collapseTree: Interactive tree visualizer

View source: R/collapseTree.R

collapseTreeR Documentation

Interactive tree visualizer

Description

Function creates an interactive visualization of collapsing & expanding clades on the tree.

Usage

collapseTree(tree, ...)

Arguments

tree

an object of class "phylo".

...

optional arguments. These mostly match the arguments of plotSimmap, but also include the argument drop.extinct=TRUE which will (if the input tree is ultrametric) drop any 'extinct' lineages from the tree that is returned by the function.

Details

Function first plots a fan style tree, and then the user collapses node on the tree by clicking on them. Collapsed nodes are collapsed to the common ancestor of the clade. Nodes that have been collapsed can also be expanded by clicking. Right-click to end.

Value

Returns the final plotted tree.

Author(s)

Liam Revell liam.revell@umb.edu

References

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

See Also

plotTree, plotSimmap

Examples

## Not run: 
data(anoletree)
pruned<-collapseTree(anoletree)
## End(Not run)

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