Accepted answer

The short answer is that you can't. The longer answer is that the force layout that D3 implements does nothing to prevent overlapping links and there are no parameters you can set to do that. What you can do is try to adjust the parameters that are there and see if they happen to help with this problem.

The force layout implemented in sigma js does try to minimise the number of links that cross, so if you don't absolutely need D3, this would be an alternative you could look into.

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