I have two signalling networks that I want to merge with "retaining network layout". I simply merged the networks with network merging utility in cytoscape however, doing this I lost the manually adjusted layout of both the networks.
Perhaps you've already resolved this on your own, judging by the date of your entry. I would have answered sooner, but just signed up to RG this week.
I haven't encountered this problem before, as I never merge networks directly in Cytoscape, although I have used the app that allows you to locate the same node from two networks in identical Cartesian positions. Makes it easier to find the node in both networks. Cytoscape has a useful tool for the types of questions such as yours, and you may have already found this, but in case you haven't, go to...
http://www.cytoscape.org/community.html
Hope that helps.
I would still rephrase the question: How do you merge networks and retain their layouts? in fact it is not enough to have their positions retained but the edges structures (like in a hierachical layout) should be kept....
If I were you I would not use cytoscape, I used it before and I don't really like it that much. Try using STRING or NetworkAnalyst (personal favourites), but if you have to use cytoscape then integrate the platforms of different softwares then you won't have to deal with any technical difficulties.
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