cladelabels: Add labels to subtrees of a plotted phylogeny

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

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 [e-mail]

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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

nodelabels

phytools documentation built on June 22, 2024, 10:39 a.m.