In my last posting, I showed a variety of node ordering schemes that could be applied to the combined glucose/oleate network. Of course, the only way to actually do these different layouts is to create a .noa node attribute file that specifies a node ordering and then install it using the Layout->Layout Using Node Attributes... feature. To make that whole process more understandable, I've posted the code for the little standalone Java program I used to create the files up at my BioFabric Github repository at:
It's a quick-and-dirty implementation that is totally hardwired to this specific example, but taking a look at that code can give you an idea of how to extend it to your particular situation.
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