Zoom on a Portion of a Phylogeny

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

zoom(phy, focus, subtree = FALSE, col = rainbow, ...)

This function aims at exploring very large trees. The main argument is a phylogenetic tree, and the second one is a vector or a list of vectors specifying the tips to be focused on. The vector(s) can be either numeric and thus taken as the indices of the tip labels, or character in which case it is taken as the corresponding tip labels.

The whole tree is plotted on the left-hand side in a narrower sub-window (about a quarter of the device) without tip labels. The subtrees consisting of the tips in `focus' are extracted and plotted on the right-hand side starting from the top left corner and successively column-wise.

If the argument `col' is a vector of colours, as many colours as the number of subtrees must be given. The alternative is to give a function that will create colours or grey levels from the number of subtrees: see rainbow for some possibilities with colours.

See Also

plot.phylo, drop.tip, layout, rainbow, grey

zoom(chiroptera, 1:20, subtree = TRUE)
zoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
zoom(chiroptera, list(grep("Plecotus", chiroptera$tip.label),
                      grep("Pteropus", chiroptera$tip.label)))
Documentation reproduced from package ape, version 3.0-2, License: GPL (>= 2)

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