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 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...
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
_______________________________________________
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-phylo@r-project.org/