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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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Add option to colour by significant NES only #446

Closed risserlin closed 3 years ago

risserlin commented 3 years ago

currently when you color using NES all NES values are used. If you want to show only significant ones you have to modify your input file to only contain significant values or you have to manually set NES values that are significantly in the node table.

It would be helpful to have the option in the dropdown "Significant NES columns" and only colour the node by NES if it passes the significance threshold.

mikekucera commented 3 years ago

Hi Ruth, how do I know if an NES value is significant?

risserlin commented 3 years ago

If the corresponding p-value and q-value pass the specified thresholds. There is no specific value where an NES values are significant.

mikekucera commented 3 years ago

ok thanks

mikekucera commented 3 years ago

Ok I've added the NES significant chart. Ruth can you please test this when you get a chance, to make sure its what you are looking for. If its not working as you expected then please reopen this issue.

risserlin commented 3 years ago

Is there a pre-release version I can downloade to try it out?