improve layout with subnodes/ keep edges straight

[HizJ]

Hi,

I am building a network where between major nodes I have 'subnodes'. The subnodes represent distances e.g. 2 subnode on edge between major node - distance of 2.

when building large networks and using a 'force-directed' layout I encounter an issue where the subnodes are treated like other nodes resulting in the graph becoming entangled and messy. 

for example if I plot my network without the subnodes it looks like this. Ideally when plotting with the subnodes, they should appear as dots on the straight lines

however instead it looks like this:

I assume this issue arises as the layout algorithm is trying to maintain distance between the subnodes too.

can anyone help me to keep the edges between the major nodes as straight as possible and prevent this entaglement. 

Thanks

[Dexter Pratt]

Hi 

Which layout algorithm(s) are you using?  Can you share your two example networks, perhaps by saving them to NDEx and sharing them via a sharable URL? (www.ndexbio.org, see the NDEx icon in the left corner of the Cytoscape menubar)

Dexter