Generate PCA plot — plotPCA • rTASSEL

This function will generate a general 2D scatterplot for a given set of principal components.

Usage

plotPCA(
  pcaObj,
  x = 1,
  y = 2,
  cluster = FALSE,
  nClust = 2,
  metadata = NULL,
  mCol = NULL,
  interactive = FALSE,
  pointColor = "black"
)

Arguments

pcaObj: A PCAResults object containing eigenvalue data ( e.g PC_Datum).
x: Principal component number to plot on x-axis.
y: Principal component number to plot on y-axis.
cluster: Plot points by hierachical clustering groups? Defaults to FALSE.
nClust: Number of clusters to report.
metadata: A data.frame object of additional categorical information for each sample/taxa. Defaults to NULL.
mCol: What metadata column do you want to plot? Needs metadata object to work.
interactive: Do you want to produce an interactive visualization? Defaults to FALSE.
pointColor: color of non-categorical PCA data points.