plotPCA {singleCellTK} | R Documentation

## Plot PCA run data from its components.

### Description

Plot PCA run data from its components.

### Usage

    plotPCA(
      inSCE,
      colorBy = "No Color",
      shape = "No Shape",
      pcX = "PC1",
      pcY = "PC2",
      reducedDimName = "PCA",
      runPCA = FALSE,
      useAssay = "logcounts"
    )

### Arguments

`inSCE` | Input SingleCellExperiment object.
`colorBy` | The variable to color clusters by
`shape` | Shape of the points
`pcX` | User choice for the first principal component
`pcY` | User choice for the second principal component
`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.
`runPCA` | Run PCA if the reducedDimName does not exist. the Default is FALSE.
`useAssay` | Indicate which assay to use. The default is "logcounts".

### Value

A PCA plot

### Examples

    data("mouseBrainSubsetSCE")
    plotPCA(mouseBrainSubsetSCE, colorBy = "level1class",
            reducedDimName = "PCA_counts")

[Package singleCellTK version 2.0.0 Index]