I also just pushed an update to phytools that now permits exact
duplicate tip labels in a cophylo plot. You can get this update by running:
library(devtools)
install_github("liamrevell/phytools")
with devtools installed.
More details about the update can be seen on my blog:
http://blog.phytools.org/2019/06/update-to-plotcophylo-to-permit.html.
All the best, Liam
Liam J. Revell
Associate Professor, University of Massachusetts Boston
Profesor Asistente, Universidad Católica de la Ssma Concepción
web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
Academic Director UMass Boston Chile Abroad (starting 2019):
https://www.umb.edu/academics/caps/international/biology_chile
On 6/17/2019 9:00 AM, Liam J. Revell wrote:
> Yes. Just to echo Juan, there should be no problem in your case if you
> specify the desired matching in your association table, provided to
> cophylo via the argument assoc.
>
> In your case, for instance, you may have M._loti_1 and M._loti_2 in one
> tree, but just M._loti in the other, in which case your assoc table
> would have:
>
> "M._loti_1" "M._loti"
> "M._loti_2" "M._loti"
>
> as two of its rows. There is an example of how to use the association
> table on my blog in a few places, including here:
> http://blog.phytools.org/2016/08/new-user-control-of-plot-method-for.html.
>
> Note that the method does produce an error if two tips in a single tree
> have tip labels that match exactly. I'm not sure that this needs to be
> the case so I may try to fix it.
>
> Liam J. Revell
> Associate Professor, University of Massachusetts Boston
> Profesor Asistente, Universidad Católica de la Ssma Concepción
> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
>
> Academic Director UMass Boston Chile Abroad (starting 2019):
> https://www.umb.edu/academics/caps/international/biology_chile
>
> On 6/17/2019 6:40 AM, Juan Antonio Balbuena wrote:
>> Hi
>>
>> I don't see why you cannot it with cophylo. All comes down to
>> configuring assoc (matrix containing the tip labels in tr1 to match to
>> the tip labels in tr2) correctly.
>>
>> All the best
>>
>> Juan A. Balbuena
>>
>> El 17/06/2019 a las 12:03, Sa
>> El 17/06/2019 a las 12:03, Saleh Rahimlouye Barabi escribió:
>>>
>>> Hello,
>>>
>>> I want to plot two phylogenetic trees face-to-face using
>>> phytools::cophylo function. I see there is no possibility to connect
>>> 2 or 3 same taxa in a tree to one taxon in the other tree (attached).
>>> Is there anyway doing this in R?
>>>
>>> Best
>>>
>>> Saleh Rahimlou
>>>
>>> Ph.D. Candidate
>>>
>>> Department of Botany and Ecology
>>>
>>> University of Tartu
>>>
>>> 14A Ravila, 50411 Tartu
>>>
>>> Estonia
>>>
>>> Email: saleh.rahim...@ut.ee <mailto:saleh.rahim...@ut.ee>
>>>
>>>
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>>>
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