plotDEGViolin: plot the violin plot to show visualize the expression...

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

Description

plot the violin plot to show visualize the expression distribution of DEGs identified by differential expression analysis

Usage

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

Arguments

inSCE	SingleCellExperiment inherited object. runMAST() has to be run in advance.
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

Value

A ggplot object of violin plot

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.