Style updates for EM networks

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

31 stars 12 forks source link

Style updates for EM networks #517

Closed mikekucera closed 1 year ago

mikekucera commented 1 year ago

Style updates for EM networks

Map node size and label font size to -log10(pvalue)
- Question: If there is more than one dataset, should the -log10(pvalue) column be the average?
- Question: What about q-value?
The label of the most significant node in a cluster should be significantly larger so that it stands out.
- Note: The style is part of EM, but clusters are created by AA. So for this to work AA would need to detect an EM network and set a style bypass. This bypass would need to be reset every time the annotation set is changed.
Add transparency to nodes
Change label color to dark grey instead of black

risserlin commented 1 year ago

Question: If there is more than one dataset, should the -log10(pvalue) column be the average?

I don't think it should be the average because then a strong signal from an individual dataset won't stand out. Or will it be the average of datasets that are significant? Will this be a setting that it is easy to adjust? (between using p-value and q-value)

mikekucera commented 1 year ago

We could add options to the style section to choose which dataset to use for the mapping, and to choose p or q value.

risserlin commented 1 year ago

By default I would set it to the max -log(pval) for all the datasets

mikekucera commented 1 year ago

Opened separate issue in AA for "label of the most significant node in a cluster should be significantly larger": https://github.com/BaderLab/AutoAnnotateApp/issues/196