Rgraphviz for Windows
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@zhangqi007yahoocom-883
Last seen 7.2 years ago
Dear all, I tried to use GOstats package, and realized that Rgraphviz package is required for displaying the graph that I created (is this true?). Then I found out that the Rgraphviz package for Windows is not available. Any work-around for this? Thanks a lot for your help. Qi Zhang
Rgraphviz GOstats Rgraphviz GOstats • 754 views
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@sean-davis-490
Last seen 7 weeks ago
United States
Qi Zhang, I can't confirm that there is not a graphviz build for windows--any help? I think there are functions in ontoTools to output graphs in dot format that can be plotted by graphviz. You could take these to a Mac (for which a binary for graphviz is available) or other computer which has graphviz. Alternatively, you might be able to install cygwin and then install graphviz on top of that (but I would suggest checking with someone else before trying that option.) Sean On Aug 17, 2004, at 1:24 PM, <zhangqi007@yahoo.com> wrote: > Dear all, > > I tried to use GOstats package, and realized that > Rgraphviz package is required for displaying the graph > that I created (is this true?). Then I found out > that the Rgraphviz package for Windows is not > available. Any work-around for this? Thanks a lot > for your help. > > Qi Zhang > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
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> graphviz. Alternatively, you might be able to install cygwin and then > install graphviz on top of that (but I would suggest checking with > someone else before trying that option.) The problem here is that cygwin and R don't play nicely together in these situations. Building Graphviz w/ cygwin causes problems when Rgraphviz tries to link to it.
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Jeff, I was thinking more along the lines of having a platform for building graphviz for display purposes, if for no other reason than most of the world has access to Windows, but not everyone has access to unix and a quick fix might be enough. I assumed that cygwin was not a great answer in terms of operating with R. If one has the graphviz binaries and a dot file, one can render it, which would avoid having to move outside the windows platform. I like your answers better, though--don't use windows right now and "help is on the way!". Sean On Aug 17, 2004, at 2:16 PM, Jeff Gentry wrote: >> graphviz. Alternatively, you might be able to install cygwin and then >> install graphviz on top of that (but I would suggest checking with >> someone else before trying that option.) > > The problem here is that cygwin and R don't play nicely together in > these > situations. Building Graphviz w/ cygwin causes problems when Rgraphviz > tries to link to it.
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Hi, An inelegant but probably functional workaround is to communicate with graphviz through files. I don't know whether there is already an export function from "graph" objects in Bioconductor to .dot files, or whether someone would like to contribute one? .dot files can be read from graphviz's dot, neato etc. on the command line (and you may even automate that using the "system" command in R). It's not pretty, but works. Best wishes Wolfgang Sean Davis wrote: > Jeff, > > I was thinking more along the lines of having a platform for building > graphviz for display purposes, if for no other reason than most of the > world has access to Windows, but not everyone has access to unix and a > quick fix might be enough. I assumed that cygwin was not a great answer > in terms of operating with R. If one has the graphviz binaries and a > dot file, one can render it, which would avoid having to move outside > the windows platform. > > I like your answers better, though--don't use windows right now and > "help is on the way!". > > Sean > > On Aug 17, 2004, at 2:16 PM, Jeff Gentry wrote: > >>> graphviz. Alternatively, you might be able to install cygwin and then >>> install graphviz on top of that (but I would suggest checking with >>> someone else before trying that option.) >> >> >> The problem here is that cygwin and R don't play nicely together in these >> situations. Building Graphviz w/ cygwin causes problems when Rgraphviz >> tries to link to it. > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber
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> An inelegant but probably functional workaround is to communicate with > graphviz through files. I don't know whether there is already an export > function from "graph" objects in Bioconductor to .dot files, or whether > someone would like to contribute one? Well, there's agwrite(), but iti s in Rgraphviz, which of course doesn't exist for Windows. :) But it will output a .dot file ... I'm not very familiar, but I believe that there might be some mechanism of graph->GXL->dot.
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I think I mentioned it, but in ontoTools, there is a command, toDot, that writes out dot format from graphNEL? Jeff, correct me if I'm wrong. Sean On Aug 17, 2004, at 3:02 PM, Jeff Gentry wrote: >> An inelegant but probably functional workaround is to communicate with >> graphviz through files. I don't know whether there is already an >> export >> function from "graph" objects in Bioconductor to .dot files, or >> whether >> someone would like to contribute one? > > Well, there's agwrite(), but iti s in Rgraphviz, which of course > doesn't > exist for Windows. :) But it will output a .dot file ... > > I'm not very familiar, but I believe that there might be some > mechanism of > graph->GXL->dot. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
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> I think I mentioned it, but in ontoTools, there is a command, toDot, > that writes out dot format from graphNEL? Jeff, correct me if I'm > wrong. I bleieve that's what I was thinking of, but I honestly haven't personally used it before, so can't say.
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Jeff Gentry wrote: >>I think I mentioned it, but in ontoTools, there is a command, toDot, >>that writes out dot format from graphNEL? Jeff, correct me if I'm >>wrong. > I bleieve that's what I was thinking of, but I honestly haven't personally > used it before, so can't say. > Would it make sense to move that function into the "graph" package? Bw Wolfgang -- ------------------------------------- Wolfgang Huber Division of Molecular Genome Analysis German Cancer Research Center Heidelberg, Germany Phone: +49 6221 424709 Fax: +49 6221 42524709 Http: www.dkfz.de/abt0840/whuber
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Jeff Gentry ★ 3.9k
@jeff-gentry-12
Last seen 7.2 years ago
> I tried to use GOstats package, and realized that > Rgraphviz package is required for displaying the graph > that I created (is this true?). Then I found out > that the Rgraphviz package for Windows is not > available. Any work-around for this? Thanks a lot > for your help. Well, for the short term, the main workaround is to not use Windows. We are looking at trying to get a Rgraphviz build for Windows in the not too distant future, though.
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