Creating a cytoscape bubble figure

Question

[Dave Carlson]

Hi all,

I'm interested in creating a figure similar to figure 4C-D in Ganassi et al. 2022:

The text from the paper says the following:

Bubble plots demonstrating networks of enriched Gene Ontologies (GOs), clustered according to main biological processes, of differentially expressed myopathogenes during early satellite cell dynamics. C. Main biological processes enriched in downregulated myopathogenes (green). D. Main biological processes enriched in upregulated myopathogenes (magenta). GOs (bubbles) were retrieved using Metascape (metascape.org; [240]) and Panther Gene Ontology (geneontology.org; [241]) and visualised using Cytoscape (cytoscape.org; v3.8.2; [242]).

I'm not very familiar with these tools. I've looked through some of the Cytoscape tutorials, but I have not found any info on how to make a figure that looks like this. Does anybody have any ideas regarding what specific Cytoscape apps might have been used?

Any suggestions would be appreciated!

Thanks! Dave

Answer 1

[Scooter]

Hi Dave,

That's actually easier than it looks. Start by doing a layout of the entire network, then select each class of nodes (e.g. Skeletal Muscle Contraction) and do a circle layout of selected nodes and move those to the side. Repeat for all of your groups and then move the groups around to fit the esthetics.

-- scooter

[Dave Carlson]

Fantastic. Thanks a lot!