I am very new to Cytoscape and have what feels like an easy-to-solve problem. I am using the drag and drop functionality of Cytoscape to build networks (I am basically translating photographs of insect trail networks into Cytoscape representations - this makes it much easier to build the networks). The problem is that I need to export the edge table from Cytoscape into R for further analysis. Cytoscape exports a .csv file that has a column that looks like this:
"Node 5 (undirected) Node 2" <- all in a single column
What I need is either a .csv file that contains either an adjacency matrix or an edge list (where edges are represented as pairs of nodes, with each node in its own column). Is there an easy way to do this? Thank you in advance!
There are several solutions:
The http://apps.cytoscape.org/apps/adjexporter allows you to export the network as adjecency matrix
You can connect directly to Cytoscape from R using the CyREST interface: http://apps.cytoscape.org/apps/cyrest
You can replace all (undirected) terms with a tab
Hope this helps, Piet