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

Eric Talevich eric.talevich at gmail.com
Fri Jan 30 06:07:26 UTC 2015


Hmm, I don't have access to a Mac so I'm not going to be able to fix this
one myself. Can anyone else take a shot at fixing this bug? Jan?

On Tue, Jan 27, 2015 at 7:48 AM, Jan Zaucha <Jan.Zaucha at bristol.ac.uk>
wrote:

> Hi Eric,
>
> This is brilliant, the problem is solved on the linux, and I'm totally
> happy with that (as can get on with my work :) ), but please be advised
> that this seems to have created some issue the matplotlib mac OSX backend
> doesn't like:
>
> on mac OSX pylab.show() yields:
>
> ---------------------------------------------------------------------------
> TypeError                                 Traceback (most recent call last)
> /Users/janzaucha/anaconda/lib/python2.7/site-packages/matplotlib/artist.pyc
> in draw_wrapper(artist, renderer, *args, **kwargs)
>      57     def draw_wrapper(artist, renderer, *args, **kwargs):
>      58         before(artist, renderer)
> ---> 59         draw(artist, renderer, *args, **kwargs)
>      60         after(artist, renderer)
>      61
>
> /Users/janzaucha/anaconda/lib/python2.7/site-packages/matplotlib/figure.pyc
> in draw(self, renderer)
>    1077         dsu.sort(key=itemgetter(0))
>    1078         for zorder, a, func, args in dsu:
> -> 1079             func(*args)
>    1080
>    1081         renderer.close_group('figure')
>
> /Users/janzaucha/anaconda/lib/python2.7/site-packages/matplotlib/artist.pyc
> in draw_wrapper(artist, renderer, *args, **kwargs)
>      57     def draw_wrapper(artist, renderer, *args, **kwargs):
>      58         before(artist, renderer)
> ---> 59         draw(artist, renderer, *args, **kwargs)
>      60         after(artist, renderer)
>      61
>
> /Users/janzaucha/anaconda/lib/python2.7/site-packages/matplotlib/axes/_base.pyc
> in draw(self, renderer, inframe)
>    2090
>    2091         for zorder, a in dsu:
> -> 2092             a.draw(renderer)
>    2093
>    2094         renderer.close_group('axes')
>
> /Users/janzaucha/anaconda/lib/python2.7/site-packages/matplotlib/artist.pyc
> in draw_wrapper(artist, renderer, *args, **kwargs)
>      57     def draw_wrapper(artist, renderer, *args, **kwargs):
>      58         before(artist, renderer)
> ---> 59         draw(artist, renderer, *args, **kwargs)
>      60         after(artist, renderer)
>      61
>
> /Users/janzaucha/anaconda/lib/python2.7/site-packages/matplotlib/text.pyc
> in draw(self, renderer)
>     536         renderer.open_group('text', self.get_gid())
>     537
> --> 538         bbox, info, descent = self._get_layout(renderer)
>     539         trans = self.get_transform()
>     540
>
> /Users/janzaucha/anaconda/lib/python2.7/site-packages/matplotlib/text.pyc
> in _get_layout(self, renderer)
>     309         tmp, lp_h, lp_bl =
> renderer.get_text_width_height_descent('lp',
>     310
>  self._fontproperties,
> --> 311
>  ismath=False)
>     312         offsety = (lp_h - lp_bl) * self._linespacing
>     313
>
> /Users/janzaucha/anaconda/lib/python2.7/site-packages/matplotlib/backends/backend_macosx.pyc
> in get_text_width_height_descent(self, s, prop, ismath)
>     164         size = self.points_to_pixels(points)
>     165         width, height, descent =
> self.gc.get_text_width_height_descent(
> --> 166             six.text_type(s), family, size, weight, style)
>     167         return  width, height, 0.0*descent
>     168
>
> Best wishes,
> Jan Zaucha
>
> On 26 January 2015 at 21:06, Eric Talevich <eric.talevich at gmail.com>
> wrote:
>
>> Thanks, Jan, that was helpful for debugging. I pushed a fix to GitHub, so
>> if you can install the development version of Biopython, it should work for
>> you now.
>>
>> The problem was a bug in networkx release 1.9.1 (and maybe others) that
>> existed between August 2013 and September 2014. The networkx "draw"
>> function would pass all keywords to "draw_networkx", except that while
>> "draw_networkx" has a keywords argument "with_labels" that defaults to
>> True, "draw" would override this to "False" unless it had been specified
>> explicitly. It has since been fixed in networkx and should be included in
>> the next release:
>>
>> https://github.com/networkx/networkx/blame/master/networkx/drawing/nx_pylab.py
>>
>>
>> On Mon, Jan 26, 2015 at 2:41 AM, Jan Zaucha <Jan.Zaucha at bristol.ac.uk>
>> wrote:
>>
>>> 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
>>>
>>
>>
>
>
> --
> Jan Zaucha
> Bristol Centre for Complexity Sciences
> Computational Genomics Group
> University of Bristol
>
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