How to merge networks in cytoscape with retaining network layout

[Lina Thomas]

[Alexander Pico]

I don't think that's possible using the built-in Merge Networks tool. You can copy/paste networks (or subnetworks) into new network windows and retain layout, but that does not perform a merging function, i.e., duplicates are not unified.

 - Alex

On Tuesday, July 9, 2013 3:01:48 PM UTC-7, Lina Thomas wrote:

[tobias....@mdc-berlin.de]

Hi all,

Sorry to open this old thread again.

However, for me (cytoscape 2.8.3, because I need some other plugins) the Advanced Network Merge Plugin only works sometimes. I can not reproduce the odd behavior. However, the parts of the Dialogue where I could select the merge Attribute etc are completely empty and inactive...

And if the merge works, the attributes of the smaller network are empty, only a new Identifier is generated, which makes the merge virtually useless.

Any suggestions?

Best, Tobias

[Lionel Bic]

I had the same problem in keeping the kegg visual style while merging two networks.
I posted on this link my answer in a powerpoint file. You can use LayoutSaver plugin in cytoscape 2.8.3.
https://groups.google.com/forum/?fromgroups#!searchin/cytoscape-discuss/lionello/cytoscape-discuss/xB_nYtXjOAE/jsavLG-S1Y0J
Hoping this can be useful,
cheers,
Lionello

Il giorno mercoledì 10 luglio 2013 00:01:48 UTC+2, Lina Thomas ha scritto:

[Sky Pangolin]

It is quite possible that no one cares about this anymore, but if per chance someone is trying to do this there is an alright method in cytoscape.

After merging the two networks go to Layout->Copycat Layout. 

From here select the network with the layout you'd like as the source network and the merged network as the target network.  This will set the nodes in your merged (which are present in the source network) to the locations they were in the source network.  Remaining nodes will need to be hand placed. 

~Sky