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POProblems with draw_networkx() when saving a figure in pdf format
 

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  1. POProblems with draw_networkx() when saving a figure in pdf format
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    <p>When I alter the line width used for edges by specifiying the width argument in the networks draw_networkx() function, e.g:</p> <pre><code>nx.draw_networkx(G, width = 0.03) </code></pre> <p>the image that results from using </p> <pre><code>plt.show() </code></pre> <p>is as expected (in that I can control the edge widths). However, when I use:</p> <pre><code>plt.savefig('foo.pdf') </code></pre> <p>the resulting pdf appears to have an unaffected edge width. Saving as png seems to work fine, but I really need a pdf output. I slightly altered a sample code from the networkx website as an example:</p> <pre><code>import networkx as nx import matplotlib.pyplot as plt G=nx.random_geometric_graph(200,0.125) pos=nx.get_node_attributes(G,'pos') dmin=1 ncenter=0 for n in pos: x,y=pos[n] d=(x-0.5)**2+(y-0.5)**2 if d&lt;dmin: ncenter=n dmin=d p=nx.single_source_shortest_path_length(G,ncenter) plt.figure(figsize=(8,8)) nx.draw_networkx_edges(G,pos,nodelist=[ncenter],alpha=1, width = 0.03) nx.draw_networkx_nodes(G,pos,nodelist=p.keys(), node_size=80, node_color=p.values(), cmap=plt.cm.Reds_r) plt.xlim(-0.05,1.05) plt.ylim(-0.05,1.05) plt.savefig('random_geometric_graph.pdf') plt.show() </code></pre> <p>which results in the images at (pdf on the rhs) <a href="http://i49.tinypic.com/2501h6c.jpg" rel="nofollow">http://i49.tinypic.com/2501h6c.jpg</a></p> <p>I've tried oping the pdf in Mac's preview, and in adobe, and the problem persists.</p> <p>Any help/suggestions much appreciated!</p>
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    1. PTQuestion
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    1. USVictoria
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      1. VTUpMod
    1. COcheck the `savefig` for options on what is saved out and how (and maybe you can try ps instead if pdf that doesn't work.
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      1. POProblems with draw_networkx() when saving a figure in pdf format
      1. USdeinonychusaur
    2. COpossible duplicate: http://stackoverflow.com/questions/7906365/matplotlib-savefig-plots-different-from-show
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      1. POProblems with draw_networkx() when saving a figure in pdf format
      1. USzenpoy
    3. COI've just found that if I open the pdf file in colorsync utility there's no longer a problem. My matplotlib rc file has identical settings for pdfs png sag etc so I don't think this is the problem as in the link zenpoy references. Does anyone know what may be causing this? It seems to be a problem in viewing the pdf rather than a coding problem now? @deinonychusaur ps results in the same problems when I include the figure in a latex document...
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      1. POProblems with draw_networkx() when saving a figure in pdf format
      1. USVictoria
 

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