Custom fill nodes by dataset

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

Custom fill nodes by dataset #454

Closed rosscm closed 3 years ago

rosscm commented 3 years ago

Hi,

I'm attempting to set custom fills for EM nodes but unable to do so. Two methods tried so far:

EM -> Chart Data = Color by Dataset -> Style Fill Color (Column = Dataset_Chart; Mapping type = Discrete). This method seems to only affect the border paint, where the preset blue/green colours remain visible.
EM -> Chart Data = None -> Style Fill Color (Column = Dataset_Chart; Mapping type = Discrete). This method changes the fill colours, but nodes shared by multiple datasets are overridden by a single colour.

Is it possible to custom fill nodes by dataset?

risserlin commented 3 years ago

What version of EM are you using?

In the latest version of EM there is an option in EM panel to specify the colour:

rs:

risserlin commented 3 years ago

I think it was introduce in version 3.3.0

rosscm commented 3 years ago

Ohh I see, I didn't try actually clicking the colour boxes to specify custom ones (I'm using EM version 3.3.1 for reference). Thanks Ruth! Screen Shot 2021-03-22 at 1 08 36 PM

Do you know by any chance if this dataset colouring can be automated via RCy3? Or is that a question I should ask there? (setNodeColorMapping() creates the situation where blue/green preset dominates over custom colours)

risserlin commented 3 years ago

I don't think it can be automated by RCy3 yet. But definitely something we can put a ticket in for. I know it is something I would love to do via RCy3 as well!

I added a ticket to add this feature - https://github.com/BaderLab/EnrichmentMapApp/issues/455