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 <[email protected]> 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 > > _______________________________________________ > R-sig-phylo mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ _______________________________________________ R-sig-phylo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
