Question: Correlating Node Size With The Amount Of Edges In Cytoscape
2
gravatar for toshnam
7.3 years ago by
toshnam620
Seoul, Republic of Korea
toshnam620 wrote:

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.

cytoscape • 9.5k views
ADD COMMENTlink written 7.3 years ago by toshnam620

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

ADD REPLYlink written 7.3 years ago by Russh1.2k
6
gravatar for Duff
7.3 years ago by
Duff660
United Kingdom
Duff660 wrote:

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

ADD COMMENTlink written 7.3 years ago by Duff660

Really thank you for your kind comments. :-)

ADD REPLYlink written 7.3 years ago by toshnam620

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

ADD REPLYlink written 5.4 years ago by diltsjeri440
2
gravatar for Gjain
7.3 years ago by
Gjain5.3k
Göttingen, Germany
Gjain5.3k wrote:

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

ADD COMMENTlink written 7.3 years ago by Gjain5.3k
1

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

ADD REPLYlink written 7.3 years ago by Michael Schubert6.9k

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?

ADD REPLYlink written 7.3 years ago by toshnam620
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