plotScanpyViolin

plotScanpyViolin

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