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ape

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, subtree = FALSE, col = rainbow, ...)

Arguments

`phy`	an object of class `"phylo"`.
`focus`	a vector, either numeric or character, or a list of vectors specifying the tips to be focused on.
`subtree`	a logical indicating whether to show the context of the extracted subtrees.
`col`	a vector of colours used to show where the subtrees are in the main tree, or a function .
`...`	further arguments passed to `plot.phylo`.

Details

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.

Author(s)

Emmanuel Paradis

Examples

## Not run: 
data(chiroptera)
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)))

## End(Not run)

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24