RVAideMemoire (version 0.9-5)

MVA.biplot: 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"), 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") or both ("nf", default).

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, drawint

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.

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"))