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

Source: R/plotTSNE.R

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

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")