dishevelled.org venn-cytoscape3-app provides a Cytoscape 3  app for generating Venn and Euler diagrams. The Venn and Euler diagram Cytoscape app requires java version 1.6 or later and Cytoscape version 3.0 or later.
The app provides a diagram view and a details view for comparing two or more Cytoscape groups at a time.
The diagram view is an interactive Venn or Euler diagram showing the number of nodes in each logical grouping. Clicking on any area in the diagram selects the corresponding nodes in the current Cytoscape network view. The diagram can be exported to an image file in PNG and SVG formats.
The Venn diagram view uses a symmetrical layout that supports two to four Cytoscape groups. Venn diagram views for two and three Cytoscape groups use two and three circles respectively. For four Cytoscape groups, a symmetrical construction of four ellipses is used.
The Euler diagram view uses an area-proportional layout that supports two or more Cytoscape groups. A Euler diagram is similar to a Venn diagram but does not display all possible intersections. The Euler layout allows an exact area-proportional Venn or Euler diagram to be generated when the data allow it and a statistically-justified approximation of a Venn or Euler diagram when the data do not [2, 3].
The details view shows the nodes in each logical grouping. The selection model of the details view synchronizes the selection for all of the list views (i.e. selecting a node in any one list will select it in all lists) and exports the selection to the current Cytoscape network view (selecting a node in the details view will select it in the current Cytoscape network view, but not vice versa). The details view supports two to four Cytoscape groups.
 Leland Wilkinson, "Exact and Approximate Area-Proportional Circular Venn and Euler Diagrams," IEEE Transactions on Visualization and Computer Graphics, pp. 321-331, February, 2012-2013