Dear all,

Using the ReactomePA package I have visualised the enrichment results by means of the enrichMap function (for an example see the original publication, Figure 1 http://pubs.rsc.org/en/content/articlepdf/2016/mb/c5mb00663e).

I am wondering though what the connections between the nodes mean? When does a connection arise? When there is (sufficient) overlap between the gene sets of the pathway or do the connections come from Reactome database? 

Thank you for your help/answers!

The connection between the dots is half the Dice coefficient. The intersection of genes in each pathway divided by the total amount of genes in these two pathways.

The color of the nodes is a representation of the p-value of the pathway. And the size represents the number of genes in the pathway. 

See the source code.