Community detection

[ugurdogrusoz]

Communities in a graph could be calculated (e.g. Louvain modularity) and clustering/grouping (alternative to existing Markov clustering) could be done based on that. Let's investigate whether anything is available in JS for this and then make a decision.

• [x] 1. Put this under Group sub-tab after None with title "By the Louvain modularity algorithm"
• [x] 2. Put a new option (radio button) under Settings with title "Group using" and choices "Compounds" (default) and "Cluster IDs". By default detected groups are shown with compounds as we do now. When the other is opted, we should maintain clustering info in node data (e.g. clusterID field).
• [x] 3. Integrate a second layout method CiSE using this extension. This layout will take the clustering info computed by a grouping method as input and do the layout accordingly, where each cluster will be laid out on a distinct separate circle. For now, we will apply this layout only when Group using by cluster IDs is chosen and grouping is applied.

[ugurdogrusoz]

1 Wrong location 3 Let's improve this by implement this and using for grouping by cluster IDs (all but 'none' option). 3 We should apply CiSE layout only when the user clicks on Apply under Group, all other operations should continue using fCoSE layout. Looks like once CiSE is applied, currently it sticks!

[ugurdogrusoz]

Problems:

• [x] 10. When I expand/collapse compounds to represent community structures, the layout performed upon these operations does not seem to be incremental any longer (things move all around as opposed to be stable like before).