plotScanpyMarkerGenesViolin

plotScanpyMarkerGenesViolin

plotScanpyMarkerGenesViolin(inSCE, groups = NULL, features = NULL, nGenes = 10)

Arguments

inSCE

Input SingleCellExperiment object.

groups

The groups for which to show the gene ranking. Default NULL means that all groups will be considered.

features

List of genes to plot. Is only useful if interested in a custom gene list

nGenes

Number of genes to show. Default 10

Value

plot object

Examples

data(scExample, package = "singleCellTK")
if (FALSE) {
sce <- runScanpyNormalizeData(sce, useAssay = "counts")
sce <- runScanpyFindHVG(sce, useAssay = "scanpyNormData", method = "seurat")
sce <- runScanpyScaleData(sce, useAssay = "scanpyNormData")
sce <- runScanpyPCA(sce, useAssay = "scanpyScaledData")
sce <- runScanpyFindClusters(sce, useReducedDim = "scanpyPCA")
sce <- runScanpyFindMarkers(sce, colDataName = "Scanpy_louvain_1" )
plotScanpyMarkerGenesViolin(sce, groups = '0')
}