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## zoom.R (2009-07-27)
## Zoom on a Portion of a Phylogeny
## Copyright 2003-2009 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
zoom <- function(phy, focus, subtree = FALSE, col = rainbow, ...)
{
if (!is.list(focus)) focus <- list(focus)
n <- length(focus)
for (i in 1:n)
if (is.character(focus[[i]]))
focus[[i]] <- which(phy$tip.label %in% focus[[i]]) # fix by Yan Wong
if (is.function(col)) {
col <- if (deparse(substitute(col)) == "grey") grey(1:n/n) else col(n)
}
ext <- vector("list", n)
for (i in 1:n)
ext[[i]] <- drop.tip(phy, phy$tip.label[-focus[[i]]],
subtree = subtree, rooted = TRUE)
nc <- round(sqrt(n)) + 1
nr <- ceiling(sqrt(n))
M <- matrix(0, nr, nc)
x <- c(rep(1, nr), 2:(n + 1))
M[1:length(x)] <- x
layout(M, c(1, rep(3/(nc - 1), nc - 1)))
phy$tip.label <- rep("", length(phy$tip.label))
colo <- rep("black", dim(phy$edge)[1])
for (i in 1:n)
colo[which.edge(phy, focus[[i]])] <- col[i]
plot.phylo(phy, edge.color = colo, ...)
for (i in 1:n)
plot.phylo(ext[[i]], edge.color = col[i], ...)
}
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