Diagram diagram = ViewService.createDiagram(....);
for (Object view : diagram.getChildren()) {
	if (view instanceof Node) {
		Node node = (Node) view;
		LayoutConstraint layoutData = node.getLayoutConstraint();
		if (layoutData instanceof Bounds) {
			((Bounds) layoutData).setX(0); // calculated x (you need to come up with an algorithm)
			((Bounds) layoutData).setY(0); // same
			((Bounds) layoutData).setWidth(0); // same
			((Bounds) layoutData).setHeight(0); // same
		}
	}
}