I use graphviz to create graphs of graphs. First I use neato, to create several small graphs. Then I use dot, to create a big graph, using the postscript-files of the small graphs as custom shapefiles.
using version 2.6 edges from a lower level of the graph end below the included shapefiles
using version 2.16 edges from a lower level of the graph cross the included shapefile
it look like the size of the shapefile is ignored
Input file: b1740.dot
Output file: b1740.ps
[erg] Version 2.16 is almost two years old. We currently deprecate using shapefile and shape=epsf. Instead, there is the image attribute available to all polygonal nodes. You can combine this with shape=none and label="" to get what you want.