collapseTree {phytools}

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 (or select Finish button in RStudio) to end.

Note, for the animation to work probably when run in the RStudio IDE the "zoom" level should be set to 100%.

Value

Returns the final plotted tree.

Author(s)

Liam Revell [e-mail]

References

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

See Also

plotTree, plotSimmap

Examples

## Not run: 
data(liolaemid.tree)
pruned<-collapseTree(liolaemid.tree,fsize=0.5)
## End(Not run)