plotUMAP {singleCellTK} | R Documentation

## 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 SingleCellExperiment object with saved dimension reduction components. 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 SingleCellExperiment 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

    data(scExample, package = "singleCellTK")
    sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
    sce <- getUMAP(inSCE = sce, useAssay = "counts", reducedDimName = "UMAP")
    plotUMAP(sce, shape = "No Shape", reducedDimName = "UMAP",
             runUMAP = TRUE, useAssay = "counts")

[Package singleCellTK version 2.2.0 Index]