plotScanpyMarkerGenesViolin: plotScanpyMarkerGenesViolin

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

plotScanpyMarkerGenesViolin

Description

plotScanpyMarkerGenesViolin

Usage

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")
## Not run: 
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')

## End(Not run)

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.