Visualize gene expression or cell metadata with violin plot — plotGeneViolin • rliger

Visualize gene expression or cell metadata with violin plot

Usage

plotGeneViolin(object, gene, byDataset = TRUE, groupBy = NULL, ...)

plotTotalCountViolin(object, groupBy = "dataset", ...)

plotGeneDetectedViolin(object, groupBy = "dataset", ...)

Arguments

object: A liger object.
gene: Character gene names.
byDataset: Logical, whether the violin plot should be splitted by dataset. Default TRUE.
groupBy: Names of available categorical variable in cellMeta slot. Use FALSE for no grouping. Default NULL looks clustering result but will not group if no clustering found.
...: Additional arguments passed to plotCellViolin.

Value

ggplot if using a single gene and not splitting by dataset. Otherwise, list of ggplot.

Examples

plotGeneViolin(pbmcPlot, varFeatures(pbmcPlot)[1],
               groupBy = "leiden_cluster")
#> $ISG15.ctrl

#> 
#> $ISG15.stim

#> 
plotTotalCountViolin(pbmc)

plotGeneDetectedViolin(pbmc, dot = TRUE, box = TRUE, colorBy = "dataset")
#> Warning: Duplicated `override.aes` is ignored.