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.rev...@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$Nnode, e.g.,, all internal nodes. You
can see that
55+(1:47)
gives a vector of node numbers that is not the same as 55 to 47.
If it isn't working right - maybe it is that you have polytomies? I think you
should have n-1 internal nodes (53 in your case). Try multi2di (from ape) for
polytomy resolution and see if it works as desired.
~Dan Rabosky
Kind regards,
Thierry
Thierry Janssens
Postdoctoral researcher
Delft University of Technology
Bionanoscience
Kavli Institute of Nanoscience
Lorentzweg 1
2628LJ Delft
the Netherlands
Tel: +31 15 2781175
Fax:+31 15 2781202
e-mail: t.k.s.janss...@tudelft.nl
-----Original Message-----
From: Liam J. Revell [mailto:liam.rev...@umb.edu]
Sent: donderdag 17 maart 2011 16:11
To: Thierry Janssens - TNW
Cc: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] reverse order plotting of newick tree/phylo
object
Hi Thierry,
There might be a more elegant way to do this, but you can just apply the
"ape" function rotate() to each node number of the tree (excluding
tips).
I.e.
tr2<-tree
for(i in length(tr2$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.rev...@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.janss...@tudelft.nl<mailto:t.k.s.janss...@tudelft.nl>
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