in reply to Lattice , Planar graphs and GraphViz

Doesn't GraphViz do it by default? It always tries to reduce crossings. You can probably help by grouping edges into subgraphs if you can "manually" decide which nodes should be together in the neighbourhood.
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Re^2: Lattice , Planar graphs and GraphViz
by spx2 (Deacon) on Oct 15, 2009 at 14:42 UTC

    after I group nodes into subgraphs can I still plot the subgraphs as one big graph ?

    I guess you mean to cluster the nodes, no ?

      Yes, cluster nodes. And yes, subgraphs will be part of one graph. And it will probably do what you want (connecting nodes). I wanted the opposite - connect borders of subgraphs and it was very tricky. If you work on Windows then you will have many graphviz examples in directory C:\Program Files\Graphviz2.22\share\graphviz\graphs, e.g. C:\Program Files\Graphviz2.22\share\graphviz\graphs\directed\clust2.gv which show well how graphviz (well, actually dot, not graphviz: dot.exe -Tpng clust2.gv > clust2.gv.png) renders it.