Dear Klaus,

Thanks a lot for your help

and what is in that case xx and yy?


From: Klaus Schliep []
Sent: Friday, February 24, 2017 6:13 PM
To: Eduardo Ascarrunz
Cc: Wierzbinska, Justyna;
Subject: Re: [R-sig-phylo] distances between the nodes

Dear Justyna
tr$edge does not store coordinates, see help(phylo).
if you want the coordinates of the nodes of your last plotted tree you can get 
tree = rtree(5)
last_plot = get("last_plot.phylo", envir = .PlotPhyloEnv)
last_plot$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.

On Fri, Feb 24, 2017 at 11:03 AM, Eduardo Ascarrunz 
<<>> 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 

Does that do what you wanted?



2017-02-23 16:41 GMT+01:00 Wierzbinska, Justyna 

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.


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,

Division of Epigenomics and Cancer Risk Factors (C010)

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 280
69120 Heidelberg
+49 6221 42<tel:+49%206221%2042> 3359<>

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Klaus Schliep
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Revell Lab, University of Massachusetts Boston
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