using cytoscape to visualize enrichMap produced by DOSE clusterProfiler ReactomePA

enrichMap is very useful to generate a meaningful graph of clusters of enriched pathways.

Although we can use fixed=FALSE parameter and then nodes and edges can be moved around, some user prefer using Cytoscape to further customize the graph.

DOSE/clusterProfiler/ReactomePA support this feature indirectly.

User can use:

info <- enrichMap(x)

to store related information in info, which is a list of two data.frames: edge_data and vertex_data for edge and node information respectively.

User can then export the info to two csv files and import them into Cytoscape to play with.

NOTE: The enrichMap() is only available in doseplot