plotScanpyMarkerGenesHeatmap

plotScanpyMarkerGenesHeatmap

plotScanpyMarkerGenesHeatmap(
  inSCE,
  groups = NULL,
  groupBy,
  nGenes = 10,
  features = NULL,
  log2fcThreshold = NULL
)

Arguments

inSCE

Input SingleCellExperiment object.

groups

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

groupBy

The key of the observation grouping to consider. By default, the groupby is chosen from the rank genes groups parameter.

nGenes

Number of genes to show. Default 10

features

Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes). The var_names could be a dictionary or a list.

log2fcThreshold

Only output DEGs with the absolute values of log2FC larger than this value. Default NULL.

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" )
plotScanpyMarkerGenesHeatmap(sce, groupBy = 'Scanpy_louvain_1')
}