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

In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

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

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 SCtkExperiment object with saved dimension reduction components or a variable with saved results. 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 SCtkExperiment 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

plotUMAP(mouseBrainSubsetSCE, shape = "No Shape", reducedDimName = "UMAP",
         runUMAP = TRUE, useAssay = "counts")

mmkhan19/singleCellTK documentation built on March 22, 2022, 7:43 a.m.