Add Clusters Without Changing The Layout

I'm creating a graph that shows the association between files and databases. When I don't use any subgraph clusters I get map1.jpg. Which looks awesome! :D But then I wanted to highlight a row of nodes (all the nodes in the same rank) and label them. After looking at some of the documentation, I used clustering, but it messes up the layout and brings the nodes really close together (see map2.jpg). How can I draw a box around the nodes in a row without messing up the layout? This is the command I used to make my images: dot -Tjpg %dotDir%example.txt -o %dotDir%map.jpg

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