vegan (version 2.7-6)

orditorp: 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, ...)

Value

The function returns invisibly the 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. If function is used in an ordiplot pipe, it will return the input ordiplot object, but amend the plotted scores with this vector as attribute "orditorp". The returned vector can be used as the select argument in ordination text and

points functions.

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). Function can also be used in a pipe (|>) where the first command is a vegan ordination plot command or ordiplot.

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.

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", labels = 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)
## only selected items are labelled, and the labels must be in the some
## order as in the scores
orditorp(mod, "sp", labels = cnam[sort(take)], priority=stems, select = take,
         pch="+", pcol="grey")
# \dontshow{
## example(orditorp) should not set random seed in the user session
rm(.Random.seed)
# }