biplot.rda {vegan} | 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 = 2, display = c("sites", "species"), type, xlim, ylim, col = c(1,2), const, ...)

`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` . |

`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. |

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 = 3) ## different type for species and site scores biplot(mod, scaling = 3, type = c("text", "points"))

[Package *vegan* version 1.16-32 Index]