man/plotScanpyMarkerGenesViolin.Rd
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 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/scanpyFunctions.R
 \name{plotScanpyMarkerGenesViolin}
 \alias{plotScanpyMarkerGenesViolin}
 \title{plotScanpyMarkerGenesViolin}
 \usage{
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 plotScanpyMarkerGenesViolin(inSCE, groups = NULL, features = NULL, nGenes = 10)
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 }
 \arguments{
 \item{inSCE}{Input \code{SingleCellExperiment} object.}
 
 \item{groups}{The groups for which to show the gene ranking. Default \code{NULL}
 means that all groups will be considered.}
 
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 \item{features}{List of genes to plot. Is only useful if interested in a 
 custom gene list}
 
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 \item{nGenes}{Number of genes to show. Default \code{10}}
 }
 \value{
 plot object
 }
 \description{
 plotScanpyMarkerGenesViolin
 }
 \examples{
 data(scExample, package = "singleCellTK")
 \dontrun{
 sce <- runScanpyNormalizeData(sce, useAssay = "counts")
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 sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
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 sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
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 sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
 sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
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 sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
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 plotScanpyMarkerGenesViolin(sce, groups = '0')
 }
 }