plotSeuratReduction Plots the selected dimensionality reduction method

plotSeuratReduction Plots the selected dimensionality reduction method

plotSeuratReduction(
  inSCE,
  useReduction = c("pca", "ica", "tsne", "umap"),
  showLegend = FALSE,
  groupBy = NULL,
  splitBy = NULL
)

Arguments

inSCE

(sce) object which has the selected dimensionality reduction algorithm already computed and stored

useReduction

Dimentionality reduction to plot. One of "pca", "ica", "tsne", or "umap". Default "umap".

showLegend

Select if legends and labels should be shown on the output plot or not. Either "TRUE" or "FALSE". Default FALSE.

groupBy

Specify a colData column name that be used for grouping. Default is NULL.

splitBy

Specify a colData column name that be used for splitting the output plot. Default is NULL.

Value

plot object

Examples

data(scExample, package = "singleCellTK")
if (FALSE) {
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
sce <- runSeuratPCA(sce, useAssay = "counts")
plotSeuratReduction(sce, useReductionPlot = "pca")}