expand.clade: Expands (or contracts) the tip-spacing of a given clade or...
In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

expand.clade

R Documentation

Expands (or contracts) the tip-spacing of a given clade or clades

Description

Modify the tip-spacing of a plotted tree.

Usage

expand.clade(tree, node, factor=5)
## S3 method for class 'expand.clade'
plot(x, ...)

Arguments

`tree`	tree an object of class `"phylo"` or `"simmap"`.
`node`	node index or vector of node indices.
`factor`	expansion factor for the tip-spacing of the taxa descended from node or nodes in `node`.
`x`	for `plot` method, an object of class `"expand.clade"`.
`...`	optional arguments to be passed to `plotTree` or `plotSimmap`, depending on the class of `x$tree`.

Details

The purpose of this function is to compute a custom tip-spacing for users who want to expand or contract the tip-spacing of the descendant taxa from a given node or nodes.

Value

The function returns an object of class "expand.clade" which consists of the (possibly re-ordered) tree and a numerical vector with the calculated tip spacing based on the expansion factor specified by the user.

This object can be plotted using the S3 plot method for the object class; or it can be plotted simply by calling a standard plotting function on the tree & tip spacings.