R/plotDEAnalysis.R
plotDEGViolin.Rd
plot the violin plot to show visualize the expression distribution of DEGs identified by differential expression analysis
plotDEGViolin( inSCE, useResult, threshP = FALSE, labelBy = NULL, nrow = 6, ncol = 6, defaultTheme = TRUE, isLogged = TRUE, check_sanity = TRUE )
inSCE | SingleCellExperiment inherited object.
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useResult | character. A string specifying the |
threshP | logical. Whether to plot threshold values from adaptive
thresholding, instead of using the assay used by |
labelBy | A single character for a column of |
nrow | Integer. Number of rows in the plot grid. Default |
ncol | Integer. Number of columns in the plot grid. Default |
defaultTheme | Logical scalar. Whether to use default SCTK theme in
ggplot. Default |
isLogged | Logical scalar. Whether the assay used for the analysis is
logged. If not, will do a |
check_sanity | Logical scalar. Whether to perform MAST's sanity check
to see if the counts are logged. Default |
A ggplot object of violin plot
data("sceBatches") logcounts(sceBatches) <- log(counts(sceBatches) + 1) 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") plotDEGViolin(sce.w, "w.aVSb")