[BioC] Question about graph package

[Florian Hahne]

Hi Markus,
we extended the capabilities or Rgraphviz a bit to allow for different 
edge marks. Please note that currently there are two interfaces to 
control graph plotting, and the edge marks are only supported in the new 
one (which we anyways recommend since it is much cleaner). There is a 
new section that hopefully explains everything at the end of the "A New 
Interface to Plot Graphs Using Rgraphviz" vignette. Please take a look 
and tell me if something is not working as expected or if something in 
the documentation is unclear.
Cheers,
Florian


Robert Gentleman wrote:
> Markus Kalisch wrote:
>   
>> Dear Robert,
>>
>> thanks a lot for the super-fast response:)! 
>>
>> Right now, I think Rgraphviz is not on CRAN anymore (do you know
>> whether there is a long term problem with Rgraphviz?). The last
>>     
>
>  No, we just don't have the energy/resources to support dual hosting. In fact,
> with some recent changes to the Windows build of graphviz it is better than it
> has been for a few years.
>
>   
>> version I know supports to my knowledge "arrowhead" and "empty" as
>> edgemarks. It would be fabulous, if this could be extended to
>>
>> - at least one more edge mark (e.g. "circle")
>> - a version where arbitrary arrangements of edgemarks are
>> possible in one graph.
>>
>>     
>   you have to control that with some sort of edge attribute (or so it seems to me).
>
>   
>> Do you think that would be doable? I believe that there will be
>> greater demand for these functionalities in near future in the
>> whole community.
>>     
>
>   who knows - if you have a use case we can have a look, and will let you know
> later this week if/when we can get it done.  But then we need you to do some
> testing.
>   
>> Thanks again for your help! I really appreciate it!
>>
>> Best
>> markus 
>>
>> Robert Gentleman writes:
>>  > Markus,
>>  >   graph is a package for representing graphs, and it should allow edges (and
>>  > nodes) to have arbitrary attributes.  I suspect that whether that is possible
>>  > may depend on the underlying representation, with graphNEL being most complete.
>>  >  I would be happy to take, and fix, any bug reports associated with issues of
>>  > that sort for graph.
>>  >   Rendering/drawing of graphs is strictly the role of Rgraphviz (not graph). And
>>  > there, we use R graphics mainly, so in principle, anything is possible.  I am
>>  > not sure what is implemented, but it should be pretty simple to add things, if
>>  > you have a specific list, and particularly if you can pick some out of the
>>  > graphviz tool kit, then we could see about adding that functionality to Rgraphviz.
>>  >   I am cc'ing Florian Hahne, in case he knows more about what the state of
>>  > Rgraphviz than I do, as I think he last worked on improvements to the rendering,
>>  > and is using it in a few applications.
>>  > 
>>  >   best wishes
>>  >     Robert
>>  > 
>>  > 
>>  > Markus Kalisch wrote:
>>  > > Dear Robert,
>>  > > 
>>  > > I'm planning to write some functions using ancestral
>>  > > graphs. Therefore, I would need to place different edge marks on
>>  > > an edge (e.g. "no mark", "arrowhead", "circle"). As far as I am
>>  > > aware, this is not possible in the graph package. Is that true?
>>  > > Do you know of any other R package, which I could use for this
>>  > > task? 
>>  > > 
>>  > > It would be great, if you could give me a quick comment and
>>  > > share your huge experience in that field!
>>  > > 
>>  > > Thanks a lot!!
>>  > > 
>>  > > Yours 
>>  > > Markus Kalisch
>>  > 
>>  > -- 
>>  > Robert Gentleman, PhD
>>  > Program in Computational Biology
>>  > Division of Public Health Sciences
>>  > Fred Hutchinson Cancer Research Center
>>  > 1100 Fairview Ave. N, M2-B876
>>  > PO Box 19024
>>  > Seattle, Washington 98109-1024
>>  > 206-667-7700
>>  > rgentlem at fhcrc.org
>>  > 
>>  > 
>>  > !DSPAM:493eaf25104238090361717!
>>     
>
>   


-- 
Florian Hahne, PhD
Computational Biology Program
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-3148
fhahne at fhcrc.org