cladelabels: Add labels to subtrees of a plotted phylogeny

View source: R/utilities.R

cladelabelsR Documentation

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", stretch=1, ...)

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.

stretch

argument for arc.cladelabels to be passed to arctext.

...

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.

See Also

nodelabels


phytools documentation built on Sept. 2, 2022, 1:06 a.m.