Re: [R-sig-phylo] cophylo

2019-06-17 Thread Liam Revell 
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 
>>>
>>>
>>> ___
>>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylodata=02%7C01%7Cliam.revell%40umb.edu%7C5ef523436a534817f90908d6f3103b50%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C636963648377367229sdata=EBU1sn4OJ7b0PG57yevqBu0Er79LrQdU4kr%2FPqvSDsU%3Dreserved=0
>>>  
>>>
>>> Searchable archive at 
>>> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7C5ef523436a534817f90908d6f3103b50%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C636963648377367229sdata=Vp65xsQlCHdpj%2FvSrFRMgepSg%2BVYOC6H0Nd30TsjdWw%3Dreserved=0
>>>  
>>>

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Re: [R-sig-phylo] cophylo

2019-06-17 Thread Gian Maria Niccolò Benucci 
Maybe look at the function tanglegram() in the dendexted R package.

Good luck!

G.



On Mon, 17 Jun 2019 at 06:03, Saleh Rahimlouye Barabi 
wrote:

> 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
>
>
> ___
> 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/
>


-- 
Gian Maria Niccolò Benucci, Ph.D.
Postdoctoral research associate
Michigan State University
Department of Plant, Soil and Microbial Sciences
Great Lakes Bioenergy Research Center (GLBRC)
1066 Bogue Street - 48825 East Lansing, MI
Lab: +1 (517) 844-6966
Emails: gian.benu...@gmail.com, *benu...@msu.edu *

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protect the environment! -*

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Re: [R-sig-phylo] cophylo

2019-06-17 Thread Liam Revell 
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 
>>
>>
>> ___
>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylodata=02%7C01%7Cliam.revell%40umb.edu%7C5ef523436a534817f90908d6f3103b50%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C636963648377367229sdata=EBU1sn4OJ7b0PG57yevqBu0Er79LrQdU4kr%2FPqvSDsU%3Dreserved=0
>>  
>>
>> Searchable archive at 
>> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2Fdata=02%7C01%7Cliam.revell%40umb.edu%7C5ef523436a534817f90908d6f3103b50%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C636963648377367229sdata=Vp65xsQlCHdpj%2FvSrFRMgepSg%2BVYOC6H0Nd30TsjdWw%3Dreserved=0
>>  
>>

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Re: [R-sig-phylo] cophylo

2019-06-17 Thread Juan Antonio Balbuena 

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 


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--

Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
Symbiont Ecology and Evolution Lab
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


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[R-sig-phylo] cophylo

2019-06-17 Thread Saleh Rahimlouye Barabi 
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



Rplot03.pdf
Description: Rplot03.pdf
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