[BioC] problem with manipulating graphs created from dot files read by agread()

[Wolfgang Huber]

Dear Alexis

when you open the URL below and follow the link "SCM Repository" you will see instruction for how to download it, via subversion. Works fine for me. 


	Best wishes
	Wolfgang


Il giorno Dec 21, 2012, alle ore 9:46 PM, alexis.dinno at pdx.edu ha scritto:

> 
> Hi Paul,
> 
>> There's a 'gridGraphviz' package on R-Forge that is in very early stages;  it has lots of holes, but I have plugged a couple so that you get a reasonable result for your example below.
>> 
>> With the latest version on ...
>> 
>> https://r-forge.r-project.org/projects/gridgraph/
> 
> It is not remotely clear how to install packages from this link. However, I found version 0.1 on CRAN.
> 
>> ... try the following code ...
>> 
>> library(gridGraphviz)
>> g <- agread("Levins.dot")
>> grid.graph(g)
>> 
>> ... which gets the edges better and the following ...
> 
> But which does not draw the nodes or their labels at all.
> 
>> grid.newpage()
>> pushViewport(viewport(width=.9, height=.9, gp=gpar(lex=4)))
>> grid.graph(g, newpage=FALSE, nodesOnTop=FALSE)
>> 
>> ... makes the "arrows" look better.
> 
> Not on my system (v. 2.15.2 x86_64-apple-darwin9.8.0/x86_64 (64-bit)):
> 
>> grid.graph(g, newpage=FALSE, nodesOnTop=FALSE)
> Error in grid.graph(g, newpage = FALSE, nodesOnTop = FALSE) :
>  unused argument(s) (nodesOnTop = FALSE)
> 
> 
> But thank you for bringing your incipient package to my attention! :)
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor