wolffd@0: <h1>Visualizing graph structures in matlab</h1>
wolffd@0: 
wolffd@0: We discuss some methods for visualizing graphs/ networks, including automatic
wolffd@0: layout of the nodes.
wolffd@0: We assume the graph is represented as an adjacency matrix.
wolffd@0: If using BNT, you can access the DAG using
wolffd@0: <pre>
wolffd@0: G = bnet.dag;
wolffd@0: </pre>
wolffd@0: 
wolffd@0: <h2>Matlab's biograph function</h2>
wolffd@0: 
wolffd@0: The Mathworks computational biology toolbox
wolffd@0: has many useful graph related functions, including visualization.
wolffd@0: <br>
wolffd@0: Click 
wolffd@0: <a href="http://www.mathworks.com/products/bioinfo/demos.html?file=/products/demos/shipping/bioinfo/graphtheorydemo.html#4">
wolffd@0: here</a>
wolffd@0: for a demo.
wolffd@0: 
wolffd@0: 
wolffd@0: 
wolffd@0: <h2>Cemgil's draw_graph</h2>
wolffd@0: 
wolffd@0: You can visualize an arbitrary graph (such as one learned using the
wolffd@0: structure learning routines) with Matlab code written by
wolffd@0: <a href="http://www-sigproc.eng.cam.ac.uk/~atc27/matlab/layout.html">
wolffd@0: Ali Taylan Cemgil</a>
wolffd@0: from the University of Cambridge.
wolffd@0: A modified version of this code
wolffd@0: is <a href="GraphViz.zip">here</a>
wolffd@0: (this is already bundled with BNT).
wolffd@0: Just type
wolffd@0: <pre>
wolffd@0: draw_graph(G);
wolffd@0: </pre>
wolffd@0: For example, this is the output produced on a
wolffd@0: <a href="http://www.cs.ubc.ca/~murphyk/Software/BNT/usage.html#qmr">random QMR-like model</a>:
wolffd@0: <p>
wolffd@0: <img src="Figures/qmr.rnd.jpg">
wolffd@0: <p>
wolffd@0: 
wolffd@0: <h2>Pajek</h2>
wolffd@0: 
wolffd@0: <a href="http://vlado.fmf.uni-lj.si/pub/networks/pajek">Pajek</a>
wolffd@0: is an excellent, free Windows program for graph layout.
wolffd@0: Use <a href="adj2pajek2.m">adj2pajek2.m</a> to convert a graph to the
wolffd@0: Pajek file format.
wolffd@0: <br>
wolffd@0: Then Choose File->Network->Read from the menu.
wolffd@0: 
wolffd@0: <h2>AT&T Graphviz</h2>
wolffd@0: 
wolffd@0: <a href="http://www.research.att.com/sw/tools/graphviz">graphhviz</a>
wolffd@0: is an 
wolffd@0: open-source graph visualization package from AT&T.
wolffd@0: Use
wolffd@0: <a href="graph_to_dot.m">graph_to_dot</a>
wolffd@0: to convert an adjacency matrix to 
wolffd@0: the AT&T file format (the "dot" format).
wolffd@0: You then use dot to convert it to postscript:
wolffd@0: <pre>
wolffd@0: graph_to_dot(G, 'filename', 'foo.dot');
wolffd@0: dot -Tps foo.dot -o foo.ps
wolffd@0: ghostview foo.ps &
wolffd@0: </pre>