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More memory efficient graph generation #180

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ChristopherMancuso opened this issue Aug 10, 2022 · 0 comments

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ChristopherMancuso commented Aug 10, 2022

Currently, to make output edgelist of the top genes, it needs to read/parse the whole edgelist. Some quick thoughts

Save edgelist files as json with node as key and all neighbors as values. May take more memory to store but could be much faster and less memory to look up
Above could also be forced to be in same order as NodeOrder files
For large, dense, weighted graph, possibly could set a threshold or else above won't help much

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ChristopherMancuso added the enhancement label

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