rliger (version 2.2.0)

plotEnhancedVolcano: Create volcano plot with EnhancedVolcano

Description

Create volcano plot with EnhancedVolcano

Usage

plotEnhancedVolcano(result, group, ...)

Value

ggplot

Arguments

result

Data frame table returned by runMarkerDEG or runPairwiseDEG.

group

Selection of one group available from result$group. If only one group is available from result, default NULL uses it.

...

Arguments passed to EnhancedVolcano::EnhancedVolcano(), except that toptable, lab, x and y are prefilled by this wrapper.

Examples

# \donttest{
if (requireNamespace("EnhancedVolcano", quietly = TRUE)) {
    defaultCluster(pbmc) <- pbmcPlot$leiden_cluster
    # Test the DEG between "stim" and "ctrl", within each cluster
    result <- runPairwiseDEG(
        pbmc,
        groupTest = "stim",
        groupCtrl = "ctrl",
        variable1 = "dataset",
        splitBy = "defaultCluster"
    )
    plotEnhancedVolcano(result, "0.stim")
}
# }