MATLAB - GraphViz interface

Interface GraphViz graph layout and MATLAB user interface power.

Description

Feb 2004 Massachusetts Institute of Technology, AI Lab
MATLAB <-> GraphViz by Dr. Leon Peshkin: pesha @ ai.mit.edu | http://www.csail.mit.edu/~pesha

this is a README file for `ad hoc' MATLAB package created to interface AT&T GraphViz graph layout and MathWorks MATLAB user Interface powers. Please make sure you have both MATLAB and GraphViz properly installed on your system. The package works on Unix and even on Windows. Use at your own risk.

README - this file
graph_to_dot.m - Creates a GraphViz formated file from a graph given by an adjacency matrix.
dot_to_graph.m - Extracts an adjacency matrix, node labels, and layout from a GraphViz file.
graph_draw.m - Draws a graph in MATLAB with a given layout
  make_layout.m - used to do a lame layout in case no layout is fed to graph_draw
draw_dot.m - a sample code illustrating use of package functions.
                  draws a graph defined by adjacency matrix, by
                    -first converting it to a GraphViz file (graph_to_dot)
                    -then calling NEATO of GraphViz to do a layout
                    -then importing layout file back into Matlab (dot_to_graph)
                    -finally calling graph_draw to display the layout
sample_click.m - an auxiliary sample code which allows to right-mouse-click on the nodes of
                  a graph to call a dummy function currently just printing that node's label
my_setdiff.m - my version of setdiff() which works much faster

• Acknowledgements: This submission has inspired the following:; MATLAB GraphViz Layout importer
• MATLAB release: MATLAB 6.1 (R12.1)
• Other requirements: GraphViz from AT&T

[Nick Valuy]

long awaited tool, must be a standard distr.

[Ben Zana]

nice!

[Nick Henderson]

I have been using the tool to visualize gene networks. I found and fixed a small bug in graph_to_dot. I have already emailed the author. But, for the time being you may use this link:

http://www.owlnet.rice.edu/~nwh/repfug/ode/graph_to_dot.m

Other than that, I am a big fan of Graphviz and the matlab interface!

[Koni Wolka]

I wish this came as a toolbox from Matlab!
Great job!

[Sébastien Vast]

Very interesting tools but lack of certain
features for my usage in biochemical network
But it is easy to add these

[Etienne Lefebvre]

 

[Jing Tang]

excellent work! I will use it in my project..

[son hong]

intgrate

[Stephen Cowen]

Good. Definitely Beta, but good. Would be nice if it had a demo script that would generate some sample graphs to illustrate the functions.

[Michael Jachan]

i rely on it :)

[Yuri Medvedev]

Highly professional work.

[Valentina Rossetti]

I was just looking for something like that - thank you, it's very nice!

[Mark Bolan]

Matlab keeps indicating error: neato command not found. How do I resolve this issue?

[Marco Canini]

I found a bug on line 92 of dot_to_graph.m. The original uses %d in the sscanf but it should be like this:
[node_pos] = sscanf(line(pos_pos:length(line)), ' pos = "%f,%f"')';

[Shicai Yang]

[node_pos] = sscanf(line(pos_pos:length(line)), ' pos = "%f,%f"')';

it does work. thank you.

[Jonathan C. Lansey]

??? Undefined function or variable 'range'.
I replaced range with max(x)-min(x) and i worked!

[Wilmer]

I try to run sample_click.m, but I have the error:
??? Error: File: sample_click.m Line: 7 Column: 1
Function definitions are not permitted in this context.

Thanks....