Display neighborhood

[logmosier]

Right now the neighborhood graph that is being fetched, are so large the graph is unreadable. The smallest I have found is 295 nodes and 856 edges.

But they can get much larger (1572 nodes 15752 edges) to the point of taking 3+ min to display.

(both of these are limited to 4 interaction types)
Would the best way to handle this be by modifying the data that is fetched (cut away nodes before displaying) or is there a better way?

[jvwong]

I assume this is a client-side bottleneck. Is it possible to spend time finding an example query that returns fewer interactions?

[logmosier]

I was able to find some much smaller graphs, Q8IWf7 and Q9BQY4 are good.

[maxkfranz]

You can load and render 20k elements in about a second (maybe 2s on a slower machine).

Here are some tests done back on [email protected]: https://github.com/cytoscape/cyjs2.6-cyjs2.7-desktop-comparison And 3.2 is faster than 2.7.

Try using the Chrome profiler to see what's going on. Or use console.time() to track how long different parts of the code are taking.

I suspect you have a slow layout and/or the PC query is taking a while. You can also try using the grid layout or the random layout to see how much of a difference layout expense makes -- those are cheap layouts.

[maxkfranz]

What layout are you using now?

[logmosier]

I was using the cose-bilkent as I was reusing baseNetworkView, I switched over to grid layout and saw a drop form 26512.44ms to 1279.80ms for the layout.run() call.

[IgorRodchenkov]

Or try PATHSBETWEEN graph query instead of neighborhood (with one ID is ok)...

[IgorRodchenkov]

I bet this (that a PC neighborhood query produces a large "hairball") has to do with
PathwayCommons/cpath2#284 and BioPAX/Paxtools#34 - both will be fixed in the next PC db release (PC10).