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


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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