plotScanpyMarkerGenes

plotScanpyMarkerGenes

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