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>
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--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/
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