Florian and list, What is your preferred method to go about this? phy$tip.label? If so, how would one label a tip label from each clade of foo's without having to hard code the clade number? I am trying to prevent any hard coding.
BL On Wed, Sep 14, 2016 at 3:46 PM, Florian Boucher <floflobouc...@gmail.com> wrote: > Hi Branchlizard and list, > > in order to do this you would first need to rename one of the foo's in > each clade (I would always rename the first one) as '6 foo's', '4 foo's', > etc. > Then you can apply drop.tip on all the foos, as you did before. > > I hope this helps. > > Cheers, > Florian > > 2016-09-14 21:32 GMT+02:00 branchlizard . <branch.liz...@gmail.com>: > >> I would like to turn this >> >> http://i.imgur.com/chLdFmZ.jpg >> >> into this >> >> http://i.imgur.com/vSoe6mu.jpg >> >> >> My dataset and phylogeny is much more complex than this, but this is the >> basic idea. >> >> >> BL >> >> >> >> On Mon, Sep 12, 2016 at 8:16 PM, Liam J. Revell <liam.rev...@umb.edu> >> wrote: >> >> > I'm sure this is possible, but I really don't understand the question. >> > Maybe you could draw what you have in mind on a piece of paper and post >> a >> > picture of the paper.... >> > >> > 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 2:46 PM, branchlizard . wrote: >> > >> >> I have posted this question at Stack Overflow. I hope this doesn't >> violate >> >> any community rules about double posting. >> >> >> >> I probably could have worded the title better, but I am wanting to >> >> collapse >> >> any clade within a phylogenetic tree (even if the clade has one member) >> >> which has a tip label of "foo" and then count the number of tips which >> >> were >> >> dropped from that specific clade and create a branch with a tip label >> >> displaying 35 foos. >> >> >> >> The counting portion is easy; however, when I use >> >> >> >> drop.tip(rooted.tree,tip=which(rooted.tree$tip.label=='foo') >> >> ,subtree=TRUE) >> >> >> >> the dropped tips do not maintain their position in the tree. Rather, >> they >> >> are all grouped at the end (counted properly however). Is there anyway >> to >> >> collapse a clade by tip labels and maintain its position >> >> >> >> >> >> >> >> BranchLizard >> >> >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> >> 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-ph...@r-project.org/ >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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-ph...@r-project.org/ >> > > [[alternative HTML version deleted]] _______________________________________________ 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/
