Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position
Liam,
Your solution worked as well! Thanks for the help and your wonderful blog
post.
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.r
Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position
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/
Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position
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/
Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position
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$tip.label=='foo') >> ,subtree=TRUE) >> >> the dropped tips do not maintain their position in the tree. Rather, they >> are all grouped at the end (counted properly however). Is there anyway to >> collapse a clade by tip labels and maintain its position >> >> >> >> BranchLizard >> >> [[alternative HTML version deleted]] >> >> ___ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at http://www.mail-archive.com/r- >> sig-ph...@r-project.org/ >> >> [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position
I have posted this question at Stack Overflow. I hope this doesn't violate any community rules about double posting. I probably could have worded the title better, but I am wanting to collapse any clade within a phylogenetic tree (even if the clade has one member) which has a tip label of "foo" and then count the number of tips which were dropped from that specific clade and create a branch with a tip label displaying 35 foos. The counting portion is easy; however, when I use drop.tip(rooted.tree,tip=which(rooted.tree$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-phylo@r-project.org/
