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

plotTSNE(inSCE, colorBy = "No Color", shape = "No Shape",
  reducedDimName = "TSNE", runTSNE = FALSE, useAssay = "logcounts")

Arguments

inSCE

Input SCtkExperiment object. Required

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")