Suggest About Layout.

[Matt-V50]

It seems this layout is better than Breadth first

Breadth first

As you can see, there is no actual connection here.

[CoderAllan]

You are right that some of the layouts hide some of the connection, but I actually don't have control over the layout.
Those layout types you can choose in the dropdown box, is the layouts that the Cytoscape.js library provides.
I will leave the issue open in case somebody smarter the me comes up with a solution.