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
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
> 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.
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.
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
> 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.
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
> 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.
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
> 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.
