plot.ancestral.R
## plot.ancestral.R (2005-12-04)
## Plotting Ancestral Characters on a Tree
## Copyright 2005 Julien Dutheil
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
plot.ancestral <- function(x, which=names(x$node.character),
n.col=10, col.fun=function(n) rainbow(n, start=0.4, end=0),
plot.node.values=FALSE,
ask = prod(par("mfcol")) < length(which) && dev.interactive(),
...)
{
if (!("ancestral" %in% class(x)))
stop("object \"phy\" is not of class \"ancestral\"")
states <- rbind(x$node.character, x$tip.character)
cols <- col.fun(n.col)
if(ask) {
op <- par(ask = TRUE)
on.exit(par(op))
}
for(state in which) {
a <- states[x$edge[,2],state]
b <- round((n.col-1)*(a-min(a))/(max(a)-min(a)))+1
if(plot.node.values) {
x$node.label <- x$node.character[,state]
plot.phylo(x, edge.color=cols[b], show.node.label=TRUE, sub=state, ...)
} else {
plot.phylo(x, edge.color=cols[b], sub=state, ...)
}
}
}