[R] help on drawing a tree with "ape"?

[Hua Li]

Thanks again, Ben.

Specifically my question should be;

If I know that I'll be using variables to represent
the distances between species:

a = AB
b = AC
d = CD

and I also know my tree can be written as
"((A:51.78,(C:24.6,D:24.6):27.18):40.06,B:91.84):0.0;"

is there a way to allow me mark the edges without
having to see the tree topology first, so that when I
use "edgelabels", the symbols and the order (
c("a-b","b","b-d","d","d","a") ) should be
automatically arranged other than being specified by
me. In other words, I don't want to be the one who
tells R the command
"edgelabels(c("a-b","b","b-d","d","d","a"))". I'd
rather a way R finds out itself. (for example, after
some calculation, R knows the edgelabes should be the
way specified above other than, say, c("a", "b", "c",
"a-b", "a-c", "b-c"). )

Thank you!

Hua





--- Ben Bolker <bolker at ufl.edu> wrote:

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> Hua Li wrote:
> > Thank you very much for the help, Ben!
> > 
> > As a follow up, is there a way to specify the
> labels,
> > through the way the text is written, rather than
> > reading the edge positions from the graph? For
> > example, 
> > 
> > mytree =
> >
>
"((A:51.78,(C:24.6,D:24.6):27.18):40.06,B:91.84):0.0;"
> > plot(read.tree(text = mytree))
> > edgelabels(c("a-b","b","b-d","d","d","a"))
> > 
> > would give the graph I want. You may notice that
> if
> > set a = 91.84; b= 51.78; d= 24.6, the labels I put
> on
> > each edge is the corresponding lengths in variable
> > form.  The way I do it right now need me to first
> draw
> > the tree and then manually set the labels, and I
> > suppose there should be an easier way to get them
> by
> > reading the way the tree is written
> >
>
("((A:51.78,(C:24.6,D:24.6):27.18):40.06,B:91.84):0.0;")?
> > 
> > 
> > Sorry for my low level questions. Just started
> using
> > "ape" and research on phylogenetic trees.
> > 
> > Best wishes,
> > 
> > Hua
> > 
> 
> How about
> 
> 
> library(ape)
> mytree =
>
"((A:51.78,(C:24.6,D:24.6):27.18):40.06,B:91.84):0.0;"
> t1 = read.tree(text = mytree)
> plot(t1)
> edgelabels(c("a-b","b","b-d","d","d","a"))
> str(t1)
> t1$edge.length
> names(t1$edge.length)[c(2,4,6)]=c("b","d","a")
> plot(t1)
>
edgelabels(c("a-b","b","b-d","d","d","a"),adj=c(0.5,1.25))
> with(as.list(t1$edge.length),
>     
>
edgelabels(c(a-b,b,b-d,d,d,a),adj=c(0.5,-0.5),bg="lightblue"))
> 
> ?
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