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 <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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