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")
Input SCTKExperiment object. Required.
The variable to color clusters by
Shape of the points
User choice for the first principal component
User choice for the second principal component
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.
Run PCA if the reducedDimName does not exist. the Default is FALSE.
Indicate which assay to use. The default is "logcounts".
A PCA plot
data("mouseBrainSubsetSCE") plotPCA(mouseBrainSubsetSCE, colorBy = "level1class", reducedDimName = "PCA_counts")