[R-sig-phylo] ladderize + drop.tip = shuffled node labels
Hi all I have been plotting some pruned trees recently, and have run into a problem using drop.tip() after ladderize(). If you ladderize() and then drop tips from the ladderized tree, then at least in my case the node labels are no longer correct. This may be an unlikely sequence of commands, but I thought I'd post this in case it is an easy fix, or it helps anyone else avoid issues. Thanks! Rebecca ## require(ape) #read tree mytree-read.tree() ((D,(E,G)1)1,((H,J)0.8,(K,(((L,M)0.5,(N,O)0.6)1,(P,(Q,R)1)1)0.7)1)1); #ladderize tree mytree.lad-ladderize(mytree) #node labels display on both trees correctly plot(mytree,show.node.label=TRUE) plot(mytree.lad,show.node.label=TRUE) #drop tips from both trees drop.mytree-drop.tip(mytree,c(L,D,G)) drop.mytree.lad-drop.tip(mytree.lad,c(L,D,G)) #plot both trees, node labels are incorrect for ladderized tree plot(drop.mytree,show.node.label=TRUE) plot(drop.mytree.lad,show.node.label=TRUE) ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] Add species branches to genus level tree
Dear All Sorry to mass email with what could be a very basic question. I am trying to generate a tree for 1000 plus species. To reduce the search effort I first generated a tree to genus level from NCBI Itol with the intention of adding species branches to each genus after. Doing this manually has invariably proved challenging as it's difficult to locate and solve all the sources of human error that creep in when manual editing. Is there a function in R that can do this? Say something that matches the genus in the species name to the genus tip on the tree, and adds branches accordingly? It is not my intention that the tree be based on divergence times, this isn't feasible given the number and order of species I am working with, hence the reason for using the NCBI taxonomy. Any help is much appreciated cheers Tom ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Add species branches to genus level tree
Thomas- I think your interests might be served by my function expandTaxonTree in my library paleotree on CRAN. Given a genus-level tree with data on the species within each genus, it will turn each genus into an unresolved polytomy of the congeneric species. -Dave On Tue, Oct 2, 2012 at 3:08 AM, Davies, Thomas thomas.dav...@exeter.ac.uk wrote: Dear All Sorry to mass email with what could be a very basic question. I am trying to generate a tree for 1000 plus species. To reduce the search effort I first generated a tree to genus level from NCBI Itol with the intention of adding species branches to each genus after. Doing this manually has invariably proved challenging as it's difficult to locate and solve all the sources of human error that creep in when manual editing. Is there a function in R that can do this? Say something that matches the genus in the species name to the genus tip on the tree, and adds branches accordingly? It is not my intention that the tree be based on divergence times, this isn't feasible given the number and order of species I am working with, hence the reason for using the NCBI taxonomy. Any help is much appreciated cheers Tom ___ R-sig-phylo mailing list R-sig-phylo@r-project.org 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/ http://cran.r-project.org/web/packages/paleotree/index.html ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
