plotSeuratReduction: plotSeuratReduction Plots the selected dimensionality...

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

plotSeuratReduction Plots the selected dimensionality reduction method

Description

plotSeuratReduction Plots the selected dimensionality reduction method

Usage

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")
## Not run: 
sce <- runSeuratNormalizeData(sce, useAssay = "counts")
sce <- runSeuratFindHVG(sce, useAssay = "counts")
sce <- runSeuratScaleData(sce, useAssay = "counts")
sce <- runSeuratPCA(sce, useAssay = "counts")
plotSeuratReduction(sce, useReduction = "pca")

## End(Not run)

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.