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:


Let us know if the problem persists.

Saludos, Liam

Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de BiologĂ­a
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...

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

R-sig-phylo mailing list - R-sig-phylo@r-project.org
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

Reply via email to