Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!
Get Started for Free

collapseTree

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)

References

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

See Also

Examples

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

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70
GPL (>= 2)
Authors
Liam J. Revell
Initial release
2020-9-19

We don't support your browser anymore

Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.