Question: How To Force Identical Topology Between Two Subnetworks (Same Nodes, Different Edges) For Comparison In Cytoscape
gravatar for antass
7.1 years ago by
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 • 3.2k views
ADD COMMENTlink modified 7.1 years ago by David Quigley11k • written 7.1 years ago by antass30
gravatar for David Quigley
7.1 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.

ADD COMMENTlink written 7.1 years ago by David Quigley11k

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.

ADD REPLYlink modified 7.1 years ago • written 7.1 years ago by antass30

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".

ADD REPLYlink written 7.1 years ago by David Quigley11k
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