Generate violin plot to show the expression of top DEGs
plotDEGViolin(
inSCE,
useResult,
threshP = FALSE,
labelBy = NULL,
nrow = 6,
ncol = 6,
defaultTheme = TRUE,
isLogged = TRUE,
check_sanity = TRUE
)
SingleCellExperiment inherited object.
character. A string specifying the analysisName
used when running a differential expression analysis function.
logical. Whether to plot threshold values from adaptive
thresholding, instead of using the assay used by runMAST()
. Default
FALSE
.
A single character for a column of rowData(inSCE)
as
where to search for the labeling text. Default NULL
.
Integer. Number of rows in the plot grid. Default 6
.
Integer. Number of columns in the plot grid. Default 6
.
Logical scalar. Whether to use default SCTK theme in
ggplot. Default TRUE
.
Logical scalar. Whether the assay used for the analysis is
logged. If not, will do a log(assay + 1)
transformation. Default
TRUE
.
Logical scalar. Whether to perform MAST's sanity check
to see if the counts are logged. Default TRUE
A ggplot object of violin plot
Any of the differential expression analysis method from SCTK should be performed prior to using this function
data("sceBatches")
logcounts(sceBatches) <- log1p(counts(sceBatches))
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 10:28:44 2023 ... Running DE with wilcox, Analysis name: w.aVSb
plotDEGViolin(sce.w, "w.aVSb")