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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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chart data -> pvalue or q-value colors in the wrong direction #452

Closed risserlin closed 2 years ago

risserlin commented 3 years ago

If you color your data by p-value or q-value (in drop down of Style panel in EM panel)

The higher p-values or q-values get a stronger red and the lower are lighter but with p-values and q-values we want to accentuate the smaller values.

mikekucera commented 3 years ago

Just checking... is it ever possible to have negative p-values or q-values?

risserlin commented 3 years ago

no. p-value and q-value should be in the range from 0 to 1.

mikekucera commented 3 years ago

In that case the 'chart colors' combo box should show two colors and not three when p-value or q-value is selected.

risserlin commented 3 years ago

white to red? is it currently set to blue-white-red?

mikekucera commented 3 years ago

The first option when p-value is selected is RdBu-3, which shows red-white-blue in the chart color combo. But blue is not used and it currently uses white for 0 and red for the max p-value. I'm thinking it should just show red-white in the combo box and use white for max p-value and red for zero. Does that sound right?

risserlin commented 3 years ago

yes. that sounds right.