MVA.biplot: Biplot of multivariate analyses

In RVAideMemoire: Testing and Plotting Procedures for Biostatistics

Biplot of multivariate analyses

Description

Displays a biplot of a multivariate analysis. This just consists in superimposing a score plot and a correlation circle (plus centroids of factor levels in constrained analyses, RDA or CCA). The correlation circle is adjusted to fit the size of the score plot.

Usage

MVA.biplot(x, xax = 1, yax = 2, scaling = 2, sco.set = c(12, 1, 2),
  cor.set = c(12, 1, 2), space = 1, ratio = 0.9, weights = 1,
  constraints = c("nf", "n", "f", NULL), sco.args = list(),
  cor.args = list(), f.col = 1, f.cex = 1)

Arguments

x	a multivariate analysis (see Details).
xax	the horizontal axis.
yax	the vertical axis.
scaling	type of scaling (see MVA.scoreplot).
sco.set	scores to be displayed, when several sets are available (see MVA.scoreplot).
cor.set	correlations to be displayed, when several sets are available (see MVA.scoreplot).
space	space to use, when several are available (see MVA.scoreplot and MVA.corplot).
ratio	constant for adjustement of correlations to the size of the score plot (0.9 means the longest arrows is 90% of the corresponding axis).
weights	only used with constrained analyses (RDA or CCA) where some constraints are factors. Individual weights, used to calculate barycenter positions.
constraints	only used with constrained analyses (RDA or CCA). Type of constraints to display: quantitative ("n"), factors ("f"), both ("nf", default) or none ("NULL").
sco.args	list containing optional arguments to pass to MVA.scoreplot. All arguments are accepted.
cor.args	list containing optional arguments to pass to MVA.corplot. All arguments are accepted except xlab, ylab, circle, intcircle, drawintaxes, add and add.const.
f.col	color(s) used for barycenters in case of a constraint analysis (RDA or CCA) containing factor constraint(s). Can be a unique value, a vector giving one color per constraint or a vector giving one color per barycenter (all factors confounded).
f.cex	size(s) used for barycenters in case of a constraint analysis (RDA or CCA) containing factor constraint(s). Can be a unique value, a vector giving one size per constraint or a vector giving one size per barycenter (all factors confounded).

Details

This function should not be use directly. Prefer the general MVA.plot, to which all arguments can be passed.

All multivariate analyses covered by MVA.corplot can be used for biplots.

Author(s)

Maxime HERVE <[e-mail]>

Examples

require(vegan)
data(iris)
RDA <- rda(iris[,1:4]~Species,data=iris)
MVA.plot(RDA,"biplot",cor.args=list(col="purple"),ratio=0.8,f.col=c("red","green","blue"))

RVAideMemoire documentation built on Nov. 6, 2023, 5:07 p.m.