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> >> >> >> _______________________________________________ >> 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-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C5ef523436a534817f90908d6f3103b50%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C636963648377367229&sdata=EBU1sn4OJ7b0PG57yevqBu0Er79LrQdU4kr%2FPqvSDsU%3D&reserved=0 >> >> >> Searchable archive at >> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C5ef523436a534817f90908d6f3103b50%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C636963648377367229&sdata=Vp65xsQlCHdpj%2FvSrFRMgepSg%2BVYOC6H0Nd30TsjdWw%3D&reserved=0 >> >> _______________________________________________ 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/
