Is "Attribute Circle Layout" of a protein-protein network standard and acceptable for a good publication?

Question

[Farah]

Hello,

I made a p-p network using StringApp, and then from that network I selected my single protein of interest and its first neighbours and did sub-networking. I want to present this sub-network (25 protein including my protein of interest) in a paper for a very good publication. For the publication, I changed the layout of this sub-network to "Attribute Circle Layout" and from it I choosed "display name".

May I kindly ask you whether this circular representation of this sub-network is standard for the publication? Or it is not acceptable and standard for a good publication?

Many thanks for any guide and advice.

[Clément Frainay]

To my opinion, the circle layout is not well suited if you expect the reader to follow paths between your nodes, compared to force directed layouts, for example. It may also hide some structural patterns in your network and overshadow densely connected communities. If this isn't the kind of information you want to display, then I don't see any problem using this layout.

As its name suggests, it is particularly useful to make a parallel between an attribute and the structure of the network. The attribute is used to position the nodes on the circle, like clockwise from smallest to highest value for example (don't know about the Cytoscape implementation though). It may then clearly show that the node with highest values seems more interconnected than the ones with small values for example.

You didn't mention any attribute of interest, so if you just want to show the connections in a small network, as long as the output is readable with few edge crossings, I don't see why any reviewers would be picky about it...

[Farah]

OK. Many thanks for your useful explanation.

[Leite]

As far as I know, There is no a standard for network representation, usually the layout is chosen to best display your data.

Best Regards

Leite

[Farah]

Thank you very much for your advice.

Answer 1

[scooter]

You may also want to take a look at the recently published paper: "Ten simple rules to create biological network figures for communication" to see if that gives you some ideas on how to proceed.

-- scooter

[Farah]

Wow. That is great. Thank you so much Scooter.