A: 

In DOT try the option "-y"

-y          - Invert y coordinate in output
Pierre
That builds a blank graph for me. But the description implies I should be getting my graph upside-down, which is not what I want. I want to pull "1" out from the strongly-connected component.
Paul Biggar
+3  A: 

Use rank specification for the subgraph. In this case sink should make it at the bottom and max will make it on the same level as 5:

digraph G {
  0;
  { rank = sink; 1; }
  5;
  4;
  7;
  8;
  0 -> 4;
  5 -> 7;
  7 -> 8;
  7 -> 1;
  8 -> 5;
  4 -> 7;
}
van
Perfect. This also clarified how rank is supposed to be used, which I obviously misunderstood. I've solved another problem using rank=same after this. Thanks.
Paul Biggar