[BioC] Rgraphviz edge weight question
huber at ebi.ac.uk
Sun Jun 11 19:22:12 CEST 2006
I believe that is not currently possible (Rgraphviz 1.11.0) without
changing some of the code in Rgraphviz (or overwriting exisitings
methods with your own ones). Seth, Jeff, please correct me if I am wrong.
The method "lines" for "AgEdge" objects (defined in
Rgraphviz/R/Ragraph.R) has and honours a parameter "lwd". Its default
is the global option par("lwd").
However, that parameter is not set (or read from any kind of graph
attribute or function call parameter) by the plot method for the
"graphNEL" class (which in turn calls the plot method for the class
"Ragraph"). Both of these are defined in Rgraphviz/R/graph.R.
It should be relatively straightforward to modify these latter two
methods to honor an element "lwd" in the edgeAttrs list and pass it on
to "lines" (for "AgEdge").
Mark, if you feel adventurous, you could try to contribute a patch for
Also, in the Bioconductor book on p.368 and Fig. 21.15 there is an
example how can really do anything you want...
PS - for the purists, when I said method for class X, I meant a method
whose signature contains X in the first position.
Kimpel, Mark William wrote:
> I am visualizing graphNEL objects using Rgraphviz. I would like to set the thickness of the edge lines, in points, proportional to the edge weights. Is this an attribute that can be set? I have looked through the Rgraphviz documentation as well as the Graphviz website without finding an answer.
> Mark W. Kimpel MD
> Official Business Address:
> Department of Psychiatry
> Indiana University School of Medicine
> Biotechnology, Research, & Training Center
> 1345 W. 16th Street
> Indianapolis, IN 46202
> Preferred Mailing Address:
> 15032 Hunter Court
> Westfield, IN 46074
> (317) 490-5129 Home, Work, & Mobile
> 1-(317)-536-2730 FAX
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
More information about the Bioconductor