plotUMAP: Plot UMAP results either on already run results or run first...

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

Description

Plot UMAP results either on already run results or run first and then plot.

Usage

plotUMAP(
  inSCE,
  colorBy = "No Color",
  shape = "No Shape",
  reducedDimName = "UMAP",
  runUMAP = FALSE,
  useAssay = "logcounts"
)

Arguments

inSCE	Input SingleCellExperiment object with saved dimension reduction components. Required
colorBy	color by a condition(any column of the annotation data).
shape	add shapes to each condition.
reducedDimName	saved dimension reduction name in the SingleCellExperiment object. Required.
runUMAP	If the dimension reduction components are already available set this to FALSE, otherwise set to TRUE. Default is False.
useAssay	Indicate which assay to use. The default is "logcounts"

Value

a UMAP plot of the reduced dimensions.

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- getUMAP(inSCE = sce, useAssay = "counts", reducedDimName = "UMAP")
plotUMAP(sce, shape = "No Shape", reducedDimName = "UMAP",
         runUMAP = TRUE, useAssay = "counts")

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.