top-down subgraphs, left-right inside subgraphs

Question

I\'d like to have my graph looks like this:

But I can only get this:

Answer 1

Using constraint=false should get the nodes in your subgraphs to turn out the way you want http://www.graphviz.org/doc/info/attrs.html#d:constraint

subgraph clusterB {
    label=B
    "0B"
    "1B"
    "2B" -> "0B" [constraint=false label=•]
}

After that you'll find that your subgraphs don't line up with each other the way you want. Something like this could resolve that.

"0A" -> "0B" -> "0C" -> "0D" -> "0E" [weight=999 style=invis];