plotScanpyViolin: plotScanpyViolin

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

plotScanpyViolin

Description

plotScanpyViolin

Usage

plotScanpyViolin(
  inSCE,
  useAssay = NULL,
  features,
  groupBy,
  xlabel = "",
  ylabel = NULL
)

Arguments

inSCE	Input SingleCellExperiment object.
useAssay	Assay to use for plotting. By default it will use counts assay.
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.
groupBy	The key of the observation grouping to consider.
xlabel	Label of the x axis. Defaults to groupBy.
ylabel	Label of the y axis. If NULL and groupBy is NULL, defaults to 'value'. If NULL and groupBy is not NULL, defaults to features.

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 <- runScanpyUMAP(sce, useReducedDim = "scanpyPCA")
markers <- c("MALAT1" ,"RPS27" ,"CST3")
plotScanpyViolin(sce, features = markers, groupBy = "Scanpy_louvain_1")

## End(Not run)

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