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

[alexis.dinno at pdx.edu]

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! :)