phytools: cladelabels – R documentation

Pricing

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

Get Started for Free

Documentation

phytools

cladelabels

Add labels to subtrees of a plotted phylogeny

Description

This function adds clade labels to a plotted tree.

Usage

cladelabels(tree=NULL, text, node, offset=NULL, wing.length=NULL, cex=1,
   orientation="vertical")
arc.cladelabels(tree=NULL, text, node=NULL, ln.offset=1.02,
   lab.offset=1.06, cex=1, orientation="curved",...)

Arguments

`tree`	an object of class `"phylo"`. If not supplied, the function will obtain the last plotted phylogeny from the environmental variable `last_plot.phylo`.
`text`	desired clade label text.
`node`	node number for the most recent common ancestor of members of the clade. For `arc.cladelabels` this defaults to `NULL` which means that the node of the clade to be labeled should be specified interactively (that is, by clicking on the graphical device).
`offset`	offset (as a multiplier of character width) for the label. Defaults to `offset=1` if `tree` is supplied or `offset=8` otherwise.
`wing.length`	length of the wings to add to the top & bottom of the label bar (in character widths).
`cex`	character expansion factor.
`orientation`	orientation of the text. Can be `orientation = "vertical"` (the default) or `"horizontal"`.
`ln.offset`	line offset (as a function of total tree height) for `arc.cladelabels`.
`lab.offset`	label offset for `arc.cladelabels`.
`...`	optional arguments for `arc.cladelabels`.

Details

cladelabels presently works only for rightward facing plotted phylogenies - but no warning will be returned if your tree does not conform to this requirement!

arc.cladelabels is designed to do a similar thing to cladelabels, but for plotted fan trees. This function checks to ensure that the most recently plotted tree was plotted with type="fan" style.

Author(s)

Liam Revell liam.revell@umb.edu

References

Paradis, E., J. Claude, and K. Strimmer (2004) APE: Analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-290.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.