Thanks Wolfgang.

Yes it does indeed produce a nice graph!

But with its own problems: Odd node sizes (tried changing fixedsize to TRUE
with fixInNamespace(plotGOTermGraph, "GOstats"), and that didn't work).  If
you change add.counts to TRUE, it doesn't show the colors.

I'm really looking to see the following.
The induced graph of all the nodes declared significant, with those nodes in
a different color, with counts, and labels that are terms, not IDs.
It seems that you've given me yet another piece of the puzzle.... but they
don't all fit together.
I can get many of these things with the various suggestions I've received, I
just can't get them all at once.
It may just be that without a lot of work R/BioC can't quite do what I'd
like.

I keep plugging away at this problem.

Thanks.

Dan.

On Fri, Sep 12, 2008 at 6:58 PM, Wolfgang Huber <huber@ebi.ac.uk> wrote:

> Dear Daniel
>
> thanks, and sorry for the delayed reply. I don't have much experience with
> this function, but it seems that if you replace the last line of your
> example code by
>
> par(mfrow=c(3,3))
>
> lapply(y, plotGOTermGraph, x,
>  node.colors=c(sig="white", not="blue"),
>  node.shape="circle", add.counts=FALSE)
>
> a result is produced. AfaIu, plotGOTermGraph wants to work on elements of
> the list y, not on y itself. I agree that the documentation in the
> function's manual page ("g : A graph object as returned by inducedTermGraph
> or termGraphs") would benefit from clarification/correction.
>
>  Best wishes
>        Wolfgang
>
> > sessionInfo()
> R version 2.8.0 Under development (unstable) (2008-09-12 r46536)
> x86_64-unknown-linux-gnu
>
> locale:
>
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
>  [1] grid      splines   tools     stats     graphics
>  [6] grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] RbcBook1_1.9.0       geneplotter_1.19.1
>  [3] lattice_0.17-14      RColorBrewer_1.0-2
>  [5] Rgraphviz_1.19.3     org.Rn.eg.db_2.2.3
>  [7] GOstats_2.7.0        Category_2.7.4
>  [9] genefilter_1.21.1    survival_2.34-1
> [11] RBGL_1.17.2          annotate_1.19.2
> [13] xtable_1.5-3         graph_1.19.1
> [15] GO.db_2.2.3          AnnotationDbi_1.3.10
> [17] RSQLite_0.7-0        DBI_0.2-4
> [19] Biobase_2.1.7        fortunes_1.3-5
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.11    GSEABase_1.3.5     KernSmooth_2.22-22
> [4] XML_1.96-0
>
>
> ----------------------------------------------------
> Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber
>
>
>
>
>
> daniel jupiter wrote:
>
>> Wolfgang,
>>
>> thanks!
>> As you suggested, here is a full script, followed by the error message,
>> and then the sessionInfo().
>>
>> Best regards,
>>
>> Dan.
>>
>> library(GO.db)
>> library(GOstats)
>> library(annotate)
>> library(org.Rn.eg.db)
>> library("Rgraphviz")
>> library("RBGL")
>> library("graph")
>> library("RColorBrewer")
>> library("geneplotter")
>> library("RbcBook1")
>>
>> # Just some dummy genes to play with
>> bkg=dbGetQuery(org.Rn.eg_dbconn(), "SELECT * from genes")
>> bkg=bkg$gene_id
>> test=bkg[1:100]
>>
>> params <- new("GOHyperGParams", geneIds = test,
>> universeGeneIds = bkg,annotation="org.Rn.eg.db",
>> conditional = FALSE, categoryName="GO", ontology="CC")
>>           x=hyperGTest(params)
>>
>> y=termGraphs(x,use.terms=TRUE , pvalue=.01)
>>
>> plotGOTermGraph(y,x, node.colors=c(sig="white",not="blue"),
>> node.shape="circle", add.counts=FALSE)
>>
>>
>> Error in function (classes, fdef, mtable)  :
>>  unable to find an inherited method for function "nodes", for signature
>> "list"
>>
>>
>>
>>  > sessionInfo()
>> R version 2.7.1 (2008-06-23)
>> i386-apple-darwin8.10.1
>>
>> locale:
>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>>  [1] grid      splines   tools     stats     graphics
>>  [6] grDevices utils     datasets  methods   base
>> other attached packages:
>>  [1] RbcBook1_1.8.0      geneplotter_1.18.0
>>  [3] lattice_0.17-8      RColorBrewer_1.0-2
>>  [5] Rgraphviz_1.18.1    org.Rn.eg.db_2.2.0
>>  [7] GOstats_2.6.0       Category_2.6.0     [9] genefilter_1.20.0
>> survival_2.34-1   [11] RBGL_1.16.0         annotate_1.18.0   [13]
>> xtable_1.5-2        graph_1.18.1      [15] GO.db_2.2.0
>> AnnotationDbi_1.2.2
>> [17] RSQLite_0.6-9       DBI_0.2-4         [19] Biobase_2.0.1
>> loaded via a namespace (and not attached):
>> [1] KernSmooth_2.22-22 cluster_1.11.11   >
>>
>>
>> On Thu, Sep 4, 2008 at 11:17 AM, Wolfgang Huber <huber@ebi.ac.uk <mailto:
>> huber@ebi.ac.uk>> wrote:
>>
>>
>>    Dear Daniel
>>
>>    thank you for your feedback! Would it be possible to
>>
>>    (i) send a code example that we can reproduce (i.e. where the
>>    variables "test" and "universe" are defined)?
>>
>>    (ii) send the output of sessionInfo() after running the example?
>>
>>     Best wishes
>>           Wolfgang
>>
>>    --    ----------------------------------------------------
>>    Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber
>>
>>
>>
>>    daniel jupiter wrote:
>>
>>        Hi all,
>>
>>        undoubtedly this is a silly question.
>>        After struggling for quite some time, I think I've been able to do
>>        hypergerometric tests for GO enrichment using hyperGTest.
>>        The documentation is a bit thin, but it's eventually become clear.
>>        The next step is to draw the DAG, with significant genes
>>        highlighted, and
>>        term names replacing GO IDs.
>>        A wrinkle: I am just interested in a particular set of genes,
>>        relative to a
>>        universe - there is no array, no annotation involved.
>>
>>        In any case, here is my code.
>>
>>        params <- new("GOHyperGParams", geneIds = test,
>>        universeGeneIds = universe,annotation="org.Rn.eg.db",
>>        conditional = FALSE, categoryName="GO", ontology="CC",
>>        pvalueCutoff=.01)
>>
>>        x=hyperGTest(params)
>>
>>        y=termGraphs(x,use.terms=TRUE , pvalue=.01)
>>
>>        plotGOTermGraph(y,x, node.colors=c(sig="white",not="blue"),
>>        node.shape="circle", add.counts=FALSE)
>>
>>        I am returned the following error:
>>        Error in function (classes, fdef, mtable)  :
>>         unable to find an inherited method for function "nodes", for
>>        signature
>>        "list"
>>
>>        Am I doing something obviously wrong?
>>
>>        Any help is greatly appreciated.
>>
>>        Thanks
>>
>>        Dan Jupiter.
>>
>>
>>
>>
>> --
>> Daniel C. Jupiter, Ph.D.
>> Postdoctoral Research Associate
>> Department of Systems Biology and Translational Medicine
>> College of Medicine
>> Texas A&M Health Science Center
>> 702 SW H.K. Dodgen Loop
>> Temple, TX 76504
>>
>> 979.997.2106 | Fax 254.742.7145
>> djupiter@tamu.edu <mailto:djupiter@tamu.edu> | www.tamhsc.edu <
>> http://www.tamhsc.edu>
>>
>


-- 
Daniel C. Jupiter, Ph.D.
Postdoctoral Research Associate
Department of Systems Biology and Translational Medicine
College of Medicine
Texas A&M Health Science Center
702 SW H.K. Dodgen Loop
Temple, TX 76504

979.997.2106 | Fax 254.742.7145
djupiter@tamu.edu | www.tamhsc.edu

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