Draws a PCA biplot with species scores indicated by biplot arrows
# S3 method for rda
biplot(x, choices = c(1, 2), scaling = "species",
display = c("sites", "species"), type, xlim, ylim, col = c(1,2),
const, correlation = FALSE, ...)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.
A rda result object.
Axes to show.
Scaling for species and site scores. Either species
(2) or site (1) scores are scaled by eigenvalues, and
the other set of scores is left unscaled, or with 3 both are
scaled symmetrically by square root of eigenvalues. With negative
scaling values in rda, species scores are divided by standard
deviation of each species and multiplied with an equalizing
constant. Unscaled raw scores stored in the result can be accessed
with scaling = 0.
The type of scores can also be specified as one of "none",
"sites", "species", or "symmetric", which
correspond to the values 0, 1, 2, and 3
respectively. Argument correlation can be used in combination
with these character descriptions to get the corresponding negative
value.
logical; if scaling is a character
description of the scaling type, correlation can be used to
select correlation-like scores for PCA. See argument scaling
for details.
Scores shown. These must some of the alternatives
"species" for species scores, and/or "sites" for site
scores.
Type of plot: partial match to text
for text labels, points for points, and none for
setting frames only. If omitted, text is selected for
smaller data sets, and points for larger. Can be of length 2
(e.g. type = c("text", "points")), in which case the first
element describes how species scores are handled, and the second how
site scores are drawn.
the x and y limits (min, max) of the plot.
Colours used for sites and species (in this order). If only one colour is given, it is used for both.
General scaling constant for scores.rda.
Other parameters for plotting functions.
Gavin Simpson, based on plot.cca by Jari Oksanen.
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.
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"))
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