[R-sig-phylo] Tree Annotation

Emmanuel Paradis Emmanuel.Paradis at ird.fr
Fri Jan 20 12:33:39 CET 2012


If you just want to color edges, what about using the option 
'edge.color' in plot? You may use which.edge() to identify the edge 
indices you want to color. edgelabels() without options also displays 
the edge indices on a plotted tree.



Todd Jones wrote on 20/01/2012 10:32:
> Hello,
> I am working on a project where I need to add annotation/comment data in
> square brackets to my tree and export it in NEXUS format so it looks like
> this:
> 0.9):0.6):0.6):0.8):0.5)*[&!color=#-65536]*:1.3):0.7):1.0)
> I need to do this so I can then import the tree into figtree and have the
> branches of the tree be colored the way I specified them to be in R
> (through the comments in the square brackets).  figtree colors branches
> based on the color=#... tag specified in the square brackets.  So far, I
> have been unable to figure out a way to accomplish this in R.  Is it
> possible?
> Thanks.

Emmanuel Paradis
IRD, Jakarta, Indonesia

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