Plot PCA run data from its components.

Plot PCA run data from its components.

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")