Florian and list, Great ideas to use getDescendants! Worked as advertised. Thanks for the help!
BL On Thu, Sep 15, 2016 at 8:55 AM, Liam J. Revell <liam.rev...@umb.edu> wrote: > I'm sure Florian's solution works, though I haven't tried it. > > Here is another one that may work that I just posted to my blog: > > http://blog.phytools.org/2016/09/collapsing-clades-of-foo-huh.html > > 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 9/15/2016 1:57 AM, Florian Boucher wrote: > >> I don't really know what you mean by 'hard-coding', but here is what I >> could think of (it is probably not optimal, but should work pretty >> quickly if your tree does not have thousands of tips): >> >> First, borrow 'getDescendants' from phytools: >> >> getDescendants<-function(tree,node,curr=NULL){ >> if(is.null(curr)) curr<-vector() >> daughters<-tree$edge[which(tree$edge[,1]==node),2] >> curr<-c(curr,daughters) >> w<-which(daughters>=length(tree$tip)) >> if(length(w)>0) for(i in 1:length(w)) >> curr<-getDescendants(tree,daughters[w[i]],curr) >> return(curr) >> } >> >> Then, traverse the tree and check whether each clade contains only tips >> named 'foo'. If this is the case, rename the first tip and label others >> 'to_rm'. >> >> # assuming your tree is dichotomic, tips are numbered 1:ntips and >> internal nodes (ntips+1):(2*ntips-1) >> ntips=length(tree$tip.label) >> reorder.phylo(tree,order='cladewise') # to make sure that we always >> traverse the tree from root to tips >> for (i in c(ntips+1):(2*ntips-1)){ >> des= getDescendants(tree,node=i,curr=NULL) >> tips=des[which(des<(ntips+1))] ; intern=des[-which(des<(ntips+1))] >> if (all(tree$tip.label[tips]=='foo')){ >> tree$tip.label[tips[1]]=paste(length(tips),"foo's",sep='_') >> tree$tip.label[tips[2:length(tips)]]='to_rm' >> } >> } >> >> plot(tree) >> >> # remove tips labelled 'to_rm' >> tree2=drop.tip(tree,tip='to_rm') >> plot(tree2) >> >> Let's hope this works as you wished. >> >> Cheers, >> Florian >> >> >> 2016-09-14 22:04 GMT+02:00 branchlizard . <branch.liz...@gmail.com >> <mailto:branch.liz...@gmail.com>>: >> >> Florian and list, >> >> What is your preferred method to go about this? phy$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 <mailto: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 <mailto: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 <mailto: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/ >> <http://faculty.umb.edu/liam.revell/> >> > email: liam.rev...@umb.edu <mailto: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 >> <mailto:R-sig-phylo@r-project.org> >> >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> >> Searchable archive at http://www.mail-archive.com/r- >> >> sig-ph...@r-project.org/ <http://sig-ph...@r-project.org/> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> <mailto:R-sig-phylo@r-project.org> >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> Searchable archive at >> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> <http://www.mail-archive.com/r-sig-phylo@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/
