plotPCA {psichomics} | R Documentation |
Create a scatterplot from a PCA object
plotPCA(pca, pcX = 1, pcY = 2, groups = NULL, individuals = TRUE, loadings = FALSE, nLoadings = NULL)
pca |
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pcX |
Character: name of the X axis of interest from the PCA |
pcY |
Character: name of the Y axis of interest from the PCA |
groups |
Matrix: groups to plot indicating the index of interest of the samples (use clinical or sample groups) |
individuals |
Boolean: plot PCA individuals |
loadings |
Boolean: plot PCA loadings/rotations |
nLoadings |
Integer: Number of variables to plot, ordered by those that
most contribute to selected principal components (this allows for faster
performance as only the most contributing variables are rendered); if
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Scatterplot as an highchart
object
pca <- prcomp(USArrests, scale=TRUE) plotPCA(pca) plotPCA(pca, pcX=2, pcY=3) # Plot both individuals and loadings plotPCA(pca, pcX=2, pcY=3, loadings=TRUE)