plotScanpyMarkerGenes: plotScanpyMarkerGenes

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

plotScanpyMarkerGenes

Description

plotScanpyMarkerGenes

Usage

plotScanpyMarkerGenes(
  inSCE,
  groups = NULL,
  nGenes = 10,
  nCols = 4,
  sharey = FALSE
)

Arguments

inSCE	Input SingleCellExperiment object.
groups	The groups for which to show the gene ranking. Default NULL means that all groups will be considered.
nGenes	Number of genes to show. Default 10
nCols	Number of panels shown per row. Default 4
sharey	Controls if the y-axis of each panels should be shared. Default FALSE allows each panel to have its own y-axis range.

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" )
plotScanpyMarkerGenes(sce, groups = '0')

## End(Not run)

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