R help - Apr 2012 - R: Colouring phylogenetic tip labels and/or edges

Hi,

I have reconstructed ancestral character states on a phylogeny using MuSSE in
the diversitree package and plotted the character state probabilities as pie
charts on the nodes. I would, however, like to colour the character states of my
extant species, i.e. the tip labels, the same colours as my pie charts, such
that all species in  state 1 are e.g. blue, species in state 2 red and  species
in state 3 yellow, and have not been successful with my attempts. I am only able
to colour them in repeating sets of 3e.g. sp1=blue, sp.2=red, sp.3=yellow,
sp.4=blue, sp5=red, sp6=yellow etc. I am also wondering how to colour the
branches or edges as the states transition from one to another over time (i.e.
as in the "Analyzing diversification with diversitree" manual by Rich
FitzJohn on page 23).

Code I've been working with is below:

library(diversitree) #loads library
tree<-read.tree("tree")#loads tree
tree<-chronopl(tree, lambda=1,CV=TRUE) #converts to ultrametric
states<-read.delim("states", header=TRUE)#load states
head(states)

#match states to tree
states<-structure(states$PC, names=states$Species)
names(states)<-tree$tip.label

#MuSSE
diversitree:::argnames.musse(NULL, 3) #number of states
lik<-make.musse(tree, states, 3)
argnames(lik)
#contstrain lambda
lik.base<-constrain(lik, lambda2~lambda1, lambda3~lambda1,
mu2~mu1,mu3~mu1,q13~q12,q21~q12,q23~q12,q31~q12,q32~q12)
#find ML point for this model
p<-starting.point.musse(tree, 3)
fit.base<-find.mle(lik.base, p[argnames(lik.base)])

#unconstrained
lik.lambda<-constrain(lik,mu2~mu1,mu3~mu1,q13~q12,q21~q12,q23~q12,q31~q12,q32~q12)
fit.lambda<-find.mle(lik.lambda, p[argnames(lik.lambda)])
anova(fit.base, free.lambda=fit.lambda)

#find ancestral state probabilities
state.probs<-asr.marginal(lik.base, coef(fit.base))#ancestral state
probabilities
state.probs
pie.probs<-t(state.probs)
pr<-apply(t(state.probs), 1, which.max)#max probability
tree$node.label<-pr #labels the nodes with the character states
write.tree(tree, file="T")#exports tree with nodes character states to
directory #configuration in figtree - node label display label

#tree pie charts
pdf("TREE_PLOT.pdf", height=11, width=8.5)
plot(tree ,cex=.8)
nodelabels(pie=pie.probs,piecol=c("blue","red","yellow"),
cex=.5)
dev.off()

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Monroe, Melanie <melanie.monroe <at> yale.edu> writes:
> I have reconstructed ancestral character states on a phylogeny using
> MuSSE in the diversitree package and plotted the character state
> probabilities as pie charts on the nodes. I would, however, like to
> colour the character states of my extant species, i.e. the tip
> labels, the same colours as my pie charts, such that all species in
> state 1 are e.g. blue, species in state 2 red and species in state 3
> yellow, and have not been successful with my attempts. I am only
> able to colour them in repeating sets of 3e.g. sp1=blue, sp.2=red,
> sp.3=yellow, sp.4=blue, sp5=red, sp6=yellow etc. I am also wondering
> how to colour the branches or edges as the states transition from
> one to another over time (i.e. as in the "Analyzing diversification
> with diversitree" manual by Rich FitzJohn on page 23).
  You probably need to ask this question on the r-sig-phylo
mailing list, which specializes in comparative methods and
phylogenetics.  For the tips you will probably want something like
tip.color=rep(c("blue","red","yellow"),nspecies/3).

  Ben Bolker