plotEnhancedVolcano: Create volcano plot with EnhancedVolcano

In rliger: Linked Inference of Genomic Experimental Relationships

Create volcano plot with EnhancedVolcano

Description

Create volcano plot with EnhancedVolcano

Usage

plotEnhancedVolcano(result, group, ...)

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.

Value

ggplot

Examples

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")
}

rliger documentation built on Oct. 30, 2024, 1:07 a.m.