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 allI 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.pdfI 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
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