top-down subgraphs, left-right inside subgraphs

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

But I can only get this:

The problem is, rankdir does not work in subgraph. So, how to emulate it?

The code:

digraph G {
    node [shape = circle]
    0 [style = invis]

    0 -> "0A"

    subgraph clusterA {
        label=A
        "0A"
        "1A"
        "2A" -> "0A" [label=•]
    }

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

        subgraph clusterC {
        label=C
        "0C"
        "1C"
        "2C" -> "0C" [label=•]
    }

    subgraph clusterD {
        label=D
        "0D"
        "1D"
        "2D" -> "0D" [label=•]
    }

    subgraph clusterE {
        label=E
        "0E"
        "1E"
        "2E" -> "0E" [label=•]
    }

    subgraph clusterF {
        label=F
            {node [shape = doublecircle] "0F" "1F"}
        "2F" -> "0F" [label=•]
    }

    "0A" -> "1B" [label=a]
    "1A" -> "2B" [label=a]
    "0B" -> "1C" [label=b]
    "1B" -> "2C" [label=b]
    "0C" -> "1D" [label=c]
    "1C" -> "2D" [label=c]
    "0D" -> "1E" [label=d]
    "1D" -> "2E" [label=d]
    "0E" -> "1F" [label=e]
    "1E" -> "2F" [label=e]
}

Solution

Reproducing particular graph layouts usually can be achieved with:

Invisible nodes and edges
rank constraints

Here's how I reproduced your graph - or at least a part of it:

digraph g {
    rankdir="LR";
    node[shape = circle, fontsize=14];
    fontsize=18;
    labeljust="l";

    edge[style=invis, fontsize=12];

    { rank=same;
        0 [style = invis];
        01 [style = invis];
        02 [style=invis];
        0 -> 01 -> 02;
    }

    subgraph clusterA {
        "0A" -> "1A" -> "2A";
        "2A" -> "0A" [label=".", constraint=false, style=solid];
        label="A";
    }

    subgraph clusterB {
        "0B" -> "1B" -> "2B";
        "2B" -> "0B" [label=".", constraint=false, style=solid];
        label="B";
    }

    subgraph clusterC {
        "0C" -> "1C" -> "2C";
        "2C" -> "0C" [label=".", constraint=false, style=solid];
        label="C";
    }

    0 -> "0A"[style=solid];
    01 -> "0B"[style=invis];
    02 -> "0C"[style=invis];

    // edges between clusters
    edge[constraint=false, style=solid];
    "0A" -> "1B" [label=a]
    "1A" -> "2B" [label=a]
    "0B" -> "1C" [label=b]
    "1B" -> "2C" [label=b]
}

This solution is not very intuitive. A couple of points to achieve this:

I chose rankdir="LR" which resulted in nicer edges than TB, though it does not really correspond with the direction of the graph
Invisible nodes and edges are use for the top rank nodes (0, 01, 02) in order to have the clusters align left.
The (invisible) top nodes are forced to the same rank and are linked by invisible edges - this will ensure that the clusters linked to each node appear in the correct order.

The result is:

graphviz output