Add Text or Points to Ordination Plots

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. If the function is used in ordiplot pipe, this should be missing and first argument be display.
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 of scores will be used if this is missing. If select is used, labels are given only selected items in the order they occur in the scores.
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 or number of scores.
select: Items to be displayed. This can either be a logical vector which is TRUE for displayed items or a vector of indices, or labels and if these are missing, row names of scores. 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). 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.

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.

Author

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", 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")

#> Warning: object '.Random.seed' not found