# subtreeplot

From ape v2.7-3
0th

Percentile

##### Zoom on a Portion of a Phylogeny by Successive Clicks

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.

Keywords
hplot
##### 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.
##### 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).

plot.phylo, drop.tip, subtrees

• subtreeplot
##### Examples
#example 1: simple
tree1<-rtree(50) #random tree with 50 leaves
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))) #allows three succssive zooms.
Documentation reproduced from package ape, version 2.7-3, License: GPL (>= 2)

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