I'm trying to use GraphViz to draw graphical models. However, I didn't find a way to make draw overlapping clusters. For example, how can I make "nodeA->nodeB" to lie inside both clusterA and clusterB?
AFAIK you can't.
Clusters as described in the documentation:
If the name of the subgraph begins with cluster, Graphviz notes the subgraph as a special cluster subgraph. If supported, the layout engine will do the layout so that the nodes belonging to the cluster are drawn together, with the entire drawing of the cluster contained within a bounding rectangle.
The whole idea of clusters is not to overlap, but to group nodes (and graphviz raises an error when a node is part of two subgraphs).
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