-## zoom.R (2004-12-17)
+## zoom.R (2009-07-27)
## Zoom on a Portion of a Phylogeny
-## Copyright 2003-2004 Emmanuel Paradis
+## Copyright 2003-2009 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
n <- length(focus)
for (i in 1:n)
if (is.character(focus[[i]]))
- focus[[i]] <- which(phy$tip.label == focus[[i]])
- if (is.function(col))
- if (deparse(substitute(col)) == "grey")
- col <- grey(1:n/n) else col <- col(n)
- ext <- list()
- length(ext) <- n
+ focus[[i]] <- which(phy$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$tip.label[-focus[[i]]],
- subtree = subtree)
+ subtree = subtree, rooted = TRUE)
nc <- round(sqrt(n)) + 1
nr <- ceiling(sqrt(n))
M <- matrix(0, nr, nc)
x <- c(rep(1, nr), 2:(n + 1))
M[1:length(x)] <- x
- layout(M, c(1, rep(3 / (nc - 1), nc - 1)))
+ layout(M, c(1, rep(3/(nc - 1), nc - 1)))
phy$tip.label <- rep("", length(phy$tip.label))
colo <- rep("black", dim(phy$edge)[1])
for (i in 1:n)