ape (version 5.5)

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.

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

# NOT RUN {
#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
# }