Dear Klaus, Thanks a lot for your help
and what is in that case xx and yy? Justyna From: Klaus Schliep [mailto:klaus.schl...@gmail.com] Sent: Friday, February 24, 2017 6:13 PM To: Eduardo Ascarrunz Cc: Wierzbinska, Justyna; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] distances between the nodes Dear Justyna tr$edge does not store coordinates, see help(phylo). if you want the coordinates of the nodes of your last plotted tree you can get them: library(ape) tree = rtree(5) nodelabels() tiplabels() last_plot = get("last_plot.phylo", envir = .PlotPhyloEnv) last_plot$xx and last_plot$yy contain the coordinates of the nodes. there is also a (generic) function cophenetic() in ape to compute the patristic distance and for larger trees this is much faster than distTips. Regards, Klaus On Fri, Feb 24, 2017 at 11:03 AM, Eduardo Ascarrunz <ear...@gmail.com<mailto:ear...@gmail.com>> wrote: Hi Justyna, If you want patristic distances (or node distances) you can use distTips from the adephylo package. To make edgelabels show the branch lengths you can use edgelabels(tr$edge.length) Does that do what you wanted? Cheers, Eduardo 2017-02-23 16:41 GMT+01:00 Wierzbinska, Justyna <j.wierzbin...@dkfz-heidelberg.de<mailto:j.wierzbin...@dkfz-heidelberg.de>>: Dear Ape users, I’be grateful for your help with my ape problems. I find it difficult to figure out how I can look at the distances between the main nodes generated in the phylogenetic tree below. My idea is to extract the distances between NBCs to hiMBCs. Somehow looking at the exemplary object tr and using tr$edge and tr$edge.length it doesn’t seem to be an easy task. [cid:part1.C97E7A27.01EB5ADD@uq.edu.au] I’ve tried to add node labels using nodelabels() and edge labels but somehow the assigned labels are different then the coordinates stored in the tr$edge would suggest (when I look at the tip projection). Any ideas how I can do it in an automatic way? Is it just a plotting problem that the coordinates of edges don’t correspond to what I see in the tree. Thank you very much. Kind regards, Justyna Division of Epigenomics and Cancer Risk Factors (C010) German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 280 69120 Heidelberg Germany +49 6221 42<tel:+49%206221%2042> 3359 j.wierzbin...@dkfz-heidelberg.de<mailto:j.wierzbin...@dkfz-heidelberg.de> [cid:image002.png@01D2929C.51A0C590] Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org<mailto:R-sig-phylo@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.org/
_______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
