Re: Memory problems with large-scale social network visualization using RCytoscape
Paul Shannon
Sorry for taking several days to get back to you.
I just ran some tests in which
1) an adjacency matrix is created in R
2) an R graphNEL is then created from the matrix
3) (optionally) node & edge attributes are added
4) a CytoscapeWindow is created, displayed, and layed out, and redrawn
(all times are in seconds)
nodes edges attributes? matrix graph cw display layout redraw total
70 35 no 0.001 0.001 0.5 5.7 2.5 0.016 9.4
70 0 no 0.033 0.001 0.2 4.2 0.5 0.49 5.6
700 350 no 0.198 0.036 6.0 8.3 1.6 0.037 16.7
1000 500 no 0.64 0.07 12.0 9.8 1.8 0.09 24.9
1000 500 yes 0.42 30.99 15.7 29.9 1.7 0.08 79.4
2000 1000 no 3.5 0.30 73.5 14.9 4.8 0.08 96.6
2500 1250 no 2.7 0.45 127.1 18.3 11.5 0.09 160.7
3000 1500 no 4.2 0.46 236.8 19.6 10.7 0.10 272.8
4000 2000 no 8.4 0.98 502.2 27.9 21.4 0.14 561.8
To my complete surprise, and chagrin, there is an exponential slowdown in 'cw' (the new.CytoscapeWindow method) --which makes no sense at all. It may be that your memory exhaustion is related to that, and is quite fixable.
I will explore this, and probably have a fix in the next week.
By the way, did you know that you can create a graphNEL directly from an adjacency matrix?
g = new ("graphAM", adjMat = matrix, edgemode="directed")
Thanks, Ignacio, for your most helpful report. I should have done these timing tests long ago!
- Paul