From 8070dc963753142bb86c4ed698d91fd623ed28e7 Mon Sep 17 00:00:00 2001
From: ziejd2
Date: Thu, 28 Sep 2017 15:04:40 -0500
Subject: BNW using Octave instead of Matlab.
This version of BNW should perform the same as the original version. The only difference is that it uses Octave instead of Matlab when running BayesNet Toolbox during parameter learning.
I am calling this BNW_1.02. It can be accessed at:
compbio.uthsc.edu/BNW_1.02
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+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 &
+
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