plotDEGViolin: Generate violin plot to show the expression of top DEGs

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

Generate violin plot to show the expression of top DEGs

Description

Generate violin plot to show the expression of top DEGs

Usage

plotDEGViolin(
  inSCE,
  useResult,
  threshP = FALSE,
  labelBy = NULL,
  nrow = 6,
  ncol = 6,
  defaultTheme = TRUE,
  isLogged = TRUE,
  check_sanity = TRUE
)

Arguments

inSCE	SingleCellExperiment inherited object.
useResult	character. A string specifying the analysisName used when running a differential expression analysis function.
threshP	logical. Whether to plot threshold values from adaptive thresholding, instead of using the assay used by runMAST(). Default FALSE.
labelBy	A single character for a column of rowData(inSCE) as where to search for the labeling text. Default NULL.
nrow	Integer. Number of rows in the plot grid. Default 6.
ncol	Integer. Number of columns in the plot grid. Default 6.
defaultTheme	Logical scalar. Whether to use default SCTK theme in ggplot. Default TRUE.
isLogged	Logical scalar. Whether the assay used for the analysis is logged. If not, will do a log(assay + 1) transformation. Default TRUE.
check_sanity	Logical scalar. Whether to perform MAST's sanity check to see if the counts are logged. Default TRUE

Details

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

Value

A ggplot object of violin plot

Examples

data("sceBatches")
logcounts(sceBatches) <- log1p(counts(sceBatches))
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")
plotDEGViolin(sce.w, "w.aVSb")

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