[BioC] GOstats package - Graphical representation of enriched terms - Help needed

[Srinivas Iyyer]

Dear Group, 
I did hyperGTest in GOStats package and trying to plot
the enriched terms onto GO tree.


>gp <- new("GOHyperGParams", 
          geneIds =  upids,
          universeGeneIds = euniv,
          ontology = "BP", 
          annotation = "rgug4130a", 
          pvalueCutoff = hgCutoff, 
          conditional = TRUE,
          testDirection = "over")

>hgO <- hyperGTest(gp)

>treedat <- GOGraph(summary(hgO)$GOBPID,GOBPPARENTS)
>pdf ("bpCutLeavestreeTest.pdf", width=100, height =
100,paper="special")
> plot(treedat)
Error in as.double(y) : cannot coerce to vector


Could I get some help in this error.  what is wrong
here?

thanks
Srini








--- Sean Davis <sdavis2 at mail.nih.gov> wrote:

> On Jan 4, 2008 10:56 AM, Srinivas Iyyer
> <srini_iyyer_bio at yahoo.com> wrote:
> 
> > Dear Group,
> > I used hyperGTest using 'conditional' parameter as
> > 'True'.
> >
> > I generated HTML report of all enriched terms.
> There
> > are many such HTML tables that are difficult to
> look
> > at and reason biologically.
> >
> > Are (IS) there any methods (more than one) to
> > represent enriched terms, their P-values
> graphically.
> >
> > Such as drawing GO tree and color enriched term
> nodes
> > OR a heatmap?
> >
> > If so, could you please let me know modules that
> can
> > help me in this task.
> >
> 
> Hi, Srini.  You might look at Rgraphviz.
> 
> Sean
> 



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