CODEWITHSUNDEEP
rtreedataframephylogeny
Rachit Agrawal
Rachit Agrawal

Reputation: 3343

R: newick tree from list of lists

I am working on to create a newick tree out of list of childs. I have a list of lists where the list name is the parent name and list element are the childs. Here is an example: 

$`825`
[1] 824

$`824`
[1] 823

$`823`
[1] 822

$`822`
[1] 821

$`821`
[1] 820 777

$`820`
[1] 819 816 789 787 785 783

$`789`
[1] 788

$`787`
[1] 786

$`785`
[1] 784

$`783`
[1] 782

$`777`
[1] 776

Hence the output I want is phylo tree in newick format as follows:

825(824(823(822(821(820(819,816,789(788),787,785(784),783(782)),777(776)))))

What is the best way to do this? One way is to write a recursive function that traverses in depth first order and creates the tree. But in R recursions are known to be bad.

Thanks.

Upvotes: 3

Views: 810

Answers (1)

Róisín Grannell
Róisín Grannell

Reputation: 1978

If you are looking for a pre-canned solution I believe the bioconductor/ape library has a list -> newick converter

http://www.r-phylo.org/wiki/HowTo/InputtingTrees

Otherwise, I wrote some code a while ago that did just this for the neighbour-joining algorithm; it's extremely terse (written in a tight deadline), but perhaps it will help.

https://github.com/rgrannell1/NJ/blob/master/main.R

hope that helps somewhat

Upvotes: 1

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