
Hi Naomi,

You should also get Rgraphviz loaded in order to plot grph

> library(Rgraphviz)

Ariel./

-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Naomi Altman
Sent: Mon 11/27/2006 12:14 PM
To: James W. MacDonald
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] GOstat
 
Thanks, Jim, but this did not work.

What I did was  (HG.out is the output from GOHy0perGResult):

grph <- GOGraph(summary(HG.out$GOBPID, GOBPPARENTS)
plot(grph)

Error in as.vector(x, "double") : cannot coerce to vector


grph
A graphNEL graph with directed edges
Number of Nodes = 40
Number of Edges = 47

So it looks like GOGraph works, but there is no plot method for 
grph.  Perhaps I need to load another library?

--Naomi

At 11:11 AM 11/27/2006, James W. MacDonald wrote:
>Hi Naomi,
>
>Naomi Altman wrote:
> > I am starting to use GOstat, and there are several things I do 
> not understand.
> >
> > I managed to get output from HyperGTest.  I was able to view the
> > enriched categories using htmlReport.
> >
> > I would like to try out the graphing methods, but I have not been
> > able to figure out the input.  In particular, I assume that since I
> > have created a GOHyperGResult object, I should use
> >
> > getGoGraph
> >
> > but I have not figured out what goes into the goIds argument.  I
> > presume it is some type of node identifier, but where do I find it?
>
>The getGoGraph() function wants a GOHyperGParams object, rather than a
>GOHyperGResult object. The goIds would then be the GO IDs that you are
>interested in, which can be read from the table produced by htmlReport().
>
>Anyway, I can't get getGoGraph() to ouput what I would expect. It
>appears to use GOXXCHILDREN to produce the graph, whereas the other
>functions in the examples for that (and related) function(s) use
>GOXXPARENTS.
>
>To get what I would expect, you can simply use GOGraph(). Say the top
>three GO IDs in your table are ("GO:0019219" "GO:0019222" "GO:0006350").
>Then you can get a graph by:
>
>grph <- GOGraph(c("GO:0019219" "GO:0019222" "GO:0006350"), GOBPPARENTS)
>plot(grph)
>
>HTH,
>
>Jim
>
>
> >
> > Thanks for any assistance.
> >
> > Naomi
> >
> >
> >
> > Naomi S. Altman                                814-865-3791 (voice)
> > Associate Professor
> > Dept. of Statistics                              814-863-7114 (fax)
> > Penn State University                         814-865-1348 (Statistics)
> > University Park, PA 16802-2111
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>--
>James W. MacDonald, M.S.
>Biostatistician
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
>734-647-5623
>
>
>**********************************************************
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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