plot.symcoca {cocorresp}R Documentation

Biplots for symmetric co-correspondence analysis

Description

Produces biplots of the response and predictor from the results of a symmetric co-correspondence analysis.

Usage

## S3 method for class 'symcoca':
plot(x, choices = c(1:2),
     display = c("species", "site"), scaling = FALSE,
     oneFig = TRUE, type = c("points", "text", "none"),
     ask = prod(par("mfcol")) < 2 && dev.interactive(),
     cex = c(0.7, 0.7), pch = c(par("pch"), 3),
     col = c("black", "red"), ylab, xlab, main, sub = "",
     axes = TRUE, ann = par("ann"), ...)

Arguments

x an object of class "symcoca", the result of a call to symcoca.
choices a vector of length 2 indicating which predictive CoCA axes to plot.
display which sets of scores are drawn. See scores.symcoca.
scaling logical, whether scaling should be applied. See scores.symcoca.
oneFig if TRUE, biplots for the response and predictor are plotted on the same figure using par(mfrow = c(1,2)). If FALSE each biplot is plotted in turn on the active device. The first plot will be overwritten unless ask = TRUE, see below.
type one of "points", "text", or "none". Determines how the site and species scores are displayed. If type = "points", scores are plotted as points using plotting characters given in argument pch. If type = "text", then the row names of the scores matrices are plotted. If type = "none", then the scores are not plotted.
ask logical, if TRUE, the user is asked before each plot, see par.
cex a vector of length 2, containing the character expansion factors to use for the samples (sites) and the species.
col a vector of length 2, containing the colours used to draw the samples (sites) and the species markers.
pch a vector of length 2, containing the plotting character to use for the samples (sites) and the species.
xlab, ylab labels for the x and y axes, defaults to “Axis X (lamda_X = Y)”, where ‘X’ is the CoCa axis plotted and ‘Y’ is the Eigenvalue for axis ‘X’.
main a main title for the plot, defaults to the names given in x\$nam.dat. User supplied values currently ignored.
sub a sub title for the plots. Currently the same sub title is applied to each biplot.
axes a logical value indicating whether both axes should be drawn on the plot.
ann logical, if TRUE plots are annotated and not if FALSE, currently ignored.
... other graphical parameters as in 'par' may also be passed as arguments.

Note

This is an improved plot method for symcoca objects, that is far more configurable. More intuitive handling of user supplied values for main, xlab, ylab and sub will be provided in the next version.

Author(s)

Gavin L. Simpson.

References

Ter Braak, C.J.F and Schaffers, A.P. (2004) Co-Correspondence Analysis: a new ordination method to relate two community compositions. Ecology 85(3), 834–846

See Also

coca, plot.default

Examples

## symmetric CoCA
data(beetles)

## log transform the bettle data
beetles <- log(beetles + 1)

data(plants)

## fit the model
bp.sym <- coca(beetles ~ ., data = plants, method = "symmetric")
## draw the biplots

plot(bp.sym)

[Package cocorresp version 0.1-7 Index]