Is there a preferred way to represent a multi-protein complex in a cytoscape layout? I am not thinking of an internal data-representation but rather of a graphical one, i.e. is there a way to draw a box around a collection of nodes?
Actually, there are several ways to represent protein complexes (or any collection of objects).
- Metanode Plugin - Represents collection of nodes as a node. Since this collapses/expands nodes in the same network, all nodes representing proteins should be in a same network:
- Nested Network - adds references to a network from a node. This means you need to define protein complexes as small, individual networks. The following diagram is not the one for protein complexes, but the basic idea is big nodes representing complexes have reference to other networks. This is a built-in feature in Cytoscape core. You can just right-click a node and add reference to other network.
Cytoscape Core Developer Team
AFAIK there's no way to group nodes with a box, but I'm not sure. Something you could do is to make edges within a complex in a special type (wider, different color) to make it clear that these are complexes. If they form a clique, then the layout algorithms should also put the nodes close together.