[Phylobase-devl] Fwd: [R-sig-phylo] Tree manipulations (pruning and grafting)

[Brian O'Meara]

A question that might of interest for phylobase (i.e., should we try  
to advocate for mesquite<->phylo4 interactions rather than just  
mesquite<->phylo, will this change the priority of any features in  
phylobase, etc.).

Brian

Begin forwarded message:

> From: Wayne Maddison <wmaddisn at interchange.ubc.ca>
> Date: October 6, 2009 12:10:42 PM EDT
> To: Sam Brown <s_d_j_brown at hotmail.com>
> Cc: r-sig-phylo at r-project.org
> Subject: Re: [R-sig-phylo] Tree manipulations (pruning and grafting)
>
> This and the previous query about importing a phylogeny into R  
> raises a question that was embedded in an email several months ago:   
> How useful would it be for you to be able to call a function like  
> newphylo <- mesquite.editTree(phylo) that would put a tree from R  
> into a Mesquite window, you would edit it there, hit a button, and  
> then the modified tree would be returned as the function result in R?
>
> We might be able to offer a test version of that soon, if there is  
> interest.
>
> Wayne
>
>
> At 12:37 PM +1300 6.10.2009, Sam Brown wrote:
>> Dear all
>>
>> To prepare for SH tests between optimised and "expected" trees,  
>> I've been attempting to do tree manipulations in R. Pruning is easy  
>> with the dual functions of extract.clade() and drop.tip(), however  
>> grafting the clade into a different place using bind.tree() is  
>> proving much more difficult.
>>
>> What seems to be happening is that during the tree binding process,  
>> some tips are becoming nodes and vice versa.
>>
>> Any help is much appreciated!
>>
>> Thank you!
>>
>> Sam
>>
>>
>> Some code:
>>
>> library(ape)
>> data(bird.orders)
>> phy<-bird.orders
>>
>> node<-43                                  #Node with taxa of  
>> interest (Columbiformes:Passeriformes)
>> site<-21                                   #Where above group is  
>> expected to be (In a clade with Struthioniformes:Anseriformes)
>>
>> j<-allDesc(node)                        #See function definition  
>> below
>> grp<-extract.clade(phy, node)
>> rest<-drop.tip(phy, j)
>>
>> tr<-bind.tree(rest, grp, where=site)
>>
>> plot(tr)                                    #Should get an error:  
>> "Error in plot.phylo(tr) : NA/NaN/Inf in foreign function call (arg  
>> 6)"
>>
>> write.tree(tr)                             #Can see Upupiformes as  
>> sister to NODE11, among others.
>>
>>
>>
>> where:
>>
>> allDesc<-function(node){
>>    N<-length(phy$tip.label)
>>
>>    index<-which(phy$edge[,1]==node)
>>    desc<-phy$edge[index,2]
>>
>>    taxa<-desc[desc<=N]
>>
>>    desc<-desc[desc>N]
>>
>>    while(length(desc)>=1){
>>        ind<-NULL
>>        for(i in 1:length(desc)){
>>            ind<-c(ind,which(phy$edge[,1]==desc[i]))
>>        }
>>        desc<-phy$edge[ind,2]
>>        taxa<-c(taxa,desc[desc<=N])
>>        desc<-desc[desc>N]
>>    }
>>    taxa
>> }
>> 			  		  
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>>
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>
>
> -- 
> --------------------------------------------------------
> Wayne Maddison
> Professor and Canada Research Chair
>         Depts. of Zoology and Botany and
>         Biodiversity Research Centre
> & Director
>         Beaty Biodiversity Museum
> 6270 University Boulevard
> University of British Columbia
> Vancouver, BC  V6T 1Z4   Canada
>
> email: wmaddisn at interchange.ubc.ca   FAX: +1 604 822-2416
>
> Mesquite: http://mesquiteproject.org
> MacClade: http://macclade.org
> Salticidae:  http://salticidae.org
> Tree of Life: http://tolweb.org
> Beaty Biodiversity Museum: http://beatymuseum.ubc.ca
> Home page: http://salticidae.org/wpm/home.html
>
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