Right. Having a k complete graph (a graph in which all nodes are connected to each of the other k nodes in the component) in the standard visualization would be very messy.
One possibility is having shaded semi-transparent area rather than all the lines.
For example, in the most minimal case, if you had {A, B}, and (A,B) as the edge of significance, since edges are not first-class objects as yet, rather than try and create a note AB pointing to A (which would not illustrate the connection’s importance) you could somehow have
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a connection-node label that takes AB with a tag that generates AB
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then creates two visual pointers \AB, A/, \AB,B/
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Finally you could use area to transparently shade the region enclosed by the triangle {AB,A,B}. This triangle would have edges {\AB,A/, \AB,B/, (A,B)}
I’m using \ x,y / as notation to indicate not a true link but a generated visual helper.
Ultimately there should still be a link from AB, into A so as to point to the note that inspired the important connection (A,B).
TL;DR In summary, given a highly important association / link (A,B) between A and B, I imagine:
- A way to click on the link (A,B) which takes you to a note AB in which you would write out the association importance etc. I.e, making edges first class objects.
- On the standard view there would be this note “AB” with some syntax indicating its status as link-note.
- AB would point to A in the standard view
- In some alternative view enabled by a plugin, link-notes would form a triangle with the two notes between which the edge of importance lies.
- This triangle would have {AB, A, B} as nodes, and {\AB,A/,\AB,B/,(A,B)} as edges and would be lightly filled in. Clicking on the shaded region would open AB.
Similarly the transitive connection (ABC), ie a chain of thoughts would be a shaded n-gon with {(A,B),(B,C), \ABC,A/, \ABC,C/} thus allowing us to click on the shaded region and taking us to ABC, a note about the connections.