ordipointlabel: Ordination Plots with Points and Optimized Locations for Text

In vegan: Community Ecology Package

Description

The function ordipointlabel produces ordination plots with points and text label to the points. The points are in the exact location given by the ordination, but the function tries to optimize the location of the text labels to minimize overplotting text. The function may be useful with moderately crowded ordination plots.

Usage

ordipointlabel(x, display = c("sites", "species"), choices = c(1, 2),
   col = c(1, 2),  pch = c("o", "+"), font = c(1, 1), 
   cex = c(0.8, 0.8), add = FALSE, select, ...)

## S3 method for class 'ordipointlabel'
plot(x, ...)

Arguments

x	For ordipointlabel() a result object from an ordination function. For plot.ordipointlabel an object resulting from a call to ordipointlabel().
display	Scores displayed in the plot.
choices	Axes shown.
col, pch, font, cex	Colours, point types, font style and character expansion for each kind of scores displayed in the plot. These should be vectors of the same length as the number of items in display.
add	Add to an existing plot.
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. select is only used if a single set of scores is being plotted (i.e. length(display) == 1), otherwise it is ignored and a warning issued. If a logical vector is used, it must have the same length as the scores plotted.
...	Other arguments passed to points and text.

Details

The function uses simulated annealing (optim, method = "SANN") to optimize the location of the text labels to the points. There are eight possible locations: up, down, sides and corners. There is a weak preference to text right above the point, and a weak avoidance of corner positions. The exact locations and the goodness of solution varies between runs, and there is no guarantee of finding the global optimum. The optimization can take a long time in difficult cases with a high number of potential overlaps. Several sets of scores can be displayed in one plot.

The function is modelled after pointLabel in maptools package (which has chained dependencies of S4 packages).

Value

The function returns invisibly an object of class ordipointlabel with items xy for coordinates of points, labels for coordinates of labels, items pch, cex and font for graphical parameters of each point or label. In addition, it returns the result of optim as an attribute "optim". The unit of overlap is the area of character "m", and with variable cex it is the smallest alternative.

There is a plot method based on orditkplot but which does not alter nor reset the graphical parameters via par.

The result object from ordipointlabel inherits from orditkplot, and can also be replotted with its plot method. It may be possible to further edit the result object with orditkplot, but for good results it is necessary that the points span the whole horizontal axis without empty margins.

Note

The function is designed for ordination graphics, and the optimization works properly with plots of isometric aspect ratio.

Author(s)

Jari Oksanen

References

See pointLabel for references.

See Also

pointLabel for the model implementation, and optim for the optimization.

Examples

data(dune)
ord <- cca(dune)
plt <- ordipointlabel(ord)

## set scaling - should be no warnings!
ordipointlabel(ord, scaling = 1)

## plot then add
plot(ord, scaling = 3, type = "n")
ordipointlabel(ord, display = "species", scaling = 3, add = TRUE)
ordipointlabel(ord, display = "sites", scaling = 3, add = TRUE)

## redraw plot without rerunning SANN optimisation
plot(plt)

Example output

Loading required package: permute
Loading required package: lattice
This is vegan 2.4-3

vegan documentation built on May 2, 2019, 5:51 p.m.