[R-sig-phylo] reverse order plotting of newick tree/phylo object

Liam J. Revell liam.revell at umb.edu
Thu Mar 17 20:18:49 CET 2011


Dan is right on - and I also suspect that the issue of the non-rotating 
node is probably due to a polytomy at that node.

Thanks for the insight Dan.

- Liam

-- 
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.revell at umb.edu
blog: http://phytools.blogspot.com

On 3/17/2011 12:26 PM, Dan Rabosky wrote:
>
>> But can you explain to me what is the rationale behind this? There are
>> only 47 nodes and 54 tips. How can the nodes from 55 to 47 than be
>> rotated?
>
>
> Liam's code is rotating nodes 55+(1:47), rather than 55 to 47. The internal node indexing in ape's phylo class starts with "number of tips plus 1". Thus, using rotate on nodes starting with length(phy$tip.label) + 1 means it is starting with node 56 (the root node) and going through length(phy$tip.label) + phy$Nnode, e.g.,, all internal nodes. You can see that
>
> 55+(1:47)
>
> gives a vector of node numbers that is not the same as 55 to 47.
>
> If it isn't working right - maybe it is that you have polytomies? I think you should have n-1 internal nodes (53 in your case). Try multi2di (from ape) for polytomy resolution and see if it works as desired.
>
> ~Dan Rabosky
>
>
>
>>
>> Kind regards,
>>
>> Thierry
>>
>> Thierry Janssens
>> Postdoctoral researcher
>> Delft University of Technology
>> Bionanoscience
>> Kavli Institute of Nanoscience
>> Lorentzweg 1
>> 2628LJ Delft
>> the Netherlands
>> Tel: +31 15 2781175
>> Fax:+31 15 2781202
>> e-mail: t.k.s.janssens at tudelft.nl
>>
>> -----Original Message-----
>> From: Liam J. Revell [mailto:liam.revell at umb.edu]
>> Sent: donderdag 17 maart 2011 16:11
>> To: Thierry Janssens - TNW
>> Cc: r-sig-phylo at r-project.org
>> Subject: Re: [R-sig-phylo] reverse order plotting of newick tree/phylo
>> object
>>
>> Hi Thierry,
>>
>> There might be a more elegant way to do this, but you can just apply the
>> "ape" function rotate() to each node number of the tree (excluding
>> tips).
>>
>> I.e.
>>
>>> tr2<-tree
>>> for(i in length(tr2$tip)+1:tr2$Nnode) tr2<-rotate(tr2,i)>  plot(tr2)
>>
>> [rotate() may also be able to take a vector of nodes, but I was not able
>> to get this to work.]
>>
>> - Liam
>>
>> --
>> Liam J. Revell
>> University of Massachusetts Boston
>> web: http://faculty.umb.edu/liam.revell/
>> email: liam.revell at umb.edu
>> blog: http://phytools.blogspot.com
>>
>> On 3/17/2011 10:51 AM, Thierry Janssens - TNW wrote:
>>> Dear R-sig-phylo,
>>>
>>>
>>>
>>> I am looking for a method to plot an unrooted tre/phylo object e in
>>> the reverse order (of the tip labels). Like all the nodes would have
>>> rotated.
>>>
>>>
>>>
>>> Any of you has an idea?
>>>
>>>
>>>
>>> Kind regards,
>>>
>>>
>>>
>>> Thierry
>>>
>>>
>>>
>>> Thierry Janssens
>>>
>>> Postdoctoral researcher
>>>
>>> Delft University of Technology
>>>
>>> Bionanoscience
>>>
>>> Kavli Institute of Nanoscience
>>>
>>> Lorentzweg 1
>>>
>>> 2628LJ Delft
>>>
>>> the Netherlands
>>>
>>> Tel: +31 15 2781175
>>>
>>> Fax:+31 15 2781202
>>>
>>> e-mail: t.k.s.janssens at tudelft.nl<mailto:t.k.s.janssens at tudelft.nl>
>>>
>>>
>>>
>>>
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>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>
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