Comments (2)
mikekucera
commented on September 13, 2024
Hi Veronique. You are right that hiding just edges does not change the results of the prefuse force directed layout. However, this appears to have been the case for some time, as I'm getting the same results in Cytoscape 3.8. Looking at the code it appears that the layout takes hidden nodes into account, but not hidden edges. Perhaps you were hiding nodes in the past when you got different results?
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veroniquevoisin
commented on September 13, 2024
I'm quite sure it was working but it must have been a while ago. I remember adjusting the edges and then clicking on the icon to redo the layout. It makes the edge sliding bar less useful as it was. Except maybe for users who can get the idea to perform the organic layout which is not a default layout algorithm. I'm not sure what to suggest here (send a note to the Cytoscape team, dialog box to say to apply the organic layout,...). It is not for me but for users in general.
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Related Issues (20)
- Better options for controlling redundancy
- Use the node color mapping for AA clusters. HOT 1
- Provide a sorted list of pathways
- index 1 out of bounds for length 1 HOT 1
- Upgrade Java and Guice
- filtering GSEA results by NES assumes positives are in one file and negatives are in another HOT 3
- Building EnrichmentMap error HOT 6
- CreateEMNetworkTask should be cancellable
- ability to layout network by dataset
- The enrichmentmap build command always creates 2 datasets when a gmt file is provided
- Different results when running via CLI vs. CyREST HOT 3
- If rank file starts with empty line get error
- GSEA-Enrichmentmap-Cytoscape-desktop applicaion HOT 4
- Diffuse string Network HOT 1
- User unaware that multi-dataset maps are supported HOT 1
- EM version 3.4.0-SNAPSHOT" Default style node color: -log10(pvalue)_max (enhancement) HOT 8
- gray nodes (not colored by -log10(value)when creating the map HOT 7
- Input files for EnrichmentMap HOT 3
- create a subnetwork of most significant gene set per cluster HOT 6
- Issue with Parsing .txt or .xls Files in EnrichmentMap: "For input string: 'I<' Error" HOT 3
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