Is there a way to tell Dot to use a cluster but not show the rectangle around the subgraph nodes?
You can do this with style.
Example using style=invis:
digraph g{ subgraph cluster0 { style=invis; 1 -> 2; } } If you'd like to use this as a default for all subgraphs, use subgraph[style=invis] :
digraph g{ subgraph[style=invis]; subgraph cluster0 { 1 -> 2; } } Edit: 9 years later...
The best solution is to use
peripheries=0
This will actually prevent generating the rectangle in svg output, whereas penwidth=0 still includes a polygon (with stroke-width="0", but it's still there).
I've added this since this is the most upvoted answer.
You can use style=invis:
subgraph cluster1 { style=invis ... } As an alternative to the style=invis approach above, you can also set pencolor=transparent (either locally or globally).
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