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BaderLab / EnrichmentMapApp

The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
http://apps.cytoscape.org/apps/enrichmentmap
GNU Lesser General Public License v2.1
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when a geneset is empty an edge is created from it to all genesets #397

Closed risserlin closed 4 years ago

risserlin commented 4 years ago

creating an EM with just a gmt file.

Screen Shot 2020-02-26 at 4 26 54 PM

ex_rand_subtype_2 is an empty geneset

file used to create EM combinded_pathways.gmt.txt

mikekucera commented 4 years ago

If a geneset is empty should it even have a node?

risserlin commented 4 years ago

Yes. For my use case. It might be empty in one "species" but populated in another.

mikekucera commented 4 years ago

Ok, the fix I committed yesterday keeps the node. The problem was division by zero when calculating overlap. I just added a check for that. Thanks.