plotTSNE: Plot t-SNE plot on dimensionality reduction data run from...

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

Plot t-SNE plot on dimensionality reduction data run from t-SNE method.

Description

Plot t-SNE plot on dimensionality reduction data run from t-SNE method.

Usage

plotTSNE(
  inSCE,
  colorBy = NULL,
  shape = NULL,
  reducedDimName = "TSNE",
  runTSNE = FALSE,
  useAssay = "counts"
)

Arguments

inSCE	Input SingleCellExperiment object.
colorBy	color by condition.
shape	add shape to each distinct label.
reducedDimName	a name to store the results of the dimension reduction coordinates obtained from this method. This is stored in the SingleCellExperiment object in the reducedDims slot. Required.
runTSNE	Run t-SNE if the reducedDimName does not exist. the Default is FALSE.
useAssay	Indicate which assay to use. The default is "logcounts".

Value

A t-SNE plot

Examples

data("mouseBrainSubsetSCE")
plotTSNE(mouseBrainSubsetSCE, colorBy = "level1class",
         reducedDimName = "TSNE_counts")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.