How do I stop GraphViz dot making my clusters more compact? - graphviz

Question

I'm trying to use dot to layout several non-connected graphs at the same time using clusters for drawing and styling boxes around each.
The problem is that while on a rendering without clustering, the layout is very neat and separates out unconnected graphs within one cluster, but once I try to use clustering it squashes these together, using less space but rendering the output much less clearly understandable (especially once it starts packing together differently sized labels).
Here's the version without clustering:
And here's with:
And the source -- to get the version without clustering I just deleted the "r" off the end of "cluster".
digraph G {
node[shape="rectangle",fontname="Nimbus Sans"];
subgraph cluster_a {
style=filled;
bgcolor=lightgrey;
node [style=filled,color=white];
a_vq; a_lvt; a_wvw; a_yvy;
a_zgxl; a_hqz; a_yqq; a_zofv;
a_qvr; a_qlz; a_ycr; a_ilq;
a_ouw; a_ryq; a_lgl; a_qvr->a_lgl;
a_kwr; a_qlz->a_kwr; a_yl; a_ilq->a_yl;
a_kgyr; a_hqz->a_kgyr; a_llq; a_ryq->a_llq;
a_llo; a_ryq->a_llo; a_ll; a_ryq->a_ll;
a_ito; a_ll->a_ito; a_rql; a_lgl->a_rql;
a_ier; a_kwr->a_ier; a_lql; a_yl->a_lql;
a_vhgp; a_lql->a_vhgp;
a_vq->a_lvt;
a_lvt->a_wvw;
a_lvt->a_yvy;
a_vq->a_zgxl;
a_hqz->a_yqq;
a_lvt->a_zofv;
a_yvy->a_qvr;
a_zgxl->a_qlz;
a_zgxl->a_ycr;
a_ycr->a_ilq;
a_hqz->a_ouw;
a_yqq->a_ryq;
}
subgraph cluster_b {
style=filled;
bgcolor=lightgrey;
node [style=filled,color=white];
b_uel;
}
}
I tried fiddling with the packmode attribute in a few places, but it just seemed to break styling without fixing the problem and I wasn't entirely sure whether it would fix anything even if it worked properly.
I'd like to retain the neat, spatially separated graphs with clustering layouts -- does anyone know whether this can be done?

Answer 1

More of a hack than a real answer but it works for your sample - use invisible nodes and edges. I have also simplified your code, not sure whether this is suitable for your task but it makes looking at it easier.
digraph G
{
node[ shape = "rectangle", fontname = "Nimbus Sans", height = .5, width = 1 ];
subgraph cluster_a
{
style = filled;
bgcolor = lightgrey;
node[ style = invis ]; // create
inv_1; inv_2; // invisible nodes
node[ style = filled, color = white ];
// first unconnected graph
a_hqz -> { a_ouw a_yqq a_kgyr }
a_ouw -> { inv_1 } [ style = invis ] // insert invisible nodes
a_kgyr -> { inv_2 } [ style = invis ] // using invisible edges
a_yqq -> a_ryq;
a_ryq -> { a_llq a_llo a_ll }
a_ll -> a_ito;
// second unconnected graph
a_vq -> { a_lvt a_zgxl }
a_lvt -> { a_wvw a_yvy a_zofv }
a_zgxl -> { a_qlz a_ycr }
a_yvy -> a_qvr -> a_lgl -> a_rql;
a_qlz -> a_kwr -> a_ier;
a_ycr -> a_ilq -> a_yl -> a_lql -> a_vhgp;
}
subgraph cluster_b
{
style = filled;
bgcolor = lightgrey;
node[ style = filled, color = white ];
b_uel;
}
}