R: Alternative plot and identify Functions for Ordination

ordiplot {vegan} | R Documentation

## 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`, `plot.procrustes` and `plot.rad` as well.

### Usage

    ordiplot(ord, choices = c(1, 2), type="points", display, xlim, ylim,
         cex = 0.7, ...)
    ## S3 method for class 'ordiplot'
    identify(x, what, labels,  ...)
    ## S3 method for class 'ordiplot'
    points(x, what, select, ...)
    ## S3 method for class 'ordiplot'
    text(x, what, labels, select, ...)

### Arguments

`ord` | A result from an ordination.
`choices` | Axes shown.
`type` | The type of graph which may be `"points"`, `"text"` or `"none"` for any ordination method.
`display` | Display only "sites" or "species". The default for most methods is to display both, but for `cca`, `rda` and `capscale` it is the same as in `plot.cca`.
`xlim, ylim` | the x and y limits (min,max) of the plot.
`cex` | Character expansion factor for points and text.
`...` | Other graphical 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` know in addition `constraints` (for ‘LC’ scores), `centroids` and `biplot`, and `plot.procrustes` ordination plot has `heads` and `points`.
`labels` | Optional text used for labels. Row names will be used if this is missing.
`select` | Items to be displayed. This can either be a logical vector which is `TRUE` for displayed items or a vector of indices of displayed items.

### 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.

For full user control of plots, it is best to call `ordiplot` with `type = "none"` and save the result, and then add sites and species using `points.ordiplot` or `text.ordiplot` which both pass all their arguments to the corresponding default graphical functions.

### 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.

### Note

The purpose of these functions is to provide similar functionality as the `plot`, `plotid` and `specid` methods in library `labdsv`. The functions are somewhat limited in parametrization, but you can call directly the standard `identify` and `plot` functions for a better user control.

### Author(s)

Jari Oksanen

### 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

    # Draw a plot for a non-vegan ordination (cmdscale).
    data(dune)
    dune.dis <- vegdist(wisconsin(dune))
    dune.mds <- cmdscale(dune.dis, eig = TRUE)
    dune.mds$species <- wascores(dune.mds$points, dune, expand = TRUE)
    fig <- ordiplot(dune.mds, type = "none")
    points(fig, "sites", pch=21, col="red", bg="yellow")
    text(fig, "species", col="blue", cex=0.9)
    # Default plot of the previous using identify to label selected points
    ## Not run:
    fig <- ordiplot(dune.mds)
    identify(fig, "spec")
    ## End(Not run)

[Package vegan version 2.4-3 Index]