[R-sig-phylo] plot.cophylo: some edges missing

Discussion:

Juan Antonio Balbuena

2018-03-13 16:09:53 UTC

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: ***@uv.es <mailto:***@uv.es>tel. +34 963 543
658 fax +34 963 543 733
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*NOTE!*For shipments by EXPRESS COURIER use the following street address:
C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

_______________________________________________
R-sig-phylo mailing list - R-sig-***@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/

Liam J. Revell

2018-03-13 16:12:40 UTC

Permalink

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/

Post by Juan Antonio Balbuena
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)
Rotating nodes to optimize matching...
Done.
plot.cophylo(obj, links.lwd=1, link.lty=2, fsize=0.4, pts=FALSE,
link.type="curved")
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-***@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/

Juan Antonio Balbuena

2018-03-13 16:27:50 UTC

Permalink

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

Post by Liam J. Revell
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
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/

Post by Juan Antonio Balbuena
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)
Rotating nodes to optimize matching...
Done.
plot.cophylo(obj, links.lwd=1, link.lty=2, fsize=0.4, pts=FALSE,
link.type="curved")
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: ***@uv.es <mailto:***@uv.es>tel. +34 963 543
658 fax +34 963 543 733
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*NOTE!*For shipments by EXPRESS COURIER use the following street address:
C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

_______________________________________________
R-sig-phylo mailing list - R-sig-***@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-***@r-project.org/

Liam J. Revell

2018-03-13 16:38:32 UTC

Permalink

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/

Post by Juan Antonio Balbuena
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

Post by Juan Antonio Balbuena
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)
Rotating nodes to optimize matching...
Done.
plot.cophylo(obj, links.lwd=1, link.lty=2, fsize=0.4, pts=FALSE,
link.type="curved")
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

Juan Antonio Balbuena

2018-03-13 16:44:57 UTC

Permalink

Worked like a charm.

¡Gracias!

Post by Liam J. Revell
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/

Post by Juan Antonio Balbuena
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

Post by Liam J. Revell
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
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/

Post by Juan Antonio Balbuena
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)
Rotating nodes to optimize matching...
Done.
plot.cophylo(obj, links.lwd=1, link.lty=2, fsize=0.4, pts=FALSE,
link.type="curved")
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