[BioC] Rgraphviz edge attributes can't be changed on Mac

[Luo Weijun]

Thanks, Herve,
I updated R , BioConductor and Rgraphviz to the latest
versions. I still can't customize the edge attributes
as I mentioned earlier. Any ideas? 
Weijun

And this is my current session information.

> sessionInfo()
R version 2.6.0 (2007-10-03) 
powerpc-apple-darwin8.10.1 

locale:
C

attached base packages:
[1] stats     graphics  grDevices utils     datasets 
methods   base     

other attached packages:
[1] Rgraphviz_1.16.0 graph_1.16.1     XML_1.93-2      

loaded via a namespace (and not attached):
[1] cluster_1.11.9  rcompgen_0.1-15 tools_2.6.0    

--- Herve Pages <hpages at fhcrc.org> wrote:

> Hi Luo,
> 
> Please update your R + Bioconductor installation to
> the current
> release (R 2.6.0 and BioC 2.1) and see if this
> solves your problem.
> Past releases of BioC are not supported.
> FYI the current release version of Rgraphviz is
> 1.16.0 and that's the
> version you should get if you use biocLite() from R
> 2.6.0:
> 
>   http://bioconductor.org/docs/install-howto.html
> 
> Thanks!
> H.
> 
> 
> Luo Weijun wrote:
> > Hello everybody,
> > 
> > I used Rgraphviz to plot some signaling pathway.
> It
> > did work well in many aspects, including node
> > attributes. However, when I tried to customize the
> > edge attributes, it did really work. I can't
> change
> > any of these attributes, including arrowhead,
> style
> > (e.g. line style, dashed, solid etc),
> labelfontsize. I
> > did see the edge labels but their size was too big
> and
> > I couldn't change it. I doubt other attributes
> would
> > all work well. I noticed that other people
> reported
> > something similar on Mac early this year in a
> thread
> > titled "Rgraphviz: Edge attributes not
> displaying",
> > but they couldn't even see the labels. I would
> > appreciate it much if anybody can give me a little
> > help on this. Thank you!
> > Weijun
> > 
> > These is the codes I used to layout and plot the
> > graph:
> > 
> > tgf=agopen(kg1, name='kg', attrs = attrs,
> > nodeAttrs=nAttr, edgeAttrs=eAttr,
> subGList=subGList)
> > loc=getNodeXY(tgf)
> > pdf('kg.pdf')
> > plot(tgf)
> > text(loc, label = labType[1,ni], cex = 0.4)
> > dev.off()
> > 
> > Not that I have to use agopen, because I need to
> > retrieve locations of the nodes and add other
> things
> > after plot(). I tried toFile() function to output
> as
> > PS file, didn't work at all (I can't even open the
> > file). Actually toFile doesn't allow me add
> anything
> > later even if it works.
> > 
> > My operating system is Mac OS X 10.4.9, and this
> is my
> > session information
> > 
> >> sessionInfo()
> > R version 2.5.1 (2007-06-27) 
> > powerpc-apple-darwin8.9.1 
> > 
> > locale:
> > C
> > 
> > attached base packages:
> > [1] "tools"     "stats"     "graphics" 
> "grDevices"
> > "utils"     "datasets" 
> > [7] "methods"   "base"     
> > 
> > other attached packages:
> >   Rgraphviz geneplotter     lattice    annotate   
> 
> > Biobase       graph 
> >    "1.14.1"    "1.14.0"   "0.15-11"    "1.14.1"   
> > "1.14.0"    "1.14.2" 
> >         XML 
> >     "1.9-0"
> > 
> > _______________________________________________
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>
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> 
>