Hi

I am trying to visualize my GO results as a graph. So far I have managed to do this:


params <- new("GOHyperGParams", geneIds= sigLL, universeGeneIds=univ, annotation=annoPk, ontology="BP", pvalueCutoff= pVerdi_GO, conditional=TRUE, testDirection="over")
hgOver <- hyperGTest(params) 
g <- GOGraph(summary(hgOver)$GOCCID, GOMFPARENTS)
plot(g)

If there are no edges/direct connection between the nodes only the nodes are drawn, but I would like to be able to visualize the (not direct) connections between my nodes. Have tried to look for a solution but so far I have not gotten any one to work, suggestions?

Regards
Ingrid


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