Oouups, I forgot a line it should have been
library(ape)
tree = rtree(5)
plot(tree)
nodelabels()
tiplabels()
last_plot = get("last_plot.phylo", envir = .PlotPhyloEnv)
The xx and yy are the coordinates of the node (of the last plot) which are
the numbers in tree$edge.
points(last_plot$xx, last_plot$yy)
If you have these coordinates you can write your own plot function
plot(last_plot$xx, last_plot$yy)
for(i in 1:nrow(tree$edge))lines(last_plot$xx[tree$edge[i,]],
last_plot$yy[tree$edge[i,]])
Cheers,
Klaus
On Wed, Mar 1, 2017 at 8:58 AM, Wierzbinska, Justyna <
j.wierzbin...@dkfz-heidelberg.de> wrote:
> 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$yy contain the coordinates of the nodes.
>
> there is also a (generic) function cophenetic() in ape to compute the
> patristic distance and for larger trees this is much faster than distTips.
>
> Regards,
>
> Klaus
>
>
>
>
>
> On Fri, Feb 24, 2017 at 11:03 AM, Eduardo Ascarrunz <ear...@gmail.com>
> wrote:
>
> Hi Justyna,
>
>
>
> If you want patristic distances (or node distances) you can use distTips
> from the adephylo package.
>
>
>
> To make edgelabels show the branch lengths you can use
> edgelabels(tr$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
>
> +49 6221 42 <+49%206221%2042> 3359
>
> j.wierzbin...@dkfz-heidelberg.de
>
>
>
> 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
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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>
>
>
>
> _______________________________________________
> 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-ph...@r-project.org/
>
>
>
>
> --
>
> Klaus Schliep
> Postdoctoral Fellow
> Revell Lab, University of Massachusetts Boston
> http://www.phangorn.org/
>
--
Klaus Schliep
Postdoctoral Fellow
Revell Lab, University of Massachusetts Boston
http://www.phangorn.org/
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