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>
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$edge.length)
>
> Does that do what you wanted?
>
> Cheers,
>
> Eduardo
>
> 2017-02-23 16:41 GMT+01:00 Wierzbinska, Justyna <j.wierzbinska@dkfz-
> heidelberg.de>:
>
>>
>>
>> Dear Ape users,
>>
>>
>>
>> I’be grateful for your help with my ape problems.
>>
>> I find it difficult to figure out how I can look at the distances between
>> the main nodes generated in the phylogenetic tree below. My idea is to
>> extract the distances between NBCs to hiMBCs. Somehow looking at the
>> exemplary object tr and using tr$edge and tr$edge.length it doesn’t seem to
>> be an easy task.
>>
>>
>>
>>
>>
>> *[image: cid:part1.C97E7A27.01EB5ADD@uq.edu.au]*
>>
>>
>>
>> I’ve tried to add node labels using nodelabels() and edge labels but
>> somehow the assigned labels are different then the coordinates stored in
>> the tr$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
>>
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>>
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>>
>>
>>
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>>
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-- 
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/
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