Generate volcano plot for DEGs

Source: R/plotDEAnalysis.R

Generate volcano plot for DEGs

plotDEGVolcano(
  inSCE,
  useResult,
  labelTopN = 10,
  log2fcThreshold = 0.25,
  fdrThreshold = 0.05,
  featureDisplay = S4Vectors::metadata(inSCE)$featureDisplay
)

Arguments

inSCE

SingleCellExperiment inherited object.

useResult

character. A string specifying the analysisName used when running a differential expression analysis function.

labelTopN

Integer, label this number of top DEGs that pass the filters. FALSE for not labeling. Default 10.

log2fcThreshold

numeric. Label genes with the absolute values of log2FC greater than this value as regulated. Default 0.25.

fdrThreshold

numeric. Label genes with FDR value less than this value as regulated. Default 0.05.

featureDisplay

A character string to indicate a variable in rowData(inSCE) for feature labeling. NULL for using rownames. Default metadata(inSCE)$featureDisplay (see setSCTKDisplayRow)

Value

A ggplot object of volcano plot

Details

Any of the differential expression analysis method from SCTK should be performed prior to using this function to generate volcano plots.

Examples

data("sceBatches")
sceBatches <- scaterlogNormCounts(sceBatches, "logcounts")
sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'")
sce.w <- runWilcox(sce.w, class = "cell_type", classGroup1 = "alpha",
                   groupName1 = "w.alpha", groupName2 = "w.beta",
                   analysisName = "w.aVSb")
#> Sat Mar 18 10:28:48 2023 ... Running DE with wilcox, Analysis name: w.aVSb
plotDEGVolcano(sce.w, "w.aVSb")