Hi Hugh, I was testing your handy code and got the following weird behavior. For some input graphs plotGraphWithTemplate works fine with the default layout ("dot") but fails when "neato" is requested. Of course this has to do more with the Rgraphviz plot call rather than with your function , but I will be happy to hear your opinion (or any bioc user) about this. 'g' and 'gg' are two small graphs I am sending you in separate email > require(Rgraphviz) > load("gdata.Rdata") > plotGraphWithTemplate(g,agopen(gg,"foo")) #non hidden edges are blue. Ok. > plotGraphWithTemplate(g,agopen(gg,"foo"),"neato") #every single edge plotted in black > sessionInfo() R version 2.6.1 (2007-11-26) i386-redhat-linux-gnu attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rgraphviz_1.16.0 graph_1.16.1 loaded via a namespace (and not attached): [1] cluster_1.11.9 rcompgen_0.1-17 tools_2.6.1 Thanks for your help, Ariel./

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