PCA biplot

Draws a PCA biplot with species scores indicated by biplot arrows

Usage

# 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, ...)

Arguments

x

A rda result object.

choices

Axes to show.

scaling

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.

correlation

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.

display

Scores shown. These must some of the alternatives "species" for species scores, and/or "sites" for site scores.

type

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.

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 scores.rda.

...

Other parameters for plotting functions.

Details

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.

Value

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.

Author

Gavin Simpson, based on plot.cca by Jari Oksanen.

Examples

data(dune)
mod <- rda(dune, scale = TRUE)
biplot(mod, scaling = "symmetric")


## plot.cca can do the same
plot(mod, scaling = "symmetric", spe.par = list(arrows=TRUE))


## different type for species and site scores
biplot(mod, scaling = "symmetric", type = c("text", "points"))


## We can use ordiplot pipes to build similar plots with flexible
## control
plot(mod, scaling = "symmetric", type="n") |>
   points("sites", cex=0.7) |>
   text("species", arrows=TRUE, length=0.05, col=2, cex=0.7, font=3)