plot.symcoca {cocorresp} | R Documentation |
Produces biplots of the response and predictor from the results of a symmetric co-correspondence analysis.
## 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"), ...)
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. |
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.
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
## 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)