<div dir="ltr">Thanks Eric,<div><br></div><div>I'm using biopython 1.65 and networkx 1.9.1. </div><div><br></div><div>When I ran the commands you've proposed I still see the node names assigned:</div><div>[Clade(branch_length=2.0, name='foo'), Clade(branch_length=4.0, name='bar), Clade(...), ... ]<br></div><div><br></div><div>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 </div><div>from <span style="font-size:12.8000001907349px">PhyloXML. Here's the code I'm running, maybe this will help: </span><br></div><div><span style="font-size:12.8000001907349px"><br></span></div><div><span style="font-size:12.8000001907349px">###################### testing graphviz</span></div><div><div style><span style="font-size:12.8000001907349px">from Bio import Phylo</span></div><div style><span style="font-size:12.8000001907349px">from Bio.Phylo.TreeConstruction import _DistanceMatrix</span></div><div style><span style="font-size:12.8000001907349px">from Bio.Phylo.TreeConstruction import DistanceTreeConstructor</span></div><div style><span style="font-size:12.8000001907349px">import pylab</span></div><div style><span style="font-size:12.8000001907349px"><br></span></div><div style><span style="font-size:12.8000001907349px">names = ['foo', 'bar', 'cat', 'dog']</span></div><div style><span style="font-size:12.8000001907349px">matrix = [[0], [1, 0], [2, 3, 0], [4, 5, 6, 0]]</span></div><div style><span style="font-size:12.8000001907349px">m = _DistanceMatrix(names, matrix)</span></div><div style><span style="font-size:12.8000001907349px">constructor = DistanceTreeConstructor()</span></div><div style><span style="font-size:12.8000001907349px">tree = constructor.nj(m)</span></div><div style><span style="font-size:12.8000001907349px">graph = Phylo.to_networkx(tree)</span></div><div style><span style="font-size:12.8000001907349px">print graph.nodes()</span></div><div style><span style="font-size:12.8000001907349px">Phylo.draw_graphviz(tree, prog="neato", node_size=50)</span></div><div style><span style="font-size:12.8000001907349px">pylab.show()</span></div><div style="font-size:12.8000001907349px">##########################</div></div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">I still don't understand where I'm going wrong.</div><div style="font-size:12.8000001907349px"><br></div><div style="font-size:12.8000001907349px">Best wishes, </div><div style="font-size:12.8000001907349px">Jan</div><div style="font-size:12.8000001907349px"><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 23 January 2015 at 16:33, Eric Talevich <span dir="ltr"><<a href="mailto:eric.talevich@gmail.com" target="_blank">eric.talevich@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div>Hi Jan,<br><br></div>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:<br><br></div><div>graph = Phylo.to_networkx(tree)<br></div><div>graph.nodes()<br><br></div><div>Also:<br><br></div><div>- What was the source file format (e.g. Newick, Nexus, PhyloXML, NeXML)<br></div><div>- Which versions of Biopython and NetworkX are you using?<br></div><div><br></div>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.<br><br></div>Hope that helps,<br>Eric<br><div><div><br><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Thu, Jan 22, 2015 at 8:02 AM, Jan Zaucha <span dir="ltr"><<a href="mailto:Jan.Zaucha@bristol.ac.uk" target="_blank">Jan.Zaucha@bristol.ac.uk</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr"><span style="font-size:13px">Hi everyone,</span><div style="font-size:13px"><br></div><div style="font-size:13px">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. </div><div style="font-size:13px"><br></div><div style="font-size:13px">I simply use:</div><div style="font-size:13px">Phylo.draw_graphviz(tree)<br></div><div style="font-size:13px">pylab.show()</div><div style="font-size:13px"><br></div><div style="font-size:13px">There is no error, I can't work out how to force the node names to be printed. </div><div style="font-size:13px"><br></div><div style="font-size:13px">Any ideas?</div><div style="font-size:13px"><br></div><div style="font-size:13px">Thanks,</div><div style="font-size:13px">Jan Zaucha</div><span><font color="#888888"><div><br></div>-- <br><div><div dir="ltr"><div>Jan Zaucha</div><div>Bristol Centre for Complexity Sciences<br></div><div>Computational Genomics Group<br></div><div>University of Bristol</div></div></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr"><div>Jan Zaucha</div><div>Bristol Centre for Complexity Sciences<br></div><div>Computational Genomics Group<br></div><div>University of Bristol</div></div></div>
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