(Cytoscape) How to make a good network with 600 nodes and 2000 edges?
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2.6 years ago
hslee97 • 0

My cytoscape network contains 600 nodes and 2000 edges. So, Network is very complicated, and node label doesn't look clearly when I see network through "Fit Content". How do I manipulating these network effectively?

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600 nodes, in my opinion, is already a lot if you also want to show node labels. If I were looking at a network of 600 nodes and 2000 edges, I would not want to read label of every node. I would not label the nodes, but maybe group them and assign every group a different color (here assignment of group will depend on question at hand) for better and informative visualization.

I feel Gephi does much better job in visualizing large networks as compared to Cytoscape (speaking from a past experience). Here is what I did when I had a network of this scale:

-Tried visualizing it with cytoscape using different layouts (Kamada- Kawai, Fruchtermann-Rheingold etc), but lets just say the network was not looking so nice

-I exported the network in a .graphml format (you can find this option under "Files" tab in Cytoscape)

-Imported this network using the .graphml file in Gephi

-Tried the Fruchtermann-Rheingold layout in Gephi, and it started to look much better.

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Thank you manswwm sir, I will try all of them, and choose best of one.

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2.6 years ago
scooter ▴ 590

The "right" answer here is: "it depends". 600 nodes and 2000 edges is not a very large network, depending on what you are trying to show. For example, this image of yeast genetic interactions has ~4000 nodes:

Yeast Genetic Interaction Network.

If you are trying to show a pathway and see details of the connections, that's probably too many nodes, and I would recommend simplifying your network. On the other hand, if you have a couple of key nodes that you want to highlight, you can turn off the labels of most of the nodes and then only show the labels of the key nodes after making those larger. You can also tune most of the layouts in Cytoscape. I typically start with Prefuse Force Directed, and then use the Layout Settings dialog to adjust it. Some folks have reported good results with the yFiles layouts also.

-- scooter

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