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.
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.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(RVAideMemoire)
*** Package RVAideMemoire v 0.9-56 ***
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/RVAideMemoire/MVA.biplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MVA.biplot
> ### Title: Biplot of multivariate analyses
> ### Aliases: MVA.biplot
>
> ### ** Examples
>
> require(vegan)
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-0
> 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"))
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> dev.off()
null device
1
>