Hi @Dunhou
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This is for the moment not possible the auto-layouter should do it's work in your case it's seems not. Is it something 100% reproducible? Could you share with us a script that produce such output so we can fix the bug? Moreover for moment this is not possible to define the node position on a graph node. I forwarded this request to the responsible development team, but there is no guarantee that this will be implemented.
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The data dictionary can be used to define default parameters value by passing a NodePath before it's creation but the semantic is a bit complex in Python so I would advice you to use
SetDefaultValue
once a port is created as demonstrated in Modify Node Graph Example.
Cheers,
Maxime.