Vince,

that works much better, almost perfectly!
I used fixInNamespace(drawTxtLabel, "Rgraphviz") , as you suggested.
I wasn't aware of this functionality.

(Using shape="plaintext"  with fixInNameSpace gives essentially the same
results
as your getNodeXY(agGO) suggestion.)

Further, if I maximize the plot, spacing seems to improve quite a bit as
well.
Nothing will be quite perfect, as I'm actually going to use full GO term
names, which can be quite long.

Just FYI, if you or anyone else is planning to attempt to resolve some of
the communication difficulties with Graphviz/Rgraphviz/Ragraph,
I've  noticed that I also don't seem to be able to get any reaction to
fixedsize=FALSE in nodeAttrs. (Much as with your fontsize experiment.)
I haven't tried all the other parameters, but one might guess that there are
difficulties there as well, as these seem to be rather subtle issues.

Thanks again, it's greatly appreciated.

Best regards,

Dan.

On Mon, Sep 8, 2008 at 11:25 PM, Vincent Carey 525-2265 <
stvjc@channing.harvard.edu> wrote:

>
> > Vince,
> >
> > thanks for the tip.
> > Unfortunately I'm not sure how to apply it.
> > The vignette doesn't really make clear to me what it is that
> pwayRendAttrs
> > does. It is mentioned once,
> > but I'm not exactly clear on its function.
> > It also does not seem to apply to the objects of type that I am using: in
> my
> > code I have taken my graphNEL object and
> > turned it into an Ragraph object.
> >
> > Am I, as usual, missing something obvious?
>
> I don't think so.  It seems to be hard to alter the font size much,
> in the presence of other constraints on node format such as height and
> width.  pwayRendAttrs is used in plotExGraph in pathRender, and one
> can get some control over node text font size by passing a modified
> pwayRendAttrs
> (with altered default AllFontsize) as the attgen parameter to plotExGraph
> --
> not a very elegant arrangement, but one can show that the font sizes can be
> _reduced_ by doing this.
>
> if we do
>
> library(graph)
> library(Rgraphviz)
> example(randomGraph)
> plot(g1, nodeAttrs=makeNodeAttrs(g1, fontsize=4))
> plot(g1, nodeAttrs=makeNodeAttrs(g1, fontsize=4, fillcolor="green"))
>
> we can see that the plotter will respond to the color attribute but
> not to the fontsize attribute, despite the fact that fontsize is
> identified in GraphvizAttributes as a target Node Attribute.  so
> either graphviz is misbehaving with respect to font size control or some
> aspect of communication from R to graphviz needs to be corrected.
>
> The fact that you are working with an Ragraph seems to make things
> a little harder.  What I see is that the rendering for Ragraph instances
> uses drawAgNode which calls drawTxtLabel, and neither seem to make
> any use of fontsize specs.
>
> I used fixInNamespace(drawTxtLabel, "Rgraphviz") to place a cex=2
> setting on the text() call that concludes that function, and then
> plot(agGO) [based on your code] renders the node names quite legibly,
> but with some collisions.  you may be able to tweak the cex setting
> to get what you want.
>
> there is clearly room for improvement in the Rgraphviz interface ...
> I see some work in the graph package on a renderInfo class that may
> help with this.  Note you can always use getNodeXY, text, and lines
> (on the BezierCurve objects in the AgEdge) to plot an Ragraph with a
> desired layout and pretty substantial control over appearance through
> basic R graphical primitives.  A rough sketch is
>
> XY = getNodeXY(agGO)
> plot(XY, bty="n", xlab=" ", ylab=" ", pch= " ", axes=FALSE)
> text(XY, labels=sapply(agGO@AgNode, "name"), cex=.65)
> tmp = sapply(AgEdge(agGO), function(x) sapply(x@splines, lines))
>
>
> >
> > Dan.
> >
> >
> >
> > On Mon, Sep 8, 2008 at 7:05 PM, Vincent Carey 525-2265 <
> > stvjc@channing.harvard.edu> wrote:
> >
> > > > Hi all,
> > > >
> > > > I'm attempting to use Rgraphviz to do some plotting.
> > > > There is no problem in producing the plots, but I would like to
> modify
> > > font
> > > > sizes in the resulting graph, and this appears tricky.
> > > > The simple fontsize setting in makeNodeAttrs seems to have no effect.
> > >
> > > there is a function called pwayRendAttrs in the pathRender
> > > package that manipulates graphviz fontsize; plotExG vignette
> illustrates
> > > its use
> > >
> >
> >
> >
> > --
> > Daniel C. Jupiter, Ph.D.
> > Postdoctoral Research Associate
> > Department of Systems Biology and Translational Medicine
> > College of Medicine
> > Texas A&M Health Science Center
> > 702 SW H.K. Dodgen Loop
> > Temple, TX 76504
> >
> > 979.997.2106 | Fax 254.742.7145
> > djupiter@tamu.edu | www.tamhsc.edu
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>



-- 
Daniel C. Jupiter, Ph.D.
Postdoctoral Research Associate
Department of Systems Biology and Translational Medicine
College of Medicine
Texas A&M Health Science Center
702 SW H.K. Dodgen Loop
Temple, TX 76504

979.997.2106 | Fax 254.742.7145
djupiter@tamu.edu | www.tamhsc.edu

	[[alternative HTML version deleted]]

