classbiplot: Grouped biplot for PLS scores and loadings

Description

This helper plots the individuals and predictors from a fitted plsR or plsRglm model while coloring the individuals according to a grouping variable.

Usage

classbiplot(
  object,
  group = NULL,
  comps = 1:2,
  col,
  colvar = "gray30",
  pch = 19,
  cex = rep(par("cex"), 2),
  xlabs = NULL,
  ylabs = NULL,
  point.labels = FALSE,
  show.legend = TRUE,
  legendpos = "topright",
  var.axes = TRUE,
  expand = 1,
  xlim = NULL,
  ylim = NULL,
  arrow.len = 0.1,
  main = NULL,
  sub = NULL,
  xlab = NULL,
  ylab = NULL,
  ...
)

Value

Invisibly returns a list with the scores, loadings, colors, grouping factor and scaling ratio used in the plot.

Arguments

object: an object containing score and loading matrices in object$tt and object$pp, typically returned by plsR or plsRglm.
group: optional grouping vector for the individuals. When supplied, observations are colored according to the levels of group.
comps: integer vector of length 2 giving the components to display.
col: colors for the individuals. If group is provided, col can have length 1, the number of groups, or the number of individuals.
colvar: color used for variable labels, arrows and axes.
pch: plotting character for the individuals.
cex: character expansion. Length 1 is recycled to length 2: the first value is used for the individuals and the second one for the variables.
xlabs: optional labels for the individuals.
ylabs: optional labels for the variables.
point.labels: shall the individuals be displayed using text labels instead of points? Defaults to FALSE.
show.legend: shall a legend be added when group is provided? Defaults to TRUE.
legendpos: position of the legend as in legend, defaults to "topright".
var.axes: shall arrows be drawn for the variables? Defaults to TRUE.
expand: expansion factor for the variables layer, as in biplot. Defaults to 1.
xlim, ylim: limits for the scores panel. When both are missing they are chosen symmetrically as in biplot.
arrow.len: length of the arrows for the variables.
main, sub, xlab, ylab: usual graphical parameters passed to plot.
...: further graphical parameters passed to plot for the scores panel.

Author

Frédéric Bertrand
frederic.bertrand@lecnam.net
https://fbertran.github.io/homepage/

Examples

Run this code

data(Cornell)
modpls <- plsR(Y ~ ., data = Cornell, nt = 2)
grp <- factor(Cornell$Y > median(Cornell$Y), labels = c("Low", "High"))
classbiplot(modpls, group = grp, col = c("firebrick3", "steelblue3"))