# Visualizing graph structures in matlab

We discuss some methods for visualizing graphs/ networks, including automatic layout of the nodes. We assume the graph is represented as an adjacency matrix. If using BNT, you can access the DAG using

    G = bnet.dag;

## Matlab's biograph function

The Mathworks computational biology toolbox has many useful graph related functions, including visualization.
Click here for a demo.

## Cemgil's draw_graph

You can visualize an arbitrary graph (such as one learned using the structure learning routines) with Matlab code written by Ali Taylan Cemgil from the University of Cambridge. A modified version of this code is here (this is already bundled with BNT). Just type

    draw_graph(G);

For example, this is the output produced on a random QMR-like model:

## Pajek

Pajek is an excellent, free Windows program for graph layout. Use adj2pajek2.m to convert a graph to the Pajek file format.
Then Choose File->Network->Read from the menu.

## AT&T Graphviz

graphhviz is an open-source graph visualization package from AT&T. Use graph_to_dot to convert an adjacency matrix to the AT&T file format (the "dot" format). You then use dot to convert it to postscript:

    graph_to_dot(G, 'filename', 'foo.dot');
    dot -Tps foo.dot -o foo.ps
    ghostview foo.ps &