For instance I want to visualise my graph in level order hierarchy, but each node can have multiple parents and children, and i want to be able to traverse the graph in the GUI by selecting 2 nodes.
Currently the 'breadthfirst' layout allows hierarchy, while the 'cose' layout allows compound nodes (nodes that can have multiple parents and children). Is there a way to tweak the source code for either, or to make my own custom layout from scratch for cytoscape?
Try the existing layouts:
breadthfirst and dagre are DAG-specific layouts. cola supports DAG-like flow, but it's a force-directed layout.
Or write your own layout: http://js.cytoscape.org/#extensions/api
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