[BioC] KEGGgraph help

[Martin Morgan]

On 11/29/2010 09:01 AM, Jitao David Zhang wrote:
> Hi dear Yan Jiao,
> 
> Well, then it must be the problem of Rgraphviz. You may have to turn to the
> maintainers of Rgraphviz (help(package=Rgraphviz)). Before that, check out
> the installation of Rgraphviz as well as the documentation of the package.
> 
> In case the question still exists, please tell me. Paul Shannon and I are
> working on an alternative approach, which might be in beta-phase soon and
> might help.
> 
> Best wishes,
> David
> 
> 2010/11/29 Yan Jiao <y.jiao at ucl.ac.uk>
> 
>> No, it crashed

Can you be more specific?

Martin

>>
>>
>>
>>
>>
>> *From:* Jitao David Zhang [mailto:davidvonpku at gmail.com]
>> *Sent:* 29 November 2010 16:48
>>
>> *To:* Yan Jiao
>> *Cc:* bioconductor at r-project.org
>> *Subject:* Re: [BioC] KEGGgraph help
>>
>>
>>
>> Hi dear Yan,
>>
>> Maybe give a try to draw a toy network
>>
>> V <- letters[1:10]
>> M <- 1:4
>> g1 <- randomGraph(V, M, 0.2)
>> plot(g1)
>>
>> Is is okay?
>>
>> Cheers, David
>>
>> 2010/11/29 Yan Jiao <y.jiao at ucl.ac.uk>
>>
>> sessionInfo()
>>
>> R version 2.12.0 (2010-10-15)
>>
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>>
>>
>> locale:
>>
>> [1] LC_COLLATE=English_United Kingdom.1252
>>
>> [2] LC_CTYPE=English_United Kingdom.1252
>>
>> [3] LC_MONETARY=English_United Kingdom.1252
>>
>> [4] LC_NUMERIC=C
>>
>> [5] LC_TIME=English_United Kingdom.1252
>>
>>
>>
>> attached base packages:
>>
>> [1] grid      stats     graphics  grDevices utils     datasets  methods
>>
>> [8] base
>>
>>
>>
>> other attached packages:
>>
>> [1] KEGGgraph_1.6.0  XML_3.2-0.2      Rgraphviz_1.28.0 graph_1.28.0
>>
>>
>>
>> loaded via a namespace (and not attached):
>>
>> [1] tools_2.12.0
>>
>>
>>
>> *From:* Jitao David Zhang [mailto:davidvonpku at gmail.com]
>> *Sent:* 29 November 2010 16:40
>> *To:* Yan Jiao
>> *Cc:* bioconductor at r-project.org
>> *Subject:* Re: [BioC] KEGGgraph help
>>
>>
>>
>>
>> please report sessionInfo() results. Currently I have no clue. It might be
>> caused by corrupt graphviz, but I am not sure.
>>
>>
>> Best wishes,
>> David
>>
>> 2010/11/29 Yan Jiao <y.jiao at ucl.ac.uk>
>>
>> Dear all,
>>
>>
>>
>> I managed reading in a kegg graph
>>
>>
>>
>> A graphNEL graph with directed edges
>>
>> Number of Nodes = 70
>>
>> Number of Edges = 109
>>
>>
>>
>> but when I do plotKEGGgraph, R crashed, my R version is 2.12.0 , how can
>> I see the graph?
>>
>>
>>
>> Many thanks
>>
>>
>>
>> yan
>>
>>
>>
>>
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>>
>>
>>
>> --
>> Jitao David Zhang
>> Pre-doc staff of Computational Biology and Biostatistics
>> Division of Molecular Genome Analysis
>> DKFZ, Heidelberg D-69120, Germany
>>
>> http://www.NextBioMotif.com/
>>
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>>
>>
>>
>>
>> --
>> Jitao David Zhang
>> Pre-doc staff of Computational Biology and Biostatistics
>> Division of Molecular Genome Analysis
>> DKFZ, Heidelberg D-69120, Germany
>>
>> http://www.NextBioMotif.com/
>>
> 
> 
> 


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