Question: How To Force Identical Topology Between Two Subnetworks (Same Nodes, Different Edges) For Comparison In Cytoscape
2
5.3 years ago by
antass30
United States
antass30 wrote:

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 • 2.8k views
modified 5.3 years ago by David Quigley11k • written 5.3 years ago by antass30
0
5.3 years ago by
David Quigley11k
San Francisco
David Quigley11k wrote:

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.

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.