similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
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@jansoderman-11752
Last seen 2.4 years ago

Hi,

I have used the emapplot {enrichplot} function to visualize gsePathway {ReactomePA} results. However, I wonder if it is possible to extract the similarity coefficients that are used for edges between nodes, so that I can take the data into Cytoscape for visualization? Also, what measure of similarity between pathways is used?

Likewise, is it possible to extract the similarity coefficients from the simplify {clusterProfiler} function?

Sincerely, Jan