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