https://github.com/cran/ape
Tip revision: 381399d76489f39fbfa381ff592fb5f1147f88f2 authored by Emmanuel Paradis on 05 September 2007, 00:00:00 UTC
version 2.0
version 2.0
Tip revision: 381399d
zoom.Rd
\name{zoom}
\alias{zoom}
\title{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{
\item{phy}{an object of class \code{"phylo"}.}
\item{focus}{a vector, either numeric or character, or a list of
vectors specifying the tips to be focused on.}
\item{subtree}{a logical indicating whether to show the context of the
extracted subtrees.}
\item{col}{a vector of colours used to show where the subtrees are in
the main tree, or a function .}
\item{...}{further arguments passed to \code{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 \code{\link[graphics]{rainbow}} for some possibilities
with colours.
}
\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
\seealso{
\code{\link{plot.phylo}}, \code{\link{drop.tip}},
\code{\link[graphics]{layout}}, \code{\link[graphics]{rainbow}},
\code{\link[graphics]{grey}}
}
\examples{
\dontrun{
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)))
}
}
\keyword{hplot}