How to graph a connectivity/adjacency matrix?

I want to graph the structure of a network (a power grid). I have a list containing to-from nodes for each branch.

The BIOGRAPH function is almost perfect. The drawback is that the lines always go out the "bottom" of the ancestor block, and into the "top" of the descendant. As an ancestor is always displayed above its descendants, the graphs are sometimes very chaotic.

It would be much better if the graph was plotted in a way that just showed which nodes were connected, without any hierarchy, and where lines could be horizontal.

Edit: I need to be able to assign different colors to various lines / nodes, to visualize voltage issues or overloads etc, similar to what I've done using biograph (code below).

Is this possible? It doesn't need to be a perfect solution, any improvements would be great.

This is the code I use now:

%%Plot biograph
Sys = sparse(from,to,1,s,s);
SysTri = tril(Sys + Sys'); 
bg = biograph(SysTri,ids,'ShowArrows','off','ShowWeights','off');
h = view(bg);  

 %%Color faulted line:
set(h.nodes(newFaultNodes),'Color',[1 0.4 0.4]);
fowEdges = getedgesbynodeid(h,get(h.Nodes(newFaultNodes),'ID'));
revEdges = getedgesbynodeid(h,get(h.Nodes(fliplr(newFaultNodes)),'ID'));
edges = [fowEdges;revEdges];
set(edges,'LineColor',[1 0 0])
set(edges,'LineWidth',2)

Answer 1

[Kelly Kearney]

Would gplot work for the basic setup? By default, the code doesn't allow the edge color modifications that you mention, but the code can be modified pretty easily to allow this (I've written a version that allows this, and can post it to the FEX if this is the type of thing you had in mind).

[John Doe]

I believe gplot needs xy-coordinates, which I don't have. My system has a different number of nodes and branches every time I run my simulations, thus I can't manually input coordinates for one single system.

I believe it would be hard to create an algorithm that automatically assigns the best coordinates to each single node?

It occured to me that in order to view the BIOGRAPH, a function assigning coordinates (or something similar) must be called. Could you think of a way to use these functions in combination with e.g. gplot?

BIOGRAPH has a property 'LayoutType', where 'hierarchical' is default. It turned out that the alternatives 'equilibrium' and 'radial' just turned everything in to a complete chaos.

Thank you!

[Kelly Kearney]

My solution to this in the past has been to interact with Graphviz (<http://www.graphviz.org/)>; it offers a variety of layout engines. I can't be positive, but I think biograph uses something similar to the Graphviz dot layout engine (which is intended for hierarchical graphs); other engines create much more compact graphs that reduce edge crossing. You could either rely on Graphviz for all your plotting, or just use it to calculate node positions, output to plain text, read that file into Matlab, and then create a Matlab plot of your choice (and if you're interested in the latter solution, I again have some functions that could help).

[John Doe]

Hi Kelly, thanks for your help!

Graphviz looks very promising, but unfortunately I can't get it to work. I have installed the program, and I believe I have the files in the correct folders. When I run the demos, I get a plot, but I get error messages saying MATLAB can't find 'neato', or any of the other layout engines in the bin-folder.

The result is that the appropriate coordinates are not assigned, thus every node is placed either in a circle or randomly. (All other properties are assigned, like colors, arrows, shapes etc.)

I don't have time to work more on this problem now, but I will try graphviz again in a few days and let you know.

[Kelly Kearney]

What operating system are you on, and how do you start Matlab? At least on a Mac, Matlab doesn't run any of your .rc or .profile scripts when it sets up the shell it accesses for system commands, so it can be a bit of a pain to get it to recognize some external functions.

The easiest way to resolve this is to run

 setenv('PATH' [getenv('PATH') ':/path/to/neato']);

(or whatever corresponds to your operating system).

I actually solve this problem by adding

 source ~/.bash_profile

to the first line of the {matlabroot}/bin/matlab function, because this way I don't need to worry about syncing my Matlab shell with the rest of my computer when I make changes to my path, but that's probably not the recommended way to do it (since the main matlab startup script isn't really intended to be messed with).

[John Doe]

setenv worked =)

It looks like Graphviz has all the functions is need. Thank you, I really appreciate the help!