Best layout for a large network

[mayank18]

Hey, my network in cytoscape is pretty large.More than 1500 nodes and 11,000 edges. I am really confused in finding a best and optimum way to visualize the network so that i can get a best fit of network in my cytoscape window. I mean trying only different layouts supposedly will not suffice my predicament. Any other suggestions?
Thanks.

[kmezhoud]

Maybe Organic layout?

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[piet molenaar]

Hi,

In my experience toying around with different layouts and scaling factors for parts of the network gives the best result. So first use e.g. the force directed layout for the whole graph. Subsequently select dense areas and perform an organic layout on the selected nodes only followed by scaling the selection. 

Hope this helps.

Piet

On Fri, Jan 11, 2013 at 9:38 AM, kmezhoud <kmez...@gmail.com> wrote:

Maybe Organic layout?

Le 01/11/2013 09:35 AM, mayank18 a écrit :

Hey, my network in cytoscape is pretty large.More than 1500 nodes and
11,000 edges. I am really confused in finding a best and optimum way to
visualize the network so that i can get a best fit of network in my
cytoscape window. I mean trying only different layouts supposedly will
not suffice my predicament. Any other suggestions?
Thanks.

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Department of Oncogenomics, M1-131
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[Mayank Malhotra]

Okay thanks everyone for your suggestions and replies.

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Regards,

Mayank Malhotra

Department Of Bio-Technology

Delhi Technological University,Delhi.

(formerly D.C.E.)

[sai nitin]

Hi,

You can check this Power graph lay out..

http://www.biotec.tu-dresden.de/research/schroeder/powergraphs/

Best,
Nitin

Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060

[Scooter Morris]

We regularly deal with very large networks, and have pretty good success
with Force Directed. Sometimes you will need to use the Settings to tune
the layout a little, but for large networks is definitely the fastest of
the force-based layout algorithms.

-- scooter

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