Correlating Node Size With The Amount Of Edges In Cytoscape

Question

[toshnam]

Hi all,

I'm trying to draw a protein interaction network using Cytoscape. I have a .sif file only.

So, I want to correlate node size to the amount of edges in network. I guess I need an extra files about node and attribute for it. I want to know the essential file list and examples for it.

Thanks.

[Russh]

many plugins output the degree of your nodes to a nodeAttribute. This can be used to size your nodes

Answer 1

[Duff]

Hi tosnam

Open your network in Cytoscape and select the Network Analysis plugin.

Run it and save the data somewhere (you should see that option in the bottom left of the post analysis dialogue).

Go to VizMapper and select Node Size, double click on it to create a mapping.

From the list of potential mappings select Degree and in the Mapping type select Continuous.

You should now be able to set the node size proportionally to the degree (use the sliders and experiment in the setting dialogue).

If you can't do this try re-installing Cytoscape or if you're running linux make sure it's using the right (i.e. Sun / Oracle) Java and not e.g. OpenJDK / IcedTea. This has given me trouble before.

One other tip. Open only the network you want to work on. If open more than one network then settings seem to go astray (well they do for me anyway).

Best

d

[toshnam]

Really thank you for your kind comments. :-)

[diltsjeri]

I can't find the "Network Analysis" plugin. Has it changed names?

Answer 2

[Gjain]

hi,

This should help you:

new version: http://wiki.cytoscape.org/Cytoscape_User_Manual/Visual_Styles

old version:http://www.cytoscape.org/manual/Cytoscape2_6Manual.html#Visual%20Styles%20Tutorials

[toshnam]

Thank you for your answer. I already read it, but can't set node size based on the degree of connectivity of the nodes. When I set node size using VizMapper, all nodes were changed to same size based on the setting value not the degree of connectivity. Can you tell me how to do that through your experiences or some examples?

[Michael Schubert]

Short answer: find a plugin that does it or write one yourself.