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Grouped biplot for PLS scores and loadings

Source: R/classbiplot.R
classbiplot.Rd

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,
  ...
)

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.

Value

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

See also

plsR, plsRglm, biplot

Author

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

Examples

data(Cornell)
modpls <- plsR(Y ~ ., data = Cornell, nt = 2)
#> ____************************************************____
#> ____Component____ 1 ____
#> ____Component____ 2 ____
#> ____Predicting X without NA neither in X nor in Y____
#> ****________________________________________________****
#> 
grp <- factor(Cornell$Y > median(Cornell$Y), labels = c("Low", "High"))
classbiplot(modpls, group = grp, col = c("firebrick3", "steelblue3"))