R: PCA biplot

biplot.rda {vegan} | R Documentation

## PCA biplot

### Description

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(s)

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

### See Also

`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.

### Examples

    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"))

[Package vegan version 2.4-3 Index]