I noticed that some nodes in ClueGO output are connected with arrows (diamond ends) while some aren't. What does it mean when one node is connected to another by an arrow vs. when they are not? I'd be sincerely grateful for your help as I spent an hour looking for this information and couldn't.
Indeed, I couldn't find any mention or screenshot of diamond arrowhead in the ClueGO paper or manual. You can find links to those on the Cytoscape app store, if you want to look more carefully than i did.
However, as with any Cytoscape network, you should be able to open the Style panel, then the Edge tab, and then expand the target arrowhead style to see what values it is mapped to. That might give some insight into why and when a particular edge has a diamond arrowhead.
If that fails, then I'd recommend emailing the app authors directly (contact info also on the app store page). They are usually quick to reply.
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