Plots the requested PCA scores using the color scheme derived from a
Spectra object. Options are provided to add confidence
ellipses for each group in the object. The ellipses may be robust or
classical. Option to label the extreme points provided.
An object of class prcomp, modified to include a
list element called $method, a character string describing the
pre-processing carried out and the type of PCA performed (it appears on the
plot). This is automatically provided if ChemoSpec functions
c_pcaSpectra or r_pcaSpectra were used to create
pca.
pcs
A vector of two integers specifying the PCA scores to plot.
ellipse
A character vector specifying the type of ellipses to be
plotted. One of c("both", "none", "cls", "rob"). cls
specifies classical confidence ellipses, rob specifies robust
confidence ellipses. An ellipse is drawn for each group in
spectra$groups.
tol
A number describing the fraction of points to be labeled.
tol = 1.0 labels all the points; tol = 0.05 labels the most
extreme 5 percent.
use.sym
A logical; if true, the color scheme is set to black and the
points plotted with symbols.
leg.loc
Character; if "none" no legend will be drawn.
Otherwise, any string acceptable to legend.
…
Additional parameters to be passed to the plotting functions.