biplot.rda  R Documentation 
Draws a PCA biplot with species scores indicated by biplot arrows
## S3 method for class 'rda'
biplot(x, choices = c(1, 2), scaling = "species",
display = c("sites", "species"), type, xlim, ylim, col = c(1,2),
const, correlation = FALSE, ...)
x 
A 
choices 
Axes to show. 
scaling 
Scaling for species and site scores. Either species
( The type of scores can also be specified as one of 
correlation 
logical; if 
display 
Scores shown. These must some of the alternatives

type 
Type of plot: partial match to 
xlim , ylim 
the x and y limits (min, max) of the plot. 
col 
Colours used for sites and species (in this order). If only one colour is given, it is used for both. 
const 
General scaling constant for 
... 
Other parameters for plotting functions. 
Produces a plot or biplot of the results of a call to
rda
. It is common for the "species" scores in a PCA to
be drawn as biplot arrows that point in the direction of increasing
values for that variable. The biplot.rda
function provides a
wrapper to plot.cca
to allow the easy production of such a
plot.
biplot.rda
is only suitable for unconstrained models. If
used on an ordination object with constraints, an error is issued.
If species scores are drawn using "text"
, the arrows are drawn
from the origin to 0.85 * species score, whilst the labels are
drawn at the species score. If the type used is "points"
, then
no labels are drawn and therefore the arrows are drawn from the origin
to the actual species score.
The plot
function returns invisibly a plotting structure which
can be used by identify.ordiplot
to identify
the points or other functions in the ordiplot
family.
Gavin Simpson, based on plot.cca
by Jari Oksanen.
plot.cca
, rda
for something to
plot, ordiplot
for an alternative plotting routine
and more support functions, and text
,
points
and arrows
for the basic routines.
data(dune)
mod < rda(dune, scale = TRUE)
biplot(mod, scaling = "symmetric")
## different type for species and site scores
biplot(mod, scaling = "symmetric", type = c("text", "points"))
## We can use ordiplot pipes in R 4.1 to build similar plots with
## flexible control
## Not run:
if (getRversion() >= "4.1") {
plot(mod, scaling = "symmetric", type="n") >
text("sites", cex=0.8) >
text("species", arrows=TRUE, length=0.02, col="red", cex=0.6)
}
## End(Not run)
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