# Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

## Documentation for package ‘SCpubr’ version 3.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

do_ActivityHeatmap | Compute affinity of gene sets to cell populations using decoupleR.
do_AlluvialPlot | Generate Alluvial plots.
do_BarPlot | Create Bar Plots.
do_BeeSwarmPlot | BeeSwarm plot.
do_BoxPlot | Generate Box Plots.
do_CellularStatesPlot | Cellular States plot.
do_ChordDiagramPlot | Generate a Chord diagram.
do_CNVHeatmap | Display CNV scores from inferCNV as Feature Plots.
do_ColorBlindCheck | Generate colorblind variations of a given color palette.
do_ColorPalette | Generate color scales based on a value.
do_CorrelationHeatmap | Create correlation matrix heatmaps.
do_DimPlot | Wrapper for DimPlot.
do_DotPlot | This function is a wrapper for DotPlot. It provides most of its functionalities while adding extra. You can
do_EnrichmentHeatmap | Create enrichment scores heatmaps.
do_ExpressionHeatmap | Create heatmaps of averaged expression by groups.
do_FeaturePlot | Wrapper for FeaturePlot.
do_GroupwiseDEHeatmap | Compute a dotplot with the results of a group-wise DE analysis.
do_LigandReceptorPlot | Visualize Ligand-Receptor analysis output.
do_LoadingsHeatmap | Compute a heatmap summary of the top and bottom genes in the PCA loadings for the desired PCs in a Seurat object.
do_MetadataHeatmap | Compute a heatmap of categorical variables.
do_NebulosaPlot | Wrapper for Nebulosa::plot_density in Seurat.
do_PackageReport | Generate a status report of SCpubr and its dependencies.
do_PathwayActivityHeatmap | Plot Pathway Activities from decoupleR using Progeny prior knowledge.
do_RankedEnrichmentHeatmap | Compute a heatmap of enrichment of gene sets on the context of a dimensional reduction component.
do_RankedExpressionHeatmap | Compute a heatmap of expression of genes on the context of a dimensional reduction component.
do_RidgePlot | Create ridge plots.
do_SCEnrichmentHeatmap | Perform a single-cell-based heatmap showing the enrichment in a list of gene sets.
do_SCExpressionHeatmap | Perform a single-cell-based heatmap showing the expression of genes.
do_StripPlot | Generate a Strip plot.
do_TermEnrichmentPlot | Display the enriched terms for a given list of genes.
do_TFActivityHeatmap | Plot TF Activities from decoupleR using Dorothea prior knowledge.
do_ViolinPlot | Wrapper for VlnPlot.
do_VolcanoPlot | Compute a Volcano plot out of DE genes.
do_WafflePlot | Display the enriched terms for a given list of genes.
human_chr_locations | Chromosome arm locations for human genome GRCh38.