| plot.predcoca {cocorresp} | R Documentation |
Produces biplots of the response and predictor from the results of a predictive co-correspondence analysis.
## S3 method for class 'predcoca':
plot(x, choices = c(1:2),
display = c("species", "site"), 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"), ...)
x |
an object of class "predcoca", 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. |
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. |
This is an improved plot method for preccoca 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.
Gavin L. Simpson.
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
## predictive CoCA data(beetles) ## log transform the bettle data beetles <- log(beetles + 1) data(plants) ## predictive CoCA using SIMPLS and formula interface bp.pred <- coca(beetles ~ ., data = plants) ## draw the biplots plot(bp.pred)