Hi John,
Have you seen the zoom() function? If that's not what you want, try:
data(chiroptera)
plot(chiroptera)
drop.tip(chiroptera, identify(chiroptera, tips = TRUE)$tips)
If your tree is smaller, you can do:
drop.tip(tr, interactive = TRUE)
bind.tree(), extract.clade() and root() also have this option. Combining
with identify.phylo() it is possible to write short interactive scripts
for tree manipulation/visualization.
HTH
Emmanuel
John Cumbers wrote on 22/03/2011 12:15:
Hi all,
I attach a screenshot of a phylogenetic tree made in Ape. It has ~1200
tips. There are so many that I can't read them all. There are three
large clades that I want to collapse down. What is the best tool to
collapse down particular clades? Ideally, I'd like an interactive
version that I can select which branches to collapse, or a way to number
particular nodes to collapse. I've tried drop.tip in Ape, but I can't
seem to select a clade to drop. I've also tried dropping ranges of
tips, e.g drop.tip(my_tree, 1:1100), but I find that difficult to
select the exact tips I want.
Many thanks,
John
------------------------------------------------------------------------
------------------------------------------------------------------------
_______________________________________________
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
--
Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
_______________________________________________
R-sig-phylo mailing list
R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
