[BioC] RCytoscape [was Re: Rgraphviz running problem on vista]

[Paul Shannon]

For some, RCytoscape might provide an alternative to Rgraphviz.   

It uses a Cytoscape plugin (which can be installed from within either Cytoscape 2.7 or 2.8) and Duncan Temple Lang's XMLRPC R package.  Operations operations like these are possible: 

 g.random <- randomGraph (V, M, 0.4)
 g.random <- initEdgeAttribute (g.random, 'weight', 'numeric', 0.0)   # Java is strongly-typed, so we have to add this information
 cw <- CytoscapeWindow ('demo', g=g.random)
 displayGraph (cw)
 layout (cw)
 redraw (cw)

You can see the result here: http://rcytoscape.systemsbiology.net/random.png

And find RCytoscape here:

 http://bioconductor.org/help/bioc-views/release/bioc/html/RCytoscape.html

A new version is in the works, providing easier back-and-forth between Cytoscape and R, and quite a few new features, but the current release, 1.0.1, is pretty good for displaying graphs from R, selecting and retrieving nodes, and controlling visual attributes.  A first cut at user documentation is 
at 

   http://rcytoscape.systemsbiology.net

I would be happy to help with any installation problems or difficulties encountered along the way.  Indeed, at this early stage of package development, comments and suggestions are really helpful, and eagerly sought.

Cheers,

- Paul Shannon
  Institute for Systems Biology
  Seattle


On Dec 11, 2010, at 5:54 PM, Martin Morgan wrote:

> On 12/09/2010 02:16 PM, xyang2 wrote:
>> Dear all,
>> 
>> I need help on the install of Rgraphviz after install my new version of R.
>> R2.12.0 crashed after I trying to plot using Rgraphviz package.
>> Details are:
>> 
>> 
>>> library("Rgraphviz")
>> Loading required package: graph
>> Loading required package: grid
>> 
>> /> set.seed(123) /
>> /> V <- letters[1:10] /
>> /> M <- 1:4 /
>> /> g1 <- randomGraph(V, M, 0.2) /
>> //
>> 
>> but when I tried to plot it R crashed.
>> 
>> /> plot(g1) /
> 
> Hi Xinan --
> 
> I haven't tried this yet, but the package source file
> 
> http://bioconductor.org/packages/2.7/bioc/src/contrib/Rgraphviz_1.28.0.tar.gz
> 
> contains a file README saying in part
> 
> This version will not work with Vista 64 bit, so the user will
> need to compile from source, and in addition make sure that a version
> strictly greater than 2.22 is used.
> 
> It then has instructions for installing Rgraphviz from source. This
> requires the tools at
> 
> http://www.murdoch-sutherland.com/Rtools/
> 
> Martin
> 
>> 
>> My working environments are:
>> 
>> 
>>> R.version.string
>> [1] "R version 2.12.0 (2010-10-15)"
>>> win.version()
>> [1] "Windows Vista (build 6001) Service Pack 1"
>>> 
>>> packageDescription("Rgraphviz")$Version
>> [1] "1.28.0"
>>> graphvizVersion()
>> $installed_version
>> [1] ‘2.20.3’
>> 
>> $build_version
>> [1] ‘2.20.3’
>> 
>> and I do add the "C:\\Program Files\\Graphviz2.20\\Bin" into PATH of
>> environment
>> 
>> 
>>> strsplit(Sys.getenv("PATH"), ";")
>> $PATH
>> [1] "%CommonProgramFiles%\\Microsoft Shared\\Windows Live"            
>> "c:\\Rtools\\bin"                                                 
>> "c:\\Rtools\\perl\\bin"                                           
>> [4] "c:\\Rtools\\MinGW\\bin"                                          
>> "C:\\Perl\\site\\bin"                                             
>> "C:\\Perl\\bin"                                                   
>> [7] "C:\\Windows\\system32"                                           
>> "C:\\Windows"                                                     
>> "C:\\Windows\\System32\\Wbem"                                     
>> [10] "C:\\Program Files\\Intel\\DMIX"                                  
>> "C:\\Program Files\\ATI Technologies\\ATI.ACE\\Core-Static"       
>> "C:\\Program Files\\Common Files\\Roxio Shared\\DLLShared\\"      
>> [13] "C:\\Program Files\\Common Files\\Roxio Shared\\10.0\\DLLShared\\"
>> "C:/R/R-2.10.0/library/RMySQL/libs"                               
>> "C:\\Program Files\\Graphviz2.20"                                 
>> [16] "D:\\AppliedBiosystems\\SDS2.4\\lib\\algorithm\\bin\\win32"       
>> "D:\\AppliedBiosystems\\SDS2.4\\lib"                              
>> "C:\\Program Files\\Graphviz2.20\\bin"                            
>> [19] "C:\\Program Files\\Common Files\\Microsoft Shared\\Windows Live" 
>> "C:\\Program Files\\SSH Communications Security\\SSH Secure Shell"
>> "C:\\R\\R-2.7.1\\library\\RMySQL\\libs"                           
>> [22] "C:\\Program Files\\Graphviz2.20\\Bin"                            
>> 
>>> 
>> 
>> Thanks,
>> 
>> Xinan
> 
> 
> -- 
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> 
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> 
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