# Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

## Documentation for package ‘SCpubr’ version 2.0.0

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

## Help Pages

check_dependencies | Check SCpubr current function dependencies.
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_ColorPalette | Generate color scales based on a value.
do_CopyNumberVariantPlot | Display CNV scores from inferCNV as Feature Plots.
do_CorrelationPlot | 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_FunctionalAnnotationPlot | Compute functional annotation plots using GO or KEGG ontologies
do_GeyserPlot | Generate a Geyser plot.
do_GroupedGOTermPlot | Compute an overview of the GO terms associated with the input list of genes.
do_GroupwiseDEPlot | Compute a heatmap with the results of a group-wise DE analysis.
do_NebulosaPlot | Wrapper for Nebulosa::plot_density in Seurat.
do_PathwayActivityPlot | Plot Pathway Activities from decoupleR using Progeny prior knowledge.
do_RidgePlot | Create ridge plots.
do_TermEnrichmentPlot | Display the enriched terms for a given list of genes.
do_TFActivityPlot | Plot TF Activities from decoupleR using Dorothea prior knowledge.
do_ViolinPlot | Wrapper for VlnPlot.
do_VolcanoPlot | Compute a Volcano plot out of DE genes.
human_chr_locations | Chromosome arm locations for human genome GRCh38.
package_report | Generate a status report of SCpubr and its dependencies.