Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

2016-09-15 Thread branchlizard . 
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  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$tip.label[tips[2:length(tips)]]='to_rm'
>> }
>> }
>>
>> plot(tree)
>>
>> # remove tips labelled 'to_rm'
>> tree2=drop.tip(tree,tip='to_rm')
>> plot(tree2)
>>
>> Let's hope this works as you wished.
>>
>> Cheers,
>> Florian
>>
>>
>> 2016-09-14 22:04 GMT+02:00 branchlizard . > >:
>>
>> Florian and list,
>>
>> What is your preferred method to go about this? phy$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
>> > 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 .
>> >:
>>
>> 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
>> > 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
>>

Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

2016-09-15 Thread branchlizard . 
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  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$tip.label[tips[2:length(tips)]]='to_rm'
>> }
>> }
>>
>> plot(tree)
>>
>> # remove tips labelled 'to_rm'
>> tree2=drop.tip(tree,tip='to_rm')
>> plot(tree2)
>>
>> Let's hope this works as you wished.
>>
>> Cheers,
>> Florian
>>
>>
>> 2016-09-14 22:04 GMT+02:00 branchlizard . > >:
>>
>> Florian and list,
>>
>> What is your preferred method to go about this? phy$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
>> > 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 .
>> >:
>>
>> 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
>> > 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

Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

2016-09-15 Thread Liam J. Revell 

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 . >:

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
> 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 .
>:

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
> 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

Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

2016-09-15 Thread Florian Boucher 
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 . :

> 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 
> 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 . :
>>
>>> 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 
>>> 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]]

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Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

2016-09-14 Thread branchlizard . 
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 
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 . :
>
>> 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 
>> 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]]

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Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

2016-09-14 Thread Florian Boucher 
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 . :

> 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 
> 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]]
> >>
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> >>
>
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>
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Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

2016-09-14 Thread branchlizard . 
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  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]]
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>> Searchable archive at http://www.mail-archive.com/r-
>> sig-ph...@r-project.org/
>>
>>

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Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

2016-09-12 Thread Liam J. Revell 
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

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Re: [R-sig-phylo] Collapse a clade by tip labels while maintaining phylogenetic position

2016-09-12 Thread Hilmar Lapp 
Hi BranchLizard,

> On Sep 12, 2016, at 3:46 PM, branchlizard .  wrote:
> 
> I have posted this question at Stack Overflow. I hope this doesn't violate
> any community rules about double posting.

It doesn’t, but why not include the URL so that people can avoid answering what 
may already have been answered?

  -hilmar
-- 
Hilmar Lapp -:- genome.duke.edu -:- lappland.io

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