I am trying to make my graph pretty. I am using subclusters fairly extensively. The result I am getting is correct but could be prettier. Can I create more space between the subclusters?

Indirectly. Look at the margin attribute (margin | Graphviz) and also consider nesting clusters - possibly with peripheries=0

```
digraph D{
rankdir=LR
subgraph clusterA{
margin=55 //points
a1->a2->a3
}
subgraph clusterB{
margin=15 //points
b1->b2->b3
}
subgraph clusterC{
margin=55 //points
subgraph clusterD1{
margin=55 //points
peripheries=0
subgraph clusterD2{
margin=55 //points
peripheries=0
subgraph clusterD5{
margin=10 //points
subgraph clusterE{
peripheries=1
margin=55 //points
e1->e2->e3
}
d1->d2->d3
}
}
}
}
}
```

Giving: