Graham Etherington wrote:
Hi,
Using Ape, I have constructed an object of class phylo, using the
method 'nj' (lets call the object 'tree_ja').
I also have a given subset of 'tree_ja' in a vector (lets call the
vector 'subspecies').
What I want to do, is construct a nj tree - plot(tree_ja) - but have the
species in vector 'subspecies' shown as red at the tips of the tree.
The closest I've come is this:
Given that 'tree_ja$tip.label' provides the following:
[1] 1_T1 2_T1 3_T1 4_T1 5_T1 6_T1
[7] 7_T1 8_T1 9_T1 10_T1 11_T1 12_T1
and that my 'subspecies' vector is:
subspecies - c(1_T1, 2_T1, 3_T1, 4_T1, 6_T1)
which can also be written as:
subspecies - c(tree_ja$tip.label[1:4], tree_ja$tip.label[5])
I can construct a method which gives me the following statement:
plot(tree_ja, tip.col = c('red', 'red', 'red', 'red', 'black', 'red',
'black', 'black', 'black', 'black', 'black', 'black'))
But this doesn't work (at least not on my full dataset, which as 118
tips - reduced to 12 here for brevity) and I'm SURE there must be a
better way of doing it.
Could anyone help me with this?
Many thanks,
Graham
--
Dr. Graham Etherington
Post-doctoral Bioinformatician,
Department of Computational and Systems Biology
John Innes Centre
Norwich Research Park
Colney
Norwich
NR4 7UH
UK
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R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
In general the r-sig-phylo group is better for this kind of question, and
it would
be better to give us a reproducible example, but here's an example that (I
think)
does what you want:
library(ape)
set.seed(1001)
z = rcoal(10)
z
Phylogenetic tree with 10 tips and 9 internal nodes.
Tip labels:
t1, t7, t6, t10, t3, t9, ...
Rooted; includes branch lengths.
names(z)
[1] edgeedge.length tip.label Nnode
ss - z$tip.label[c(1,3,5,7)]
?plot.phylo
plot(z,tip.color=ifelse(z$tip.label %in% ss, red,black))
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R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
