[genoPlotR-help] matching ordering of phylog or dna_segs object

[Migun Shakya]

hi  Lionel,
That worked really well.

Thank you much for the quick response.

Migun
On Mar 12, 2014, at 4:41 PM, Lionel Guy <lionel.guy at icm.uu.se> wrote:

> Hi Migee,
> 
> There is no tutorial or method about that. One way to do that would the following:
> 
> Provided that your tree leaves and the names of your dna_segs are exactly the same (and are unique), you simply reorder the list containing the dna_segs according to the names of the leaves of the tree. For example, say you have 4 segments:
> 
> data(barto)
> # I'm making a fake tree:
> tree <- newick2phylog("(BQ:2.5,(BH:1.8,(BG:1,BB:0.8):1.9):3);")
> plot(tree)
> names(tree$leaves)
> # The dna_segs are ordered differently:
> names(barto$dna_segs)
> # I can now reorder the list containing the dna_segs according to the names of the leaves
> ds2 <- barto$dna_segs[names(tree$leaves)]
> # Now the dna_segs are ordered as the leaves, and I can plot accordingly:
> names(ds2)
> names(tree$leaves)
> plot_gene_map(ds2, tree=tree)
> 
> Now of course, the comparisons need to be done accordingly, thus you need to compute BQ vs BH, BH vs BG, and BG vs BB. 
> 
> HTH,
> 
> Lionel
> 
> On 12 Mar 2014, at 19:00 , Migun Shakya <microbeatic at gmail.com> wrote:
> 
>> Hello,
>> 
>> In the help page for `plot_dna-segs`, it is mentioned that the solution for matching large number of `lines` with the corresponding phylogenetic tree is to do the following:
>> 
>> "The solution is then to provide segments that are ordered in the same manner as the tree labels (or vice-versa)."
>> 
>> 
>> However, i can’t find an obvious way to do it for phylog object or the dna_segs.
>> 
>> My question is, is there any tutorial or method in the genoplotR package that tells us how to do it.
>> 
>> 
>> Thank you again
>> 
>> Migee
>> _______________________________________________
>> genoPlotR-help mailing list
>> genoPlotR-help at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genoplotr-help
> 
> --
> Lionel Guy 
> Molecular Evolution, Uppsala University, Uppsala, Sweden
> postal address: Box 596, SE-751 24 Uppsala; visiting address: BMC B7:213e, Husargatan 3, SE-752 37 Uppsala
> phone: +46 18 471 6129, mobile +46 73 976 0618
> lionel.guy at icm.uu.se
> 
> 
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