Alternative plot and identify Functions for Ordination

Function ordiplot is an alternative plotting function which works with any vegan ordination object and many non-vegan objects. In addition, plot functions for vegan ordinations return invisibly an "ordiplot" object, and this allows using ordiplot support functions with this result: identify can be used to add labels to selected site, species or constraint points, and points and text can add elements to the plot, and used in a pipe to add scores into plot by layers.

Usage

ordiplot(ord, choices = c(1, 2), type="points", display, optimize = FALSE,
    arrows = FALSE, length = 0.05, arr.mul, xlim, ylim, ...)
# S3 method for class 'ordiplot'
points(x, what, select, arrows = FALSE,
    length = 0.05, arr.mul, ...)
# S3 method for class 'ordiplot'
text(x, what, labels, select, optimize = FALSE,
    arrows = FALSE, length = 0.05, arr.mul, bg, ...)
# S3 method for class 'ordiplot'
identify(x, what, labels,  ...)

Arguments

ord: A result from an ordination.
choices: Axes shown.
type: The type of graph which may be "points", "text" or "none" for any ordination method.
display: Display only "sites" or "species". The default for most methods is to display both, but for cca, rda, dbrda and capscale it is the same as in plot.cca.
xlim, ylim: the x and y limits (min,max) of the plot.
...: Other graphical parameters.
x: A result object from ordiplot.
what: Items identified in the ordination plot. The types depend on the kind of plot used. Most methods know sites and species, functions cca and rda know in addition constraints (for LC scores), centroids, biplot and regression, and plot.procrustes ordination plot has heads and points.
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 to selected items in the order they occur in the scores.
optimize: Optimize locations of text to reduce overlap and plot point in the actual locations of the scores. Uses ordipointlabel.
arrows: Draw arrows from the origin. This will always be TRUE for biplot and regression scores in constrained ordination (cca etc.). Setting this TRUE will draw arrows for any type of scores. This allows, e.g, using biplot arrows for species. The arrow head will be at the value of scores, and possible text is moved outwards.
length: Length of arrow heads (see arrows).
arr.mul: Numeric multiplier to arrow lenghts; this will also set arrows = TRUE. The default is to automatically adjust arrow lengths with "biplot" and "regression" scores and else use unmodified scores.
bg: Background colour for labels. If bg is set, the labels are displayed with ordilabel instead of text.
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.

Details

Function ordiplot draws an ordination diagram with default of black circles for sites and red crosses for species. It returns invisibly an object of class ordiplot.

The function can handle output from several alternative ordination methods. For cca, rda and decorana it uses their plot method with option type = "points". In addition, the plot functions of these methods return invisibly an ordiplot object which can be used by identify.ordiplot to label points. For other ordinations it relies on scores to extract the scores.

For full user control of plots, it is best to call ordiplot with type = "none" and save the result, and then add sites and species using points.ordiplot or text.ordiplot which both pass all their arguments to the corresponding default graphical functions. Alternatively, points and text can be used in pipe which allows an intuitive way of building up plots by layers. In addition, function ordilabel and ordipointlabel can be used in pipe after ordiplot or other vegan ordination plot commands. See Examples.

Value

Function ordiplot returns invisibly an object of class ordiplot with used scores. In general, vegan plot functions for ordination results will also return an invisible ordiplot object. If the plot(..., type = "n") was used originally, the plot is empty, and items can be added with the invisible object. Functions points and text return their input object without modification, which allows chaining these commands with pipes. Function identify.ordiplot uses this object to label the point.

Author

Jari Oksanen

Examples

## Draw a plot for a non-vegan ordination (cmdscale).
data(dune)
dune.dis <- vegdist(wisconsin(dune))
dune.mds <- cmdscale(dune.dis, eig = TRUE)
dune.mds$species <- wascores(dune.mds$points, dune, expand = TRUE)
pl <- ordiplot(dune.mds, type = "none")
points(pl, "sites", pch=21, col="red", bg="yellow")
text(pl, "species", col="blue", cex=0.9)


## same plot using pipes (|>)
ordiplot(dune.mds, type="n") |>
  points("sites", pch=21, col="red", bg="yellow") |>
  text("species", col="blue", cex=0.9)
## Default plot using identify to label selected points
if (FALSE) { # \dontrun{
pl <- ordiplot(dune.mds)
identify(pl, "spec")} # }
## Some people think that species should be shown with arrows in PCA.
## Other ordination methods also return an invisible ordiplot object and
## we can use pipes to draw those arrows. We drop species that are
## poorly explained by the current graph.
mod <- rda(dune)
good <- goodness(mod, choices=1:2, model="CA", summarize = TRUE)
plot(mod, type="n") |>
  points("sites", pch=16, col="red") |>
  text("species", arrows = TRUE, length=0.05, col="blue", select = good > 1/3)