plotScanpyMarkerGenesHeatmap: plotScanpyMarkerGenesHeatmap

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

plotScanpyMarkerGenesHeatmap

Description

plotScanpyMarkerGenesHeatmap

Usage

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

## End(Not run)

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