Network visualization for consensus modules

[bsangiorgi]

Ola Fabricio,

Thank you for developing such a fantastic package!

I’ve been exploring the Network Comparison vignette (https://www.bioconductor.org/packages/release/bioc/vignettes/BioNERO/inst/doc/vignette_03_network_comparison.html), specifically the section on identifying consensus modules. I’d like to visualize these modules in a manner similar to the output of the plot_gcn() function. From the Gene Coexpression Network inference vignette (https://www.bioconductor.org/packages/release/bioc/vignettes/BioNERO/inst/doc/vignette_01_GCN_inference.html), I see this visualization can be achieved through the following pipeline: identifying hubs (get_hubs_gcn()), extracting subgraphs (get_edge_list()), and network visualization (plot_gcn()).

The challenge I’m facing is that the structure of the object created by consensus_modules() differs from the one generated by exp2gcn(), which prevents me from following this pipeline for network visualization. Is there a workaround for this?

Looking forward to your insights.

Thank you,

[almeidasilvaf]

Hi, @bsangiorgi

Thank you for using BioNERO!

Unfortunately, there isn't a workaround for this. To make a network visualization with nodes and edges, one needs to extract edge lists (or adjacency matrices) for genes in a module, and extracting that for consensus modules is not trivial because of the way edges are scaled across independent data sets.

I will add this to my list of enhancements to implement (if possible).

All the best,
Fabricio

[bsangiorgi]

Understood!

Thanks for the quick reply, please feel free to close the issue.

Cheers,