Hi,

Yes!! It worked! Thank you so much!

BTW, is there a way to supress the tip labels? show.tip.label=FALSE does not work.

All the best

Juan


El 13/03/2018 a las 17:12, Liam J. Revell escribió:
Hola Juan.

I'm guessing you are using an old version of phytools as this bug has been identified & should be fixed (http://blog.phytools.org/2017/08/bug-fix-in-plotcophylo-for-co.html). If you update to the latest CRAN version that should take care of it, but I recommend updating to the latest version on GitHub using devtools as follows:

library(devtools)
install_github("liamrevell/phytools")

Let us know if the problem persists.

Saludos, Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/

On 3/13/2018 11:09 AM, Juan Antonio Balbuena wrote:
Hi all

I am using cophylo in phytools to draw a large tanglegram (phylogenies with 29 and 129 terminals, and 129 associations between them). The problem is that only a fraction of the edges of the larger tree (to the right) are plotted.

This is the syntax used


obj <- cophylo(euglossini29, orchids, links, rotate.multi=TRUE)

#which apparently works well:

Rotating nodes to optimize matching...
Done.

plot.cophylo(obj, links.lwd=1, link.lty=2, fsize=0.4, pts=FALSE, link.type="curved")

# the resulting plot can be visualized here: https://www.uv.es/balbuena/PDF/Rplot.pdf


I usually work in RStudio but I got the same result in an ordinary R console. In addition, when I use cophyloplot (ape) with the same input, I am able to get the tanglegram.

I wonder what the problem might be and any help will by much appreciated.

Juan A. Balbuena



--

Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
Symbiont Ecology and Evolution Lab
University of Valencia http://www.uv.es/~balbuena <http://www.uv.es/%7Ebalbuena> P.O. Box 22085 http://www.uv.es/cophylpaco <http://www.uv.es/cavanilles/zoomarin/index.htm>
46071 Valencia, Spain
e-mail: j.a.balbu...@uv.es <mailto:j.a.balbu...@uv.es>tel. +34 963 543 658    fax +34 963 543 733
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