Worked like a charm.
¡Gracias!
El 13/03/2018 a las 17:38, Liam J. Revell escribió:
Try ftype="off".
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 11:27 AM, Juan Antonio Balbuena wrote:
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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