Re: [R-sig-phylo] plot.cophylo: how to change the colour of host-parasite associations
Hi
No, I didn't have the latest version. Now I have and it works
nicely.
Thank you very much for your continous effort to develop
phytools. The package is amazing.
All the best
Juan
El 12/09/2016 a las 16:40, Liam J.
Revell escribió:
Hi Juan.
This update is pretty new so is probably not on CRAN. Do you have
the latest version of phytools installed from GitHub? To install
from GitHub I recommend using the package devtools:
## in a fresh R session
install.packages("devtools") ## install devtools from CRAN
library(devtools)
install_github("liamrevell/phytools")
library(phytools)
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 9/12/2016 9:35 AM, Juan Antonio Balbuena wrote:
Hi
I wonder whether there is a way to change the colours of the
host-parasite associations in plot.cophylo in phytools.
I tried:
t1 <- rtree(10) t2 <- rtree(10) obj <- cophylo(t1,t2)
plot.cophylo(obj,
link.col= "red")
But the links appear in black. According to the code in
https://github.com/liamrevell/phytools/blob/master/R/cophylo.R,
link.col
is set in the internal function makelinks (l. 119), being
"black" the
default. However, in function plot.cophylo (l. 151-152), it is
indicated
if(hasArg(link.col)) link.col<-list(...)$link.col else
link.col<-"black"
So I can't see why link.color = "red" didn't work.
Eventually I wish to code each host-parasite association as a
colour in
function of a continuous trait.
Actually I managed to do it with cophyloplot in ape
cophyloplot(TreeH, TreeP, assoc=links, use.edge.length=FALSE,
gap=0, space=20, col=links$Col)
Where links$Col is a vector of colours ranging from "red" to
"blue".
However, I'd rather use plot.cophylo to the advantage of the
optimal
rotation of branches.
Any help will be most welcome.
Juan A. Balbuena
--
Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
University of Valencia
http://www.uv.es/~balbuena
P.O. Box 22085
http://www.uv.es/cophylpaco
46071 Valencia, Spain
e-mail: j.a.balbu...@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-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/
--
Dr.
Juan
A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary
Biology
University of
Valencia
http://www.uv.es/~balbuena
P.O. Box
22085
http://www.uv.es/cophylpaco
46071 Valencia,
Spain
e-mail: j.a.balbu...@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.
__
Re: [R-sig-phylo] plot.cophylo: how to change the colour of host-parasite associations
Hi Juan.
This update is pretty new so is probably not on CRAN. Do you have the
latest version of phytools installed from GitHub? To install from GitHub
I recommend using the package devtools:
## in a fresh R session
install.packages("devtools") ## install devtools from CRAN
library(devtools)
install_github("liamrevell/phytools")
library(phytools)
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 9/12/2016 9:35 AM, Juan Antonio Balbuena wrote:
Hi
I wonder whether there is a way to change the colours of the
host-parasite associations in plot.cophylo in phytools.
I tried:
t1 <- rtree(10) t2 <- rtree(10) obj <- cophylo(t1,t2) plot.cophylo(obj,
link.col= "red")
But the links appear in black. According to the code in
https://github.com/liamrevell/phytools/blob/master/R/cophylo.R, link.col
is set in the internal function makelinks (l. 119), being "black" the
default. However, in function plot.cophylo (l. 151-152), it is indicated
if(hasArg(link.col)) link.col<-list(...)$link.col else link.col<-"black"
So I can't see why link.color = "red" didn't work.
Eventually I wish to code each host-parasite association as a colour in
function of a continuous trait.
Actually I managed to do it with cophyloplot in ape
cophyloplot(TreeH, TreeP, assoc=links, use.edge.length=FALSE,
gap=0, space=20, col=links$Col)
Where links$Col is a vector of colours ranging from "red" to "blue".
However, I'd rather use plot.cophylo to the advantage of the optimal
rotation of branches.
Any help will be most welcome.
Juan A. Balbuena
--
Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
University of Valencia
http://www.uv.es/~balbuena
P.O. Box 22085
http://www.uv.es/cophylpaco
46071 Valencia, Spain
e-mail: j.a.balbu...@uv.es tel. +34 963
543 658fax +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-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/
___
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/
[R-sig-phylo] plot.cophylo: how to change the colour of host-parasite associations
Hi I wonder whether there is a way to change the colours of the host-parasite associations in plot.cophylo in phytools. I tried: t1 <- rtree(10) t2 <- rtree(10) obj <- cophylo(t1,t2) plot.cophylo(obj, link.col= "red") But the links appear in black. According to the code in https://github.com/liamrevell/phytools/blob/master/R/cophylo.R, link.col is set in the internal function makelinks (l. 119), being "black" the default. However, in function plot.cophylo (l. 151-152), it is indicated if(hasArg(link.col)) link.col<-list(...)$link.col else link.col<-"black" So I can't see why link.color = "red" didn't work. Eventually I wish to code each host-parasite association as a colour in function of a continuous trait. Actually I managed to do it with cophyloplot in ape cophyloplot(TreeH, TreeP, assoc=links, use.edge.length=FALSE, gap=0, space=20, col=links$Col) Where links$Col is a vector of colours ranging from "red" to "blue". However, I'd rather use plot.cophylo to the advantage of the optimal rotation of branches. Any help will be most welcome. Juan A. Balbuena -- Dr. Juan A. Balbuena Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia http://www.uv.es/~balbuena P.O. Box 22085 http://www.uv.es/cophylpaco 46071 Valencia, Spain e-mail: j.a.balbu...@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-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/
