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How To Force Identical Topology Between Two Subnetworks (Same Nodes, Different Edges) For Comparison In Cytoscape

I have two GR networks from which I extracted two subnetworks using the same list of genes (nodes). I want to be able to visually compare the topology of the resulting subnetworks. In other words, I want to be able to put the two subnetworks side by side and see which edges exist in one subnetwork but don't exist in the other.

So far, I have not been able to find a built-in functionality, nor a plugin, that would allow me to "freeze" a particular topology of nodes, and then add edges.

This is not a computational problem. I just want to be able to show a figure which will be easy to understand.

I could also calculate the union of edges in the two subnetworks and then color the resulting network's edges by "in subnetwork 1 only", "in subnetwork 2 only", and "common"; but I'd rather have a side by side figure.

Do any of you have any suggestions?

cytoscape
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updated by David Quigley David Quigley • written by antass • antass

1 answer

I've solved this problem in a paper I'm currently working on by constructing a single network that contains the union of both individual networks I'd like to compare. Each edge has an attribute which I use to indicate whether it came from network A, network B, or is present inboth. I arrange the nodes in a sensible manner and then manipulate the edge opacity using a custom Visual Style. In your case, you could use an attribute that takes three values: "A_only", "B_only", or "BOTH". By default you display all edges, which shows the BOTH edges. You then use a Discrete Mapper to make the opacity of "B" edges equal to zero if you are plotting network A, or vice versa.

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written by David Quigley David Quigley

Brilliant solution. Thanks David.

Just to clarify - by BOTH you meant EITHER, right? To get the union/all edges? So I may need 4 categories: net1, net2, both (intersection), either (union). I'll try it out.

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written by antass • antass

You can get the union by showing all edges and not masking anything. If you want to show the intersection of A and B, show only edges tagged with BOTH. Network A is "BOTH or A", and network B is "BOTH or B".

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written by David Quigley David Quigley

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