Perfect! Exactly the information I needed.
Thanks,
Morgan
On Wed, Aug 10, 2011 at 4:15 PM, David Bapst dwba...@uchicago.edu wrote:
Morgan-
The node labels from ace() are the ID numbers used in the edge matrix
(you can see that with tree$edge, where 'tree' is your phylogeny
object), and the are numbered from (Ntip(tree)+1) to
(Ntip(tree)+Ntip(tree)-1). Thus, to give your tree the IDs from the
edge matrix as node labels, just do:
tree$node.label-Ntip(tree)+(1:(Ntip(tree)-1))
plot.phylo (tree,show.node.label=T) #and we can see
the node labels!
I hope that helps.
-Dave
On Wed, Aug 10, 2011 at 1:49 PM, Morgan Langille
morgan.g.i.langi...@gmail.com wrote:
I have a tree with no node labels and I am running ACE many times. I
would like to somehow get ACE data, specifically reconstruction$ace
out of R. I can create node labels for my tree using function
makenodelabel, but these don't correspond to the node labels within
the phylo data structure that is used as the names within
reconstruction$ace. I see two choices:
Is there a way to easily set the node labels for my tree to correspond
to the internal R phylo object node labels?
OR
Is there a way to map the internal phylo node labels to the node
labels on the tree?
Any help is greatly appreciated!
Morgan Langille
http://morganlangille.com
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David Bapst
Dept of Geophysical Sciences
University of Chicago
5734 S. Ellis
Chicago, IL 60637
http://home.uchicago.edu/~dwbapst/
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