href: articles/single-cell-course/6.Advanced.html 40 | - text: "7. Advanced Methods (Part 2)" 41 | href: articles/single-cell-course/6.Advanced-2.html 42 | - text: "FAQ" 43 | href: articles/FAQ.html 44 | -------------------------------------------------------------------------------- /data-raw/PanglaoDB.R: -------------------------------------------------------------------------------- 1 | PanglaoDB <- 2 | read.csv("/Documents/R documents/SeuratExtend_databases/2020-3-27 PanglaoDB/PanglaoDB_markers_27_Mar_2020.tsv", 3 | sep = "\t") 4 | PanglaoDB_data <- list() 5 | Hs <- grepl("Hs",PanglaoDB$species) 6 | PanglaoDB_data[["marker_list_human"]] <- 7 | split(PanglaoDB$official.gene.symbol[Hs], PanglaoDB$cell.type[Hs]) 8 | Mm <- grepl("Mm",PanglaoDB$species) 9 | PanglaoDB_data[["marker_list_mouse"]] <- 10 | split(PanglaoDB$official.gene.symbol[Mm], PanglaoDB$cell.type[Mm]) %>% 11 | lapply(HumanToMouseGenesymbol, match = F) 12 | PanglaoDB_data[["original_data"]] <- PanglaoDB 13 | 14 | object.size(PanglaoDB_data) 15 | -------------------------------------------------------------------------------- /data-raw/colors_iwanthue.R: -------------------------------------------------------------------------------- 1 | library(openxlsx) 2 | library(tidyr) 3 | library(dplyr) 4 | file <- "d:/Documents/R documents/SeuratExtend_databases/2021-5-21 preset colors/2021-8-12 preset colors I want hue.xlsx" 5 | col.space <- c("default","intense","pastel","all","all_hard") 6 | color_presets <- list() 7 | for (i in 1:5) { 8 | col_list <- read.xlsx(file, sheet = i, colNames = F) %>% 9 | as.list() %>% 10 | lapply(function(x) x[!is.na(x)]) %>% 11 | split(f = lengths(.)) %>% 12 | lapply(function(x) { 13 | names(x) <- seq_along(x) 14 | x}) 15 | color_presets[[col.space[i]]] <- col_list 16 | } 17 | 18 | usethis::use_data(color_presets, overwrite = TRUE) 19 | # rename 20 | presets_color_iwh <- color_presets 21 | usethis::use_data(presets_color_iwh, overwrite = TRUE) 22 | -------------------------------------------------------------------------------- /data-raw/colors_pro.R: -------------------------------------------------------------------------------- 1 | setwd("~/Documents/SeuratExtend-database/2024-4-5 color pro from i want hue") 2 | 3 | files <- list.files(pattern = ".csv") 4 | files <- files[!grepl("_original",files)] 5 | theme <- c("default","light","red","yellow","green","blue","purple","bright") 6 | 7 | lines <- readLines(files[1]) 8 | color_palettes <- strsplit(lines, ",") 9 | color_palettes <- split(color_palettes, f = lengths(color_palettes)) 10 | 11 | color_pro_presets <- list() 12 | for (i in theme) { 13 | file_diff <- paste0("diffSortedPalettes_pro_",i,".csv") 14 | file_hue <- paste0("hueSortedPalettes_pro_",i,".csv") 15 | file <- c(diff = file_diff, hue = file_hue) 16 | for (j in c("hue","diff")) { 17 | lines <- readLines(file[j]) 18 | color_palettes <- strsplit(lines, ",") 19 | color_pro_presets[[i]][[j]] <- split(color_palettes, f = lengths(color_palettes)) 20 | } 21 | } 22 | 23 | presets_color_pro <- color_pro_presets 24 | usethis::use_data(presets_color_pro, overwrite = TRUE) 25 | -------------------------------------------------------------------------------- /data/PanglaoDB_data.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huayc09/SeuratExtend/e228f70b5b621198fb7e19a1f40d3ec6df94f1b8/data/PanglaoDB_data.rda -------------------------------------------------------------------------------- /data/hall50.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/huayc09/SeuratExtend/e228f70b5b621198fb7e19a1f40d3ec6df94f1b8/data/hall50.rda -------------------------------------------------------------------------------- /data/human_ensembl_genesymbol.rda: -------------------------------------------------------------------------------- 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Hide your header until you need it 3 | * Copyright (c) 2017 Nick Williams - http://wicky.nillia.ms/headroom.js 4 | * License: MIT 5 | */ 6 | 7 | !function(a){a&&(a.fn.headroom=function(b){return this.each(function(){var c=a(this),d=c.data("headroom"),e="object"==typeof b&&b;e=a.extend(!0,{},Headroom.options,e),d||(d=new Headroom(this,e),d.init(),c.data("headroom",d)),"string"==typeof b&&(d[b](),"destroy"===b&&c.removeData("headroom"))})},a("[data-headroom]").each(function(){var b=a(this);b.headroom(b.data())}))}(window.Zepto||window.jQuery); -------------------------------------------------------------------------------- /docs/docsearch.js: -------------------------------------------------------------------------------- 1 | $(function() { 2 | 3 | // register a handler to move the focus to the search bar 4 | // upon pressing shift + "/" (i.e. "?") 5 | $(document).on('keydown', function(e) { 6 | if (e.shiftKey && e.keyCode == 191) { 7 | e.preventDefault(); 8 | $("#search-input").focus(); 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56 | 57 | var hierarchy = hit._highlightResult.hierarchy; 58 | // loop to fetch from lvl0, lvl1, etc. 59 | for (var idx in hierarchy) { 60 | words = words.concat(hierarchy[idx].matchedWords); 61 | } 62 | 63 | var content = hit._highlightResult.content; 64 | if (content) { 65 | words = words.concat(content.matchedWords); 66 | } 67 | 68 | // return unique words 69 | var words_uniq = [...new Set(words)]; 70 | return words_uniq; 71 | } 72 | 73 | function updateHitURL(hit) { 74 | 75 | var words = matchedWords(hit); 76 | var url = ""; 77 | 78 | if (hit.anchor) { 79 | url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor; 80 | } else { 81 | url = hit.url + '?q=' + escape(words.join(" ")); 82 | } 83 | 84 | return url; 85 | } 86 | -------------------------------------------------------------------------------- /docs/katex-auto.js: -------------------------------------------------------------------------------- 1 | // https://github.com/jgm/pandoc/blob/29fa97ab96b8e2d62d48326e1b949a71dc41f47a/src/Text/Pandoc/Writers/HTML.hs#L332-L345 2 | document.addEventListener("DOMContentLoaded", function () { 3 | var mathElements = document.getElementsByClassName("math"); 4 | var macros = []; 5 | for (var i = 0; i < mathElements.length; i++) { 6 | var texText = mathElements[i].firstChild; 7 | if (mathElements[i].tagName == "SPAN") { 8 | katex.render(texText.data, mathElements[i], { 9 | displayMode: mathElements[i].classList.contains("display"), 10 | throwOnError: false, 11 | macros: macros, 12 | fleqn: false 13 | }); 14 | }}}); 15 | -------------------------------------------------------------------------------- /docs/link.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | 5 | 8 | 12 | 13 | -------------------------------------------------------------------------------- /docs/pkgdown.yml: -------------------------------------------------------------------------------- 1 | pandoc: 3.1.11 2 | pkgdown: 2.0.7 3 | pkgdown_sha: ~ 4 | articles: 5 | FAQ: FAQ.html 6 | GSEA: GSEA.html 7 | News: News.html 8 | SCENIC: SCENIC.html 9 | Trajectory: Trajectory.html 10 | Utilities: Utilities.html 11 | Visualization: Visualization.html 12 | quick_start: quick_start.html 13 | 1.basic-R: single-cell-course/1.basic-R.html 14 | 2.Seurat: single-cell-course/2.Seurat.html 15 | 3.Visualization: single-cell-course/3.Visualization.html 16 | 4.GSEA: single-cell-course/4.GSEA.html 17 | 5.Core-Enhancement: single-cell-course/5.Core-Enhancement.html 18 | 6.Advanced-2: single-cell-course/6.Advanced-2.html 19 | 6.Advanced: single-cell-course/6.Advanced.html 20 | last_built: 2025-05-16T12:32Z 21 | 22 | -------------------------------------------------------------------------------- /man/BarOfCluster.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ClusterDistrBar.R 3 | \name{BarOfCluster} 4 | \alias{BarOfCluster} 5 | \title{Cluster proportion bar plot} 6 | \usage{ 7 | BarOfCluster(meta, cluster, origin, method = "value", do.heatmap = T) 8 | } 9 | \arguments{ 10 | \item{meta}{meta data data.frame} 11 | 12 | \item{cluster}{variable name of cluster} 13 | 14 | \item{origin}{variable name of sample} 15 | 16 | \item{method}{'percent'or 'value'} 17 | 18 | \item{do.heatmap}{Generate plot (TRUE) or matrix (FALSE), Default: T} 19 | } 20 | \value{ 21 | ggplot object or matrix 22 | } 23 | \description{ 24 | deprecated function of \code{\link[SeuratExtend:ClusterDistrBar]{ClusterDistrBar()}} 25 | } 26 | \seealso{ 27 | \code{\link[SeuratExtend:ClusterDistrBar]{ClusterDistrBar()}} 28 | } 29 | -------------------------------------------------------------------------------- /man/BuildAUCRank.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/AUCell_basic.R 3 | \name{BuildAUCRank} 4 | \alias{BuildAUCRank} 5 | \title{Build AUCell Rank} 6 | \usage{ 7 | BuildAUCRank(seu, slot = "counts", assay = "RNA", verbose = TRUE) 8 | } 9 | \arguments{ 10 | \item{seu}{Seurat object} 11 | 12 | \item{slot}{Slot to pull feature data for, Default: 'counts'} 13 | 14 | \item{assay}{Name of assay to use, Default: 'RNA'} 15 | 16 | \item{verbose}{Should the function show progress messages? Default: TRUE} 17 | } 18 | \value{ 19 | Seurat object. 20 | } 21 | \description{ 22 | Build AUCell ranking matrix using 'AUCell' package: 23 | 24 | Aibar et al. (2017) SCENIC: single-cell regulatory network inference and clustering. 25 | Nature Methods. doi: 10.1038/nmeth.4463 26 | 27 | Aibar. et al. (2016) AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data. 28 | R/Bioconductor package. 29 | } 30 | \details{ 31 | AUCell ranking matrix is saved in seu@misc$AUCell[["cells_rankings"]] 32 | } 33 | \examples{ 34 | library(SeuratExtend) 35 | options(max.print = 20) 36 | 37 | pbmc <- BuildAUCRank(pbmc) 38 | pbmc@misc$AUCell[["cells_rankings"]][3,4] 39 | } 40 | -------------------------------------------------------------------------------- /man/CalcScoreGeneral.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/CalcStats.R 3 | \name{CalcScoreGeneral} 4 | \alias{CalcScoreGeneral} 5 | \alias{CalcScoreGeneral_v3} 6 | \alias{ScoreAndOrder} 7 | \title{CalcScoreGeneral, ScoreAndOrder} 8 | \usage{ 9 | CalcScoreGeneral( 10 | matr, 11 | f, 12 | method = "zscore", 13 | exp.transform = F, 14 | t = F, 15 | order = NULL, 16 | n = Inf, 17 | p.threshold = 0.05 18 | ) 19 | 20 | CalcScoreGeneral_v3( 21 | seu, 22 | features, 23 | group.by = NULL, 24 | cells = NULL, 25 | slot = "data", 26 | assay = NULL, 27 | method = "zscore", 28 | exp.transform = F, 29 | order = NULL, 30 | n = Inf, 31 | p.threshold = 0.05, 32 | priority = c("expr", "none") 33 | ) 34 | 35 | ScoreAndOrder( 36 | matr, 37 | f, 38 | method = "zscore", 39 | exp.transform = F, 40 | t = F, 41 | order = NULL, 42 | n = Inf, 43 | p.threshold = 0.05 44 | ) 45 | } 46 | \description{ 47 | Alias of \code{\link[SeuratExtend:CalcStats]{CalcStats()}} 48 | } 49 | \seealso{ 50 | \code{\link[SeuratExtend:CalcStats]{CalcStats()}} 51 | } 52 | -------------------------------------------------------------------------------- /man/ClusterDistrBar.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/ClusterDistrBar.R 3 | \name{ClusterDistrBar} 4 | \alias{ClusterDistrBar} 5 | \title{Cluster proportion bar plot} 6 | \usage{ 7 | ClusterDistrBar( 8 | origin, 9 | cluster, 10 | rev = F, 11 | normalize = rev, 12 | percent = T, 13 | plot = T, 14 | flip = T, 15 | reverse_order = T, 16 | width = 0.9, 17 | stack = T, 18 | cols = "light", 19 | border = "white" 20 | ) 21 | } 22 | \arguments{ 23 | \item{origin}{factor/vector of sample} 24 | 25 | \item{cluster}{factor/vector of cluster} 26 | 27 | \item{rev}{If TRUE, plot the proportion of sample in each cluster, Default: F} 28 | 29 | \item{normalize}{Normalize sample size to 100, Default: rev} 30 | 31 | \item{percent}{If FALSE, plot absolute cell number instead of percentage, Default: T} 32 | 33 | \item{plot}{Generate plot (TRUE) or matrix (FALSE), Default: T} 34 | 35 | \item{flip}{If plot bars horizontally, Default: T} 36 | 37 | \item{reverse_order}{If TRUE, will reverse the default stacking order. Default: T} 38 | 39 | \item{width}{Width of bars, Default: 0.9} 40 | 41 | \item{stack}{If TRUE, plot stacked bars, Default: T} 42 | 43 | \item{cols}{Colors to use for plotting. Default: "light"} 44 | 45 | \item{border}{Border color, Default: "white"} 46 | } 47 | \value{ 48 | ggplot object or matrix 49 | } 50 | \description{ 51 | Plot the percentage/absolute cell count of each cluster in each sample 52 | } 53 | \details{ 54 | See example 55 | } 56 | \examples{ 57 | ClusterDistrBar(origin = pbmc$orig.ident, cluster = pbmc$cluster) 58 | 59 | # absolute cell count 60 | ClusterDistrBar(origin = pbmc$orig.ident, cluster = pbmc$cluster, percent = F) 61 | 62 | # reverse x and y axis, normalized by sample size 63 | ClusterDistrBar(origin = pbmc$orig.ident, cluster = pbmc$cluster, rev = T, normalize = T) 64 | 65 | # reverse x and y axis, not normalized by sample size 66 | ClusterDistrBar(origin = pbmc$orig.ident, cluster = pbmc$cluster, rev = T, normalize = F) 67 | 68 | # vertical bar plot, and keep the default stacking order 69 | ClusterDistrBar(origin = pbmc$orig.ident, cluster = pbmc$cluster, flip = F, reverse_order = F) 70 | 71 | # not stacking bars 72 | ClusterDistrBar(origin = pbmc$orig.ident, cluster = pbmc$cluster, flip = FALSE, stack = FALSE) 73 | 74 | # export matrix 75 | ClusterDistrBar(origin = pbmc$orig.ident, cluster = pbmc$cluster, plot = F) 76 | } 77 | -------------------------------------------------------------------------------- /man/GSEAplot.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/runGSVA.R 3 | \name{GSEAplot} 4 | \alias{GSEAplot} 5 | \title{GSEA plot} 6 | \usage{ 7 | GSEAplot( 8 | seu, 9 | group.by = NULL, 10 | geneset, 11 | ident.1 = NULL, 12 | ident.2 = NULL, 13 | cells = NULL, 14 | slot = "data", 15 | assay = NULL, 16 | logFC.cutoff = c(-1, 1), 17 | p.position = c(0.8, 0.85), 18 | sample = 500, 19 | title = deparse(substitute(geneset)) 20 | ) 21 | } 22 | \arguments{ 23 | \item{seu}{Seurat object} 24 | 25 | \item{group.by}{A variable name in meta.data to 26 | group the violin plots by, or string with the same length of cells} 27 | 28 | \item{geneset}{A list of genes} 29 | 30 | \item{ident.1}{Cell type name} 31 | 32 | \item{ident.2}{(Optional) Second cell type name to compare with 'ident.1'} 33 | 34 | \item{cells}{Cell names to use, Default: all cells} 35 | 36 | \item{slot}{Slot to pull feature data for, Default: 'data'} 37 | 38 | \item{assay}{Name of assay to use, defaults to the active assay} 39 | 40 | \item{logFC.cutoff}{Range of Log2 fold change of ranked genes, Default: c(-1, 1)} 41 | 42 | \item{p.position}{Where to put ES and p value text, Default: c(0.8, 0.85)} 43 | 44 | \item{sample}{Points used for drawing curves. Default: 500} 45 | 46 | \item{title}{Title of geneset} 47 | } 48 | \value{ 49 | Plot 50 | } 51 | \description{ 52 | Generate plot that mimic the Gene Set Enrichment computational analysis 53 | published by the Broad Institute 54 | } 55 | \details{ 56 | P value is calculated using Kolmogorov-Smirnov Tests 57 | } 58 | \examples{ 59 | GSEAplot( 60 | pbmc, ident.1 = "CD4 T Naive", title = "INTERFERON_GAMMA_RESPONSE", 61 | geneset = hall50$human$HALLMARK_INTERFERON_GAMMA_RESPONSE) 62 | } 63 | -------------------------------------------------------------------------------- /man/Palantir-Magic.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Palantir.R 3 | \name{Palantir.Magic} 4 | \alias{Palantir.Magic} 5 | \title{Run MAGIC for Gene Expression Smoothing} 6 | \usage{ 7 | Palantir.Magic( 8 | seu, 9 | n_top_genes = 2000, 10 | n_components = 20, 11 | conda_env = "seuratextend", 12 | n_jobs = 1 13 | ) 14 | } 15 | \arguments{ 16 | \item{seu}{A Seurat object containing single-cell RNA-seq data to which the MAGIC algorithm will be applied.} 17 | 18 | \item{n_top_genes}{The number of top variable genes to consider in the MAGIC algorithm, which helps in focusing the smoothing on the most informative genes. Default: 2000} 19 | 20 | \item{n_components}{The number of principal components to use in dimensionality reduction before applying MAGIC. Useful for preprocessing the data to enhance the effects of MAGIC. Default: 20} 21 | 22 | \item{conda_env}{The name of the Conda environment where the necessary Python dependencies for running MAGIC are installed. This environment is used to run Python code from R, ensuring smooth integration of the two platforms. Default: 'seuratextend'} 23 | 24 | \item{n_jobs}{Number of jobs for parallel computation. Default: 1} 25 | } 26 | \value{ 27 | Updates the provided Seurat object by adding a new assay named 'magic', which contains the denoised and smoothed gene expression data. 28 | } 29 | \description{ 30 | Applies the MAGIC (Markov Affinity-based Graph Imputation of Cells) algorithm to a Seurat object to denoise and smooth gene expression data. This technique enhances data interpretability by imputing missing data and reducing technical noise. 31 | } 32 | \details{ 33 | MAGIC uses a graph-based approach to infer and smooth gene expression across similar cells, effectively filling in gaps in the data where measurements are sparse or noisy. This process is especially beneficial in datasets with high levels of technical noise or when trying to resolve subtle biological signals that might be obscured by this noise. 34 | } 35 | \examples{ 36 | library(Seurat) 37 | library(SeuratExtend) 38 | 39 | # Download the example Seurat Object 40 | mye_small <- readRDS(url("https://zenodo.org/records/10944066/files/pbmc10k_mye_small_velocyto.rds", "rb")) 41 | 42 | # Run MAGIC 43 | mye_small <- Palantir.Magic(mye_small) 44 | 45 | # Visualizing the effects of MAGIC on selected genes 46 | DimPlot2(mye_small, features = c("CD14", "magic_CD14", "FLT3", "magic_FLT3")) 47 | 48 | } 49 | -------------------------------------------------------------------------------- /man/RenameGO.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/GeneSetAnalysisGO.R, 3 | % R/GeneSetAnalysisReactome.R 4 | \name{RenameGO} 5 | \alias{RenameGO} 6 | \alias{RenameReactome} 7 | \title{Convert GO/Reactome Pathway IDs to Full Names} 8 | \usage{ 9 | RenameGO(term, add_id = T, add_n_gene = T, spe = getOption("spe")) 10 | 11 | RenameReactome(term, add_id = T, add_n_gene = T, spe = getOption("spe")) 12 | } 13 | \arguments{ 14 | \item{term}{GO/Reactome IDs, which can be either a character vector or a matrix (with IDs in rownames).} 15 | 16 | \item{add_id}{Logical: Should the IDs be displayed? Default: TRUE.} 17 | 18 | \item{add_n_gene}{Logical: Should the number of genes in each geneset be displayed? Default: TRUE.} 19 | 20 | \item{spe}{Species, either 'human' or 'mouse'. Default: getOption("spe").} 21 | } 22 | \value{ 23 | Returns either a character vector or a matrix, depending on the input. 24 | } 25 | \description{ 26 | Converts GO or Reactome IDs to their respective full geneset or pathway names. 27 | } 28 | \details{ 29 | For more examples, see \code{\link[SeuratExtend:GeneSetAnalysis]{GeneSetAnalysis()}}. 30 | } 31 | \examples{ 32 | library(SeuratExtend) 33 | 34 | RenameGO(c("GO:0002376","GO:0050896"), spe = "human") 35 | 36 | RenameReactome(c("R-HSA-109582","R-HSA-112316"), spe = "human") 37 | } 38 | -------------------------------------------------------------------------------- /man/RunPalantirDiffusionMap.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Palantir.R 3 | \name{RunPalantirDiffusionMap} 4 | \alias{RunPalantirDiffusionMap} 5 | \title{(Deprecated) Run Palantir Diffusion Map} 6 | \usage{ 7 | RunPalantirDiffusionMap(seu, reduction = "pca", n_components = 20) 8 | } 9 | \arguments{ 10 | \item{seu}{A Seurat object.} 11 | 12 | \item{reduction}{A character string specifying the dimension reduction to use. Default: 'pca'.} 13 | 14 | \item{n_components}{An integer specifying how many dimensions to use as input. Default: 20.} 15 | } 16 | \value{ 17 | A Seurat object with added dm, ms, and t-SNE embeddings. 18 | } 19 | \description{ 20 | This is a deprecated version of the Palantir Diffusion Map function. 21 | Please refer to the updated function, \code{\link{Palantir.RunDM}}, for the latest features and improvements. 22 | This older version, in addition to calculating the diffusion map (dm) and multiscale_space (ms), 23 | also calculates t-SNE. To use the t-SNE feature, the \code{multicore-tsne} package needs to be installed in the conda environment. 24 | } 25 | \examples{ 26 | \dontrun{ 27 | library(Seurat) 28 | library(SeuratExtend) 29 | pbmc <- RunPalantirDiffusionMap(pbmc) 30 | DimPlot(pbmc, reduction = "tsne", label = TRUE) 31 | } 32 | } 33 | \seealso{ 34 | \code{\link{Palantir.RunDM}} for the updated version of this function. 35 | } 36 | -------------------------------------------------------------------------------- /man/SearchPathways.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/SearchDatabase.R 3 | \name{SearchPathways} 4 | \alias{SearchPathways} 5 | \title{Search Pathways in a Given Geneset List} 6 | \usage{ 7 | SearchPathways(genesets, item, type = c("gene", "SetName")) 8 | } 9 | \arguments{ 10 | \item{genesets}{A list of genesets where the names are pathway names and the contents are genes.} 11 | 12 | \item{item}{A vector containing gene names or (parts of) pathway names to search for.} 13 | 14 | \item{type}{Specifies the types of search criteria. This can be "gene", "SetName", or both. Default is c("gene", "SetName").} 15 | } 16 | \value{ 17 | A subset of the provided geneset list containing the specified items. 18 | } 19 | \description{ 20 | This function filters a provided geneset list based on a specified gene name, or pathway name. 21 | } 22 | \details{ 23 | For more details and use-cases, see the examples section. 24 | } 25 | \examples{ 26 | library(SeuratExtend) 27 | library(dplyr) 28 | options(max.print = 10) 29 | 30 | # Check within the hallmark 50 database for pathways that contain the "CD3D" gene 31 | # or have pathway names that include "interferon". 32 | SearchPathways(genesets = hall50$human, item = c("CD3D", "interferon")) 33 | } 34 | -------------------------------------------------------------------------------- /man/StackedViolin.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Vlnplots.R 3 | \name{StackedViolin} 4 | \alias{StackedViolin} 5 | \alias{StackedViolin_v3} 6 | \title{StackedViolin} 7 | \usage{ 8 | StackedViolin( 9 | matr, 10 | f, 11 | f2 = NULL, 12 | features = NULL, 13 | t = F, 14 | cols = "light", 15 | ncol = NULL, 16 | nrow = NULL, 17 | lab_fill = "group", 18 | scales = "free_y", 19 | style = c("fill", "outline"), 20 | violin = T, 21 | box = T, 22 | width = 0.9, 23 | show.mean = FALSE, 24 | mean_colors = c("red", "blue"), 25 | pt = T, 26 | hide.outlier = F, 27 | pt.style = c("jitter", "quasirandom"), 28 | pt.size = 0.2, 29 | pt.alpha = 1, 30 | strip.position = "top", 31 | stat.method = c("none", "wilcox.test", "t.test"), 32 | stats.method = NULL, 33 | p.adjust.method = "holm", 34 | label = c("p.signif", "p", "p.adj", "p.format"), 35 | comparisons = NULL, 36 | hide.ns = TRUE, 37 | step.increase = 0.12, 38 | tip.length = 0.03, 39 | angle = NULL, 40 | hjust = NULL, 41 | vjust = NULL, 42 | ... 43 | ) 44 | 45 | StackedViolin_v3( 46 | seu, 47 | features, 48 | group.by = NULL, 49 | split.by = NULL, 50 | cells = NULL, 51 | slot = "data", 52 | assay = NULL, 53 | priority = c("expr", "none"), 54 | cols = "light", 55 | load.cols = TRUE, 56 | ncol = NULL, 57 | nrow = NULL, 58 | lab_fill = "group", 59 | scales = "free_y", 60 | style = c("fill", "outline"), 61 | violin = T, 62 | box = T, 63 | width = 0.9, 64 | show.mean = FALSE, 65 | mean_colors = c("red", "blue"), 66 | pt = T, 67 | hide.outlier = F, 68 | pt.style = c("jitter", "quasirandom"), 69 | pt.size = 0.2, 70 | pt.alpha = 1, 71 | strip.position = "top", 72 | stat.method = c("none", "wilcox.test", "t.test"), 73 | stats.method = NULL, 74 | p.adjust.method = "holm", 75 | label = c("p.signif", "p", "p.adj", "p.format"), 76 | comparisons = NULL, 77 | hide.ns = TRUE, 78 | step.increase = 0.12, 79 | tip.length = 0.03, 80 | angle = NULL, 81 | hjust = NULL, 82 | vjust = NULL, 83 | ... 84 | ) 85 | } 86 | \description{ 87 | Alias of \code{\link[SeuratExtend:VlnPlot2]{VlnPlot2()}} 88 | } 89 | \seealso{ 90 | \code{\link[SeuratExtend:VlnPlot2]{VlnPlot2()}} 91 | } 92 | -------------------------------------------------------------------------------- /man/UniprotToGenesymbol.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/GenesymbolConversion.R 3 | \name{UniprotToGenesymbol} 4 | \alias{UniprotToGenesymbol} 5 | \title{Convert UniProt IDs to Gene Symbols} 6 | \usage{ 7 | UniprotToGenesymbol(Uniprot, spe = getOption("spe")) 8 | } 9 | \arguments{ 10 | \item{Uniprot}{A vector of UniProt IDs that are to be converted to gene symbols.} 11 | 12 | \item{spe}{The species for which the conversion should be performed. The default is set to the user's global option (`getOption("spe")`), but can be explicitly specified as "human" or "mouse".} 13 | } 14 | \value{ 15 | Returns a vector of gene symbols corresponding to the input UniProt IDs. 16 | } 17 | \description{ 18 | Converts UniProt IDs to corresponding gene symbols for specified species using local databases. This function supports integration between proteomic and genomic data, enhancing the utility of proteomic identifiers in genomic analyses. 19 | } 20 | \details{ 21 | `UniprotToGenesymbol` utilizes a locally stored version of the UniProt database to convert UniProt IDs to gene symbols. This approach ensures fast and reliable conversions without the need for online database access. The local database includes comprehensive mappings from UniProt IDs to gene symbols for both human and mouse, facilitating seamless integration of proteomic and genomic data. 22 | } 23 | \examples{ 24 | # Converting UniProt IDs to human gene symbols 25 | UniprotToGenesymbol(c("Q8NF67", "Q9NPB9"), spe = "human") 26 | 27 | # Converting UniProt IDs to mouse gene symbols 28 | UniprotToGenesymbol(c("Q9R1C8", "Q9QY84"), spe = "mouse") 29 | } 30 | -------------------------------------------------------------------------------- /man/WaterfallPlot_v3.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/WaterfallPlot.R 3 | \name{WaterfallPlot_v3} 4 | \alias{WaterfallPlot_v3} 5 | \title{WaterfallPlot_v3} 6 | \usage{ 7 | WaterfallPlot_v3( 8 | seu, 9 | features, 10 | group.by = NULL, 11 | cell = NULL, 12 | cells = NULL, 13 | slot = "data", 14 | assay = NULL, 15 | priority = c("expr", "none"), 16 | ident.1 = NULL, 17 | ident.2 = NULL, 18 | exp.transform = (length == "logFC"), 19 | order = TRUE, 20 | length = "logFC", 21 | color = "p", 22 | len.threshold = 0, 23 | col.threshold = 0, 24 | color_theme = "BuRd", 25 | center_color = NULL, 26 | top.n = NULL, 27 | flip = FALSE, 28 | y.label = NULL, 29 | angle = NULL, 30 | hjust = NULL, 31 | vjust = NULL, 32 | title = NULL, 33 | style = c("bar", "segment"), 34 | border = NA, 35 | log.base = "e", 36 | pseudocount = NULL 37 | ) 38 | } 39 | \description{ 40 | Alias of \code{\link[SeuratExtend:WaterfallPlot]{WaterfallPlot()}}, Seurat version 41 | } 42 | \seealso{ 43 | \code{\link[SeuratExtend:WaterfallPlot]{WaterfallPlot()}} 44 | } 45 | -------------------------------------------------------------------------------- /man/activate_python.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Python.R 3 | \name{activate_python} 4 | \alias{activate_python} 5 | \title{Activate Python Environment for SeuratExtend} 6 | \usage{ 7 | activate_python(conda_env = "seuratextend", verbose = TRUE, packages = c("os")) 8 | } 9 | \arguments{ 10 | \item{conda_env}{Character string specifying the conda environment name. Default is "seuratextend".} 11 | 12 | \item{verbose}{Logical indicating whether to print status messages. Default is TRUE.} 13 | 14 | \item{packages}{Character vector of Python packages to import.} 15 | } 16 | \value{ 17 | Invisible TRUE if successful 18 | } 19 | \description{ 20 | This function activates a Python environment (default: "seuratextend") and imports specified packages. 21 | It's particularly important for macOS users to call this function at the beginning of their workflow 22 | to prevent R session crashes when running Python-dependent functions later. 23 | } 24 | \details{ 25 | This function serves two main purposes: 26 | 27 | 1. It activates the specified conda environment and imports the specified Python packages. 28 | 29 | 2. **For macOS users (especially on Apple Silicon M1/M2/M3/M4)**: Running this function at the start 30 | of your R session, before loading any R objects, prevents memory management issues between R and Python 31 | that can otherwise cause R to crash when running operations like PCA on AnnData objects. 32 | 33 | This is a crucial first step for macOS users working with `scVelo` functions. 34 | } 35 | \examples{ 36 | \dontrun{ 37 | # For macOS users, run this at the beginning of your session 38 | activate_python() 39 | 40 | # Then load your Seurat objects and continue with your analysis 41 | seu <- readRDS("my_seurat_object.rds") 42 | 43 | # Custom environment with verbose output 44 | activate_python(conda_env = "my_custom_env", verbose = TRUE) 45 | } 46 | } 47 | -------------------------------------------------------------------------------- /man/color_iwh.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Colors.R 3 | \name{color_iwh} 4 | \alias{color_iwh} 5 | \title{Default discrete color presets by 'I want hue'} 6 | \usage{ 7 | color_iwh( 8 | n, 9 | col.space = c("default", "intense", "pastel", "all", "all_hard"), 10 | set = 1 11 | ) 12 | } 13 | \arguments{ 14 | \item{n}{How many colors to generate} 15 | 16 | \item{col.space}{Color space, Options: "default", "intense", "pastel", 17 | "all" (k-Means) or "all_hard" (force vector)} 18 | 19 | \item{set}{Several random presets, Default: 1} 20 | } 21 | \value{ 22 | Vector of colors 23 | } 24 | \description{ 25 | Generate color presets from 'I want hue' online tool 26 | } 27 | \details{ 28 | Random color presets generated from: https://medialab.github.io/iwanthue/ 29 | } 30 | \examples{ 31 | color_iwh(10) 32 | } 33 | -------------------------------------------------------------------------------- /man/color_pro.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Colors.R 3 | \name{color_pro} 4 | \alias{color_pro} 5 | \title{Professional discrete color presets by 'I want hue'} 6 | \usage{ 7 | color_pro( 8 | n, 9 | col.space = c("default", "light", "red", "yellow", "green", "blue", "purple", "bright"), 10 | sort = c("hue", "diff"), 11 | set = 1 12 | ) 13 | } 14 | \arguments{ 15 | \item{n}{How many colors to generate} 16 | 17 | \item{col.space}{Color space, Options: "default", "light", "red", "yellow", "green", "blue", "purple", or "bright"} 18 | 19 | \item{sort}{Sort colors by hue (default) or differentiation, Options: "hue", "diff"} 20 | 21 | \item{set}{Several random presets, Default: 1} 22 | } 23 | \value{ 24 | Vector of colors 25 | } 26 | \description{ 27 | Generate professional color presets from 'I want hue' color tool 28 | } 29 | \details{ 30 | Random color presets generated from: https://medialab.github.io/iwanthue/ 31 | } 32 | \examples{ 33 | color_pro(10) 34 | } 35 | -------------------------------------------------------------------------------- /man/feature_percent.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Functions.R 3 | \name{feature_percent} 4 | \alias{feature_percent} 5 | \title{Proportion of features} 6 | \usage{ 7 | feature_percent( 8 | seu, 9 | feature, 10 | ident = NULL, 11 | group.by = NULL, 12 | DefaultAssay = NULL, 13 | above = 0, 14 | total = F, 15 | if.expressed = F, 16 | min.pct = 0.1 17 | ) 18 | } 19 | \arguments{ 20 | \item{seu}{Seurat object} 21 | 22 | \item{feature}{Features to plot (gene expression, metrics, PC scores, anything that can be 23 | retreived by FetchData)} 24 | 25 | \item{ident}{cluster name, Default: all clusters} 26 | 27 | \item{group.by}{A variable name in meta.data to group by, if you don't want to use 28 | default Idents of Seurat object} 29 | 30 | \item{DefaultAssay}{Assay to use, Default: NULL (uses object's default assay)} 31 | 32 | \item{above}{Above which value will be considered as positive cell, Default: 0} 33 | 34 | \item{total}{If to calculate proportion in total cells of selected clusters, Default: F} 35 | 36 | \item{if.expressed}{If only return logical value, Default: F} 37 | 38 | \item{min.pct}{Minimum fraction of min.pct cells in the cluster will be considered "expressed", 39 | only use this parameter when "if.expressed" is set to TRUE. Default: 0.1} 40 | } 41 | \value{ 42 | A matrix 43 | } 44 | \description{ 45 | Check the Proportion of positive cells (default: expression above 0) 46 | in certain clusters 47 | } 48 | \details{ 49 | None. 50 | } 51 | \examples{ 52 | genes <- VariableFeatures(pbmc)[1:10] 53 | 54 | feature_percent(pbmc, feature = genes) 55 | 56 | # Count one cell as positive only the expression is above 2 57 | feature_percent(pbmc, feature = genes, above = 2) 58 | 59 | # Only check subset of clusters 60 | feature_percent(pbmc, feature = genes, ident = c("B cell", "CD8 T cell")) 61 | 62 | # Group by a different variable 63 | feature_percent(pbmc, feature = genes, group.by = "orig.ident") 64 | 65 | # Also check the proportion of expressed cells in total clusters 66 | feature_percent(pbmc, feature = genes, total = T) 67 | 68 | # only show logical value; 'TRUE' if more than 20\% cells are positive 69 | feature_percent(pbmc, feature = genes, if.expressed = T, min.pct = 0.2) 70 | 71 | } 72 | -------------------------------------------------------------------------------- /man/install_SeuratExtendData.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/GeneSetAnalysis.R 3 | \name{install_SeuratExtendData} 4 | \alias{install_SeuratExtendData} 5 | \title{Select SeuratExtendData Version} 6 | \usage{ 7 | install_SeuratExtendData(version = "latest") 8 | } 9 | \arguments{ 10 | \item{version}{Character string specifying the version. Options are: 11 | 12 | - "latest" (default): The latest version with most recent database updates (April 2025) 13 | - "stable": The stable version (v0.2.1) with datasets from January 2020 14 | - "v0.2.1": Specific version tag for the January 2020 databases 15 | - "v0.3.0": Specific version tag for the April 2025 databases} 16 | } 17 | \value{ 18 | Invisible TRUE if successful 19 | } 20 | \description{ 21 | This function allows users to select which version of SeuratExtendData to install. 22 | } 23 | \examples{ 24 | # Install the latest version 25 | install_SeuratExtendData("latest") 26 | 27 | # Install the stable version 28 | install_SeuratExtendData("stable") 29 | } 30 | -------------------------------------------------------------------------------- /man/ryb2rgb.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Colors.R 3 | \name{ryb2rgb} 4 | \alias{ryb2rgb} 5 | \title{Mix RYB color} 6 | \usage{ 7 | ryb2rgb(ryb = c(0, 0, 0)) 8 | } 9 | \arguments{ 10 | \item{ryb}{numeric vector range in [0,1], 11 | e.g. c(r = 0.3, y = 0.5, b = 0.2)} 12 | } 13 | \value{ 14 | RGB code 15 | } 16 | \description{ 17 | Mix 3 primary colors (red, yellow and blue) and 18 | return RGB code 19 | } 20 | \details{ 21 | see above 22 | } 23 | \examples{ 24 | library(scales) 25 | library(dplyr) 26 | data.frame( 27 | red = c(1,0,0), 28 | yellow = c(0,1,0), 29 | blue = c(0,0,1), 30 | orange = c(1,1,0), 31 | purple = c(1,0,1), 32 | green = c(0,1,1), 33 | black = c(1,1,1), 34 | grey = c(0.5,0.5,0.5), 35 | white = c(0,0,0) 36 | ) \%>\% 37 | apply(2, ryb2rgb) \%>\% 38 | show_col() 39 | } 40 | -------------------------------------------------------------------------------- /man/save_colors.Rd: -------------------------------------------------------------------------------- 1 | % Generated by roxygen2: do not edit by hand 2 | % Please edit documentation in R/Colors.R 3 | \name{save_colors} 4 | \alias{save_colors} 5 | \title{Save Custom Color Settings to a Seurat Object} 6 | \usage{ 7 | save_colors(seu, col_list) 8 | } 9 | \arguments{ 10 | \item{seu}{A Seurat object to which the color settings will be saved.} 11 | 12 | \item{col_list}{A list of color settings where names correspond to variable names and values are the colors to be associated with each variable.} 13 | } 14 | \value{ 15 | The modified Seurat object with updated color settings in the `misc` slot. 16 | } 17 | \description{ 18 | This function stores custom color settings within a Seurat object, allowing these settings to be reused across various visualization functions within the Seurat environment. 19 | } 20 | \details{ 21 | `save_colors` enhances workflow efficiency by centralizing color management within the Seurat object. This enables consistent and coherent visualizations across multiple plots, reducing the need for repeated color specifications and ensuring that plots are both aesthetically pleasing and informative. 22 | } 23 | \examples{ 24 | library(SeuratExtend) 25 | 26 | # Define custom colors for different clusters and genes 27 | custom_colors <- list( 28 | "cluster" = "pro_blue", 29 | "CD14" = "D", 30 | "CD3D" = c("#EEEEEE", "black") 31 | ) 32 | # Save these colors to the Seurat object 33 | pbmc <- save_colors(pbmc, custom_colors) 34 | # Use the colors in DimPlot2 35 | DimPlot2(pbmc, features = c("cluster", "CD14", "CD3D")) 36 | 37 | } 38 | -------------------------------------------------------------------------------- /vignettes/GSEA_files/figure-gfm/unnamed-chunk-11-1.png: -------------------------------------------------------------------------------- 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