Cytoscape to visualize metanodes

Question

[Giovanni]

Hi!

I'd like to understand which cytoscape plugin is best for my use case. I developed a pairwise local allignment algorithm, that outputs a graph made of nodes representing drosophila and homo sapiens proteins. Each node has a field "Organism" that store the organism to which the node belongs to, and a field "array" to store a list of similar proteins belonging to the organism. There's no overlapping between the proteins of two different nodes.

I'm looking for a way to visualize my graph like eXamine Cytoscape's plugin does. Do you know how to use this or other plugins in my specific use case?

Thank you so much!

Answer 1

[xanderpico]

Not entirely sure I follow your example and understand what you want, but having looked at eXamine, here are few other options that leverage the concepts of sets in Cytoscape:

• https://apps.cytoscape.org/apps/setsapp
• https://apps.cytoscape.org/apps/boundarylayout
• Built-in support for Groups: https://cytoscape.org/cytoscape-tutorials/protocols/group-nodes/#/, including compound nodes with broundaries
• Build-in support for annotations: https://cytoscape.org/cytoscape-tutorials/protocols/advanced-annotations/#/, including background shapes