[Biopython] Phylo.draw_graphviz(tree) not showing node names

[Jan Zaucha]

Thanks Eric,

I'm using biopython 1.65 and networkx 1.9.1.

When I ran the commands you've proposed I still see the node names assigned:
[Clade(branch_length=2.0, name='foo'), Clade(branch_length=4.0, name='bar),
Clade(...), ... ]

I'm not sure what the source file format is, I created the tree myself from
a distance matrix, the examples I was looking at were importing trees
from PhyloXML. Here's the code I'm running, maybe this will help:

###################### testing graphviz
from Bio import Phylo
from Bio.Phylo.TreeConstruction import _DistanceMatrix
from Bio.Phylo.TreeConstruction import DistanceTreeConstructor
import pylab

names = ['foo', 'bar', 'cat', 'dog']
matrix = [[0], [1, 0], [2, 3, 0], [4, 5, 6, 0]]
m = _DistanceMatrix(names, matrix)
constructor = DistanceTreeConstructor()
tree = constructor.nj(m)
graph = Phylo.to_networkx(tree)
print graph.nodes()
Phylo.draw_graphviz(tree, prog="neato", node_size=50)
pylab.show()
##########################


I still don't understand where I'm going wrong.

Best wishes,
Jan


On 23 January 2015 at 16:33, Eric Talevich <eric.talevich at gmail.com> wrote:

> Hi Jan,
>
> Could you show us some more information about your tree, like the first
> few lines you see with "print tree"? Also try converting the tree to a
> NetworkX graph, which is the intermediate form used by draw_graphviz, and
> inspecting the nodes to see if names were lost or retained:
>
> graph = Phylo.to_networkx(tree)
> graph.nodes()
>
> Also:
>
> - What was the source file format (e.g. Newick, Nexus, PhyloXML, NeXML)
> - Which versions of Biopython and NetworkX are you using?
>
> It's possible the node names are assigned to a different attribute than
> the node name, in which case you can use the "label_func" argument in
> draw_graphviz to retrieve the name from the graph node.
>
> Hope that helps,
> Eric
>
>
>
> On Thu, Jan 22, 2015 at 8:02 AM, Jan Zaucha <Jan.Zaucha at bristol.ac.uk>
> wrote:
>
>> Hi everyone,
>>
>> I'm trying to visualize the trees I generate, but for some reason the
>> plots do not display the node names. When I print the tree each node has an
>> associated name (string format). Phylo.draw(tree) also works fine and plots
>> a tree with the node names.
>>
>> I simply use:
>> Phylo.draw_graphviz(tree)
>> pylab.show()
>>
>> There is no error, I can't work out how to force the node names to be
>> printed.
>>
>> Any ideas?
>>
>> Thanks,
>> Jan Zaucha
>>
>> --
>> Jan Zaucha
>> Bristol Centre for Complexity Sciences
>> Computational Genomics Group
>> University of Bristol
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython
>>
>
>


-- 
Jan Zaucha
Bristol Centre for Complexity Sciences
Computational Genomics Group
University of Bristol
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20150126/2c6166b4/attachment.html>