plotTSNE {singleCellTK} | R Documentation

## 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 = "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")

[Package singleCellTK version 1.7.0 Index]