ape (version 1.2-7)

zoom: Zoom on a Portion of a Phylogeny

Description

This function plots simultaneously a whole phylogenetic tree (supposedly large) and a portion of it.

Usage

zoom(phy, focus, type = "phylogram", use.edge.length = TRUE)

Arguments

phy

an object of class "phylo".

focus

a vector, either numeric or character, specifying the tips to be focused on.

type

a character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default), "cladogram", "unrooted", or any unambiguous abbreviation of these.

use.edge.length

a logical indicating whether to use the edge lengths of the phylogeny to draw the branches (the default) or not (if FALSE). This option has no effect if the object of class "phylo" has no `edge.length' element.

Details

This is an experimental function aimed at exploring very large trees. The main argument is a phylogenetic tree, and the second one is a vector specifying the tips to be focused on. The latter can be either numeric and is thus taken as the index of the tip labels, or character in which case it is taken as the corresponding tip labels. The plot consists of two trees: the whole tree is plotted on the left-hand side in a narrower sub-window (about a quarter of the device) without any tip labels; the sub-tree consisting of the tips in `focus' is extracted and plotted on the right-hand side. The tips in `focus' are marked on the left-hand side tree with a blue "o".

See Also

plot.phylo, drop.tip, layout

Examples

data(chiroptera)
zoom(chiroptera, 1:20)