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" )
inSCE | Input SingleCellExperiment object. |
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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". |
A PCA plot
data("mouseBrainSubsetSCE") plotPCA(mouseBrainSubsetSCE, colorBy = "level1class", reducedDimName = "PCA_counts")