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.

Usage

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. If this is not given, the text is found from the ordination object.
choices: Axes shown (passed to scores).
priority: Vector of the same length as the number of labels. 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

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")