plotDEGVolcano: Generate volcano plot for DEGs

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Generate volcano plot for DEGs

Description

Generate volcano plot for DEGs

Usage

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)

Details

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

Value

A ggplot object of volcano plot

See Also

runDEAnalysis, plotDEGHeatmap

Examples

data("sceBatches")
sceBatches <- scaterlogNormCounts(sceBatches, "logcounts")
sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'")
sce.w <- runWilcox(sce.w, class = "cell_type",
                   classGroup1 = "alpha", classGroup2 = "beta",
                   groupName1 = "w.alpha", groupName2 = "w.beta",
                   analysisName = "w.aVSb")
plotDEGVolcano(sce.w, "w.aVSb")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.