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1 <h1>Visualizing graph structures in matlab</h1>
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2
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3 We discuss some methods for visualizing graphs/ networks, including automatic
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4 layout of the nodes.
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5 We assume the graph is represented as an adjacency matrix.
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6 If using BNT, you can access the DAG using
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7 <pre>
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8 G = bnet.dag;
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9 </pre>
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10
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11 <h2>Matlab's biograph function</h2>
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12
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13 The Mathworks computational biology toolbox
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14 has many useful graph related functions, including visualization.
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15 <br>
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16 Click
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17 <a href="http://www.mathworks.com/products/bioinfo/demos.html?file=/products/demos/shipping/bioinfo/graphtheorydemo.html#4">
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18 here</a>
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19 for a demo.
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20
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21
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22
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23 <h2>Cemgil's draw_graph</h2>
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24
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25 You can visualize an arbitrary graph (such as one learned using the
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26 structure learning routines) with Matlab code written by
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27 <a href="http://www-sigproc.eng.cam.ac.uk/~atc27/matlab/layout.html">
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28 Ali Taylan Cemgil</a>
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29 from the University of Cambridge.
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30 A modified version of this code
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31 is <a href="GraphViz.zip">here</a>
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32 (this is already bundled with BNT).
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33 Just type
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34 <pre>
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35 draw_graph(G);
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36 </pre>
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37 For example, this is the output produced on a
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38 <a href="http://www.cs.ubc.ca/~murphyk/Software/BNT/usage.html#qmr">random QMR-like model</a>:
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39 <p>
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40 <img src="Figures/qmr.rnd.jpg">
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41 <p>
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42
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43 <h2>Pajek</h2>
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44
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45 <a href="http://vlado.fmf.uni-lj.si/pub/networks/pajek">Pajek</a>
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46 is an excellent, free Windows program for graph layout.
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47 Use <a href="adj2pajek2.m">adj2pajek2.m</a> to convert a graph to the
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48 Pajek file format.
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49 <br>
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50 Then Choose File->Network->Read from the menu.
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51
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52 <h2>AT&T Graphviz</h2>
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53
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54 <a href="http://www.research.att.com/sw/tools/graphviz">graphhviz</a>
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55 is an
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56 open-source graph visualization package from AT&T.
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57 Use
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58 <a href="graph_to_dot.m">graph_to_dot</a>
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59 to convert an adjacency matrix to
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60 the AT&T file format (the "dot" format).
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61 You then use dot to convert it to postscript:
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62 <pre>
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63 graph_to_dot(G, 'filename', 'foo.dot');
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64 dot -Tps foo.dot -o foo.ps
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65 ghostview foo.ps &
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66 </pre>
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