Generate volcano plot for DEGs
plotDEGVolcano(
inSCE,
useResult,
labelTopN = 10,
log2fcThreshold = 0.25,
fdrThreshold = 0.05
)
SingleCellExperiment inherited object.
character. A string specifying the analysisName
used when running a differential expression analysis function.
Integer, label this number of top DEGs that pass the filters.
numeric. Label genes with the absolute values of
log2FC greater than this value as regulated. Default 0.25
.
numeric. Label genes with FDR value less than this
value as regulated. Default 0.05
.
A ggplot
object of volcano plot
Any of the differential expression analysis method from SCTK should be performed prior to using this function to generate volcano plots.
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")
plotDEGVolcano(sce.w, "w.aVSb")