vegan (version 1.4-3)

ordiplot: Alternative plot and identify Functions for Ordination

Description

Ordination plot function especially for congested plots. Function ordiplot always plots only unlabelled points, but identify.ordiplot can be used to add labels to selected site, species or constraint points. Function identify.ordiplot can be used to identify points from plot.cca, plot.decorana or plot.procrustes as well.

Usage

ordiplot(ord, choices = c(1, 2), type="points", ...)
## S3 method for class 'ordiplot':
identify(x, what, ...)

Arguments

ord

A result from an ordination.

choices

Axes shown.

type

The type of graph which may be "points" or "none" for any ordination method, or any of the alternatives in plot.cca or plot.dec

...

Other graphcial parameters.

x

A result object from ordiplot.

what

Items identified in the ordination plot. The types depend on the kind of plot used. Most methods know sites and species, functions cca and rda

Value

• Function ordiplot returns invisibly an object of class "ordiplot" with items sites, species and constraints (if these are available in the ordination object). Function identify.ordiplot uses this object to label the point.

Details

Function ordiplot draws an ordination diagram using black circles for sites and red crosses for species. It returns invisibly an object of class "ordiplot" which can be used by identify.ordiplot to label selected sites or species, or constraints in cca and rda.

The function can handle output from several alternative ordination methods. For cca, rda and decorana it uses their plot method with option type = "points". In addition, the plot functions of these methods return invisibly an "ordiplot" object which can be used by identify.ordiplot to label points. For other ordinations it relies on scores to extract the scores.

See Also

identify for basic operations, plot.cca, plot.decorana, plot.procrustes which also produce objects for identify.ordiplot and scores for extracting scores from non-vegan ordinations.

Examples

data(dune)
ordina <- cca(dune)
tmp <- ordiplot(ordina)
# identify needs user interaction
identify(tmp, "spec")