e32a3ff8 |
% Generated by roxygen2: do not edit by hand
|
5afd7247 |
% Please edit documentation in R/plotDEAnalysis.R
\name{plotDEGViolin}
\alias{plotDEGViolin}
|
558e269c |
\title{Generate violin plot to show the expression of top DEGs}
|
e32a3ff8 |
\usage{
|
5afd7247 |
plotDEGViolin(
|
7f256fc3 |
inSCE,
useResult,
threshP = FALSE,
|
5afd7247 |
labelBy = NULL,
|
7f256fc3 |
nrow = 6,
ncol = 6,
|
c7edcb60 |
defaultTheme = TRUE,
|
cea7aaa7 |
isLogged = TRUE,
|
c7edcb60 |
check_sanity = TRUE
|
7f256fc3 |
)
|
e32a3ff8 |
}
\arguments{
|
558e269c |
\item{inSCE}{\linkS4class{SingleCellExperiment} inherited object.}
|
e32a3ff8 |
|
5afd7247 |
\item{useResult}{character. A string specifying the \code{analysisName}
used when running a differential expression analysis function.}
|
e32a3ff8 |
|
33a1ba82 |
\item{threshP}{logical. Whether to plot threshold values from adaptive
thresholding, instead of using the assay used by \code{runMAST()}. Default
\code{FALSE}.}
|
e32a3ff8 |
|
5afd7247 |
\item{labelBy}{A single character for a column of \code{rowData(inSCE)} as
where to search for the labeling text. Default \code{NULL}.}
|
33a1ba82 |
\item{nrow}{Integer. Number of rows in the plot grid. Default \code{6}.}
|
e32a3ff8 |
|
33a1ba82 |
\item{ncol}{Integer. Number of columns in the plot grid. Default \code{6}.}
|
7f256fc3 |
\item{defaultTheme}{Logical scalar. Whether to use default SCTK theme in
ggplot. Default \code{TRUE}.}
|
c7edcb60 |
|
cea7aaa7 |
\item{isLogged}{Logical scalar. Whether the assay used for the analysis is
logged. If not, will do a \code{log(assay + 1)} transformation. Default
\code{TRUE}.}
|
c7edcb60 |
\item{check_sanity}{Logical scalar. Whether to perform MAST's sanity check
to see if the counts are logged. Default \code{TRUE}}
|
e32a3ff8 |
}
\value{
|
5afd7247 |
A ggplot object of violin plot
|
e32a3ff8 |
}
\description{
|
558e269c |
Generate violin plot to show the expression of top DEGs
}
\details{
|
7d46c6eb |
Any of the differential expression analysis method from SCTK should
|
558e269c |
be performed prior to using this function
|
e32a3ff8 |
}
|
930ec858 |
\examples{
data("sceBatches")
|
b1877916 |
logcounts(sceBatches) <- log1p(counts(sceBatches))
|
930ec858 |
sce.w <- subsetSCECols(sceBatches, colData = "batch == 'w'")
|
093aea7f |
sce.w <- runWilcox(sce.w, class = "cell_type",
classGroup1 = "alpha", classGroup2 = "beta",
|
930ec858 |
groupName1 = "w.alpha", groupName2 = "w.beta",
analysisName = "w.aVSb")
plotDEGViolin(sce.w, "w.aVSb")
}
|