Thanks...here's the code. However, it looks like the output
I am processing does not actually come with post-order
labeling.
I.e., in the 2nd plot below:
node 1 should be labeled 1
node 10 should be labeled 2
node 2 should be labeled 3
node 14 should be labeled 4
node 3 should be labeled 5
...etc...
What is the name of this sort of ordering? Or are there 2
sorts of post-ordering?
Cheers,
Nick
================
trstr =
"((((1:61.9979,2:61.9979):10.0994,3:72.0973):30.5957,(4:97.17,5:97.17):5.52294):165.913,(((((6:45.8837,7:42.7899):90.6427,8:11.748):9.81895,((9:71.9983,10:30.1075):59.5189,(((11:48.3447,12:48.3447):77.8739,(13:86.8531,(14:53.665,15:53.665):33.1881):39.3656):26.0816,((16:94.7537,17:94.7537):44.1509,(18:82.3045,(19:72.9737,20:72.9737):9.33074):56.6002):13.3956):27.9983):10.886):22.824,21:214.009):34.3554,(22:186.877,23:186.877):61.4866):20.2417);"
tr = read.tree(file="", text=trstr)
plot(tr)
nodelabels()
tr2 = reorder(tr, order="pruningwise")
plot(tr2)
nodelabels()
internal_nodenums_in_postorder = unique(tr2$edge[,1])
internal_nodenums_in_postorder =
internal_nodenums_in_postorder - length(tr2$tip.label)
tr3 = tr2
tr3$node.label[internal_nodenums_in_postorder] = 1:tr3$Nnode
plot(tr3)
nodelabels(tr3$node.label)
================
On 9/14/11 6:36 PM, Liam J. Revell wrote:
Hi Nick.
If you use the function
reorder.phylo(...,order="pruningwise") the resultant tree
edge matrix is suitable for post-order traversal (i.e., the
daughters always precede the parents in top-to-bottom matrix
traversal). This might be helpful for what you would like to
do - for instance if you just label the nodes as they are
first encountered in the matrix this would be in the order
of a post-order traversal of the tree.
All the best, Liam
--
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley
Graduate Student Instructor, IB200B
Principles of Phylogenetics: Ecology and Evolution
http://ib.berkeley.edu/courses/ib200b/
http://phylo.wikidot.com/
Lab websites:
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http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page:
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page:
http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: mat...@berkeley.edu
Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140
-----------------------------------------------------
"[W]hen people thought the earth was flat, they were wrong.
When people thought the earth was spherical, they were
wrong. But if you think that thinking the earth is spherical
is just as wrong as thinking the earth is flat, then your
view is wronger than both of them put together."
Isaac Asimov (1989). "The Relativity of Wrong." The
Skeptical Inquirer, 14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
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