plot.phylospace: Plot a phylospace object.

In eliotmiller/phylospacer: Tools for creating and plotting phyloclimate and phylomorphospaces

Description

Plots a phylospace object and, if desired, available climate space, species labels, and/or node labels.

Usage

  ## S3 method for class 'phylospace'
 plot(phylospace.object,
    climate.points, species.labels = FALSE,
    node.labels = FALSE, label.adjust = 0, x.label,
    y.label, x.limits, y.limits, ...)

Arguments

phylospace.object	Phylospace object. The results of a call to phylospace.
climate.points	Two column data frame (or matrix?) of x, y points. Columns in same order as species niche data frame. Here, each row refers to separate climate point.
species.labels	Logical indicating whether species names should be plotted.
node.labels	Logical indicating whether node names should be plotted.
label.adjust	Numeric value by which species labels should be offset from their points. Currently only works well if x & y axes are on similar scales.
x.label	Optional label for x axis. Defaults to "trait1".
y.label	Optional label for y axis. Defaults to "trait2".
x.limits	Optional x limits for the plot.
y.limits	Optional y limits for the plot.
...	Some arguments can be passed to graphical parameters, in particular "lwd". See: par

Details

This function plots an object of class phylospace. Because currently the label adjust argument calculates how much to offset the labels from the species' points as a function of absolute slope (not slope as you see it plotted), this currently only works well if the x and y axes are on similar scales. This will be updated in future versions.

Value

Returns a plotted phylospace object.

References

Miller, E.T., A.E. Zanne, & R. E. Ricklefs. In press. Niche conservatism constrains Australian honeyeater assemblages in stressful environments. Ecology Letters.

Examples

#See examples under phylospace function

eliotmiller/phylospacer documentation built on May 16, 2019, 3:03 a.m.