The easiest way to achieve this is to add splines=false to the dot file – this forces the rendering of the edges to be straight lines:
digraph {
splines=false;
subgraph clusterX {
A;
B;
}
subgraph clusterY {
C;
D;
}
A -> B;
B -> C [constraint=false];
C -> D [label=yadda];
}
Output:
