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How the vertices are placed is up to d3, although we use a default gravity (https://github.com/mbostock/d3/wiki/Force-Layout#wiki-gravity) of 0.1. This causes the vertices to be drawn towards the center of the layout, and by default, the entire graph is loaded in the center. I'm not sure what problem you're experiencing but it could be that it's a bug in d3.
Is that intentional or would it be hard to place them more centrally?
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