Edge Varieties

[Jordan Langston]

Hello,

I'm relatively new to Cytoscape and am still learning all that it has to offer. I'm interesting in building a protein-protein interaction model in the program from scratch and want to incorporate different edges to show how one node is regulated by another etc. I know Cytoscape has different edge styles, but I can not find an inhibitory type edge (as well as self loops etc), is there one in the program or do you need to draw/import one on your own. 

Thanks,

Jordan

[Scooter Morris]

Cytoscape doesn't have the concept of edge "type" -- just edge "style".  What that means is you can add edges from any node to any other node (including itself, for self loops) and then use the visual styles to show the semantics of the edge.  By convention, the "interaction" column in the edge table reflects the edge type.  So, for inhibitory interactions, you could add the text "inhibits" to the interaction column.  You could also add "walks across the street" -- Cytoscape really doesn't care.  Once you've set the edge types you want in that column, you can use the visual styles to visualize the semantics for those edges.  So, you could use the "T" edge target arrow shape to indicate that this is an inhibitory interaction.  You would do that by setting up a "discrete mapping" of the interaction column to the edge target arrow style.  This is pretty well explained in the tutorial on Basic Data Visualization.

-- scooter

[Jordan Langston]

Thank you!