R: Add Text or Points to Ordination Plots

orditorp {vegan} | R Documentation

## Add Text or Points to Ordination Plots

### Description

The function adds `text` or `points` to ordination plots. Text will be used if this can be done without overwriting other text labels, and points will be used otherwise. The function can help in reducing clutter in ordination graphics, but manual editing may still be necessary.

### Usage

    orditorp(x, display, labels, choices = c(1, 2), priority,
        select, cex = 0.7, pcex, col = par("col"), pcol,
        pch = par("pch"), air = 1, ...)

### Arguments

`x` | A result object from ordination or an `ordiplot` result.
`display` | Items to be displayed in the plot. Only one alternative is allowed. Typically this is `"sites"` or `"species"`.
`labels` | Optional text used for labels. Row names will be used if this is missing.
`choices` | Axes shown.
`priority` | Text will be used for items with higher priority if labels overlap. This should be vector of the same length as the number of items plotted.
`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. If a logical vector is used, it must have the same length as the scores plotted.
`cex, pcex` | Text and point sizes, see `plot.default`..
`col, pcol` | Text and point colours, see `plot.default`.
`pch` | Plotting character, see `points`.
`air` | Amount of empty space between text labels. Values <1 allow overlapping text.
`...` | Other arguments to `scores` (and its various methods), `text` and `points`.

### Details

Function `orditorp` will add either text or points to an existing plot. The items with high `priority` will be added first and `text` will be used if this can be done without overwriting previous labels,and `points` will be used otherwise. If `priority` is missing, labels will be added from the outskirts to the centre. Function `orditorp` can be used with most ordination results, or plotting results from `ordiplot` or ordination plot functions (`plot.cca`, `plot.decorana`, `plot.metaMDS`).

Arguments can be passed to the relevant `scores` method for the ordination object (`x`) being drawn. See the relevant `scores` help page for arguments that can be used.

### Value

The function returns invisibly a logical vector where `TRUE` means that item was labelled with text and `FALSE` means that it was marked with a point. The returned vector can be used as the `select` argument in ordination `text` and `points` functions.

### Author(s)

Jari Oksanen

### Examples

    ## A cluttered ordination plot :
    data(BCI)
    mod <- cca(BCI)
    plot(mod, dis="sp", type="t")
    # Now with orditorp and abbreviated species names
    cnam <- make.cepnames(names(BCI))
    plot(mod, dis="sp", type="n")
    stems <- colSums(BCI)
    orditorp(mod, "sp", label = cnam, priority=stems, pch="+", pcol="grey")

    ## show select in action
    set.seed(1)
    take <- sample(ncol(BCI), 50)
    plot(mod, dis="sp", type="n")
    stems <- colSums(BCI)
    orditorp(mod, "sp", label = cnam, priority=stems, select = take,
             pch="+", pcol="grey")

[Package vegan version 2.4-3 Index]