Is there a way to use x,y coordinates stored as attributes of each node to layout a graph using the coordinates that were calculated by another program?
And if not, would it be possible to implement this somehow - how does one get started on this?
Is there a standard way how to provide the node positions to the cytoscape.js web viewer somehow?
Background: it is trivial to use Python networkx to calculate some layouts which are not supported in Cytoscape, and it would also be trivial to store the coordinates as node attributes. All that would then be need is some way for Cytoscape to use those coordinates to find node positions instead of using a layout algorithm.
This is a quite easy thing to do. Many examples on use this functionlity in the demos, as you can see here:
As you can see, there are an abundance of examples for this in the demos, but also in the docs. You can see one here and here:
// can use reference to eles later
var eles = cy.add([
{ group: 'nodes', data: { id: 'n0' }, position: { x: 100, y: 100 } },
{ group: 'nodes', data: { id: 'n1' }, position: { x: 200, y: 200 } },
{ group: 'edges', data: { id: 'e0', source: 'n0', target: 'n1' } }
]);
The json used in the .add() function can be created in your js application or directly in Python and added to the graph as some of the examples do.
In general, you should take some time and skim through through the docs. The ability to position nodes via x and y is quite basic and is one of the first pages in the docs.
If you don't understand the description in the docs and the examples I provided, please edit your question and add your current code as a Minimal, Reproducible Example, where you can show your efforts to implement the positioning.
As @maxkfranz pointed out, the preset layout plays a big role here. The documentation states this in the Initialisation Chapter: