ape (version 5.8)

subtreeplot: Zoom on a Portion of a Phylogeny by Successive Clicks

Description

This function plots simultaneously a whole phylogenetic tree (supposedly large) and a portion of it determined by clicking on the nodes of the phylogeny. On exit, returns the last subtree visualized.

Usage

subtreeplot(x, wait=FALSE, ...)

Arguments

x

an object of class "phylo".

wait

a logical indicating whether the node beeing processed should be printed (useful for big phylogenies).

...

further arguments passed to plot.phylo.

Author

Damien de Vienne

Details

This function aims at easily exploring very large trees. The main argument is a phylogenetic tree, and the second one is a logical indicating whether a waiting message should be printed while the calculation is being processed.

The whole tree is plotted on the left-hand side in half of the device. The subtree is plotted on the right-hand side in the other half. The user clicks on the nodes in the complete tree and the subtree corresponding to this node is ploted in the right-hand side. There is no limit for the number of clicks that can be done. On exit, the subtree on the right hand side is returned.

To use a subtree as the new tree in which to zoom, the user has to use the function many times. This can however be done in a single command line (see example 2).

See Also

plot.phylo, drop.tip, subtrees

Examples

if (FALSE) {
#example 1: simple
tree1 <- rtree(50)
tree2 <- subtreeplot(tree1, wait = TRUE) # on exit, tree2 will be a subtree of tree1

#example 2: more than one zoom
tree1 <- rtree(60)
tree2 <- subtreeplot(subtreeplot(subtreeplot(tree1))) # allow three succssive zooms
}