Add Text on Non-transparent Label to an Ordination Plot.

Function ordilabel is similar to text, but the text is on an opaque label. This can help in crowded ordination plots: you still cannot see all text labels, but at least the uppermost ones are readable. Argument priority helps to make the most important labels visible. Function can be used in pipe after ordination plot or ordiplot command.

ordilabel(x, display, labels, choices = c(1, 2), priority, select,
    cex = 0.8, fill = "white", border = NULL, col = NULL, xpd = TRUE, ...)

Arguments

x

An ordination object an any object known to scores.

display

Kind of scores displayed (passed to scores).

labels

Optional text used in plots instead of the default. If select is given, the labels are given only to selected items in the order they occur in the scores.

choices

Axes shown (passed to scores).

priority

Vector of the same length as the number of scores or selected items. The items with high priority will be plotted uppermost.

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.

cex

Character expansion for the text (passed to text).

fill

Background colour of the labels (the col argument of polygon).

border

The colour and visibility of the border of the label as defined in polygon. The default is to use text colour col.

col

Text colour.

xpd

Draw labels also outside the plot region.

...

Other arguments (passed to text).

Details

The function may be useful with crowded ordination plots, in particular together with argument priority. You will not see all text labels, but at least some are readable. Function can be used as a part of a pipe (|>) in place of text after an ordination plot command (see Examples).

Other alternatives for cluttered plots are identify.ordiplot, orditorp, ordipointlabel and orditkplot in vegan3d package.

Author

Jari Oksanen

See also

plot.cca and text.ordiplot that can use the function with argument bg.

Examples

data(dune)
ord <- cca(dune)
plot(ord, type = "n")
## add text
ordilabel(ord, dis="sites", cex=1.2, font=3, fill="hotpink", col="blue")
## You may prefer separate plots, but here species as well
ordilabel(ord, dis="sp", font=2, priority=colSums(dune))

## use in a pipe
plot(ord, type = "n") |>
   ordilabel("spec", font = 3, priority = colSums(dune)) |>
   points("sites", pch=21, bg = "yellow", col = "blue")