How to correlate node size to the amount of edges

[WoutH]

I'm fairly new to CytoScape. I'm trying to get the big hubs out of a
network (which is fairly big, 12k+ nodes). I cannot find the option
anywhere, and the manual says it should do it automatically.

My network comes in a tab delimited format, which works fine to load,
but I can't get CytoScape to correlate the size of the nodes to the
amount of edges on it. Any help is appreaciated!

Wout H

[piet molenaar]

Hi Wout,
In the manual is a section describing the use of visual styles; one of the examples (the last) maps size to node degree; ie the number of edges: http://www.cytoscape.org/manual/Cytoscape2_6Manual.html#Visual%20Styles%20Tutorials
Hope this helps, if not let me know.
Piet

--
Piet Molenaar
p.mol...@amc.uva.nl
Department of Human Genetics, M1-131
Academic Medical Center
University of Amsterdam
Meibergdreef 9
1105 AZ Amsterdam
the Netherlands

tel (+31) 20-5666592
fax (+31) 20-6918626

[Maital Ashkenazi]

Hi Wout,

The manual Piet mentioned refers to the Degree attribute. The somewhat secret trick to calculate this attribute for your own network is to choose Layouts --> Cytoscape Layouts --> Degree Sorted Circle Layout.  When you execute this layout, a degree will be calculated for each node and will be stored in a Degree attribute.  However, this layout may take a while to execute on a large network, so you may want to change the memory allocation (see second FAQ here: http://www.cytoscape.org/cgi-bin/moin.cgi/user_faq) .

Hope this helps,
Maital