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

[Alexis Dinno]

Hi,

I would love to integrate interoperability with Rgraphviz in my LoopAnalyst
package on CRAN. Unfortunately, Rgraphiz does not seem to behave well with
graphs read from dot files. The dot file
(http://doyenne.com/personal/files/Levins.dot) can be read an rendered by
agread(), but does not turn out so nicely, presumably because of how node, edge
and arrowhead attributes are handled.

Here's how dot from graphviz renders my graph:
http://doyenne.com/personal/files/Levins.png


But if in R I type:
g <- agread("/Users/Alexis/Desktop/Levins.dot")
plot(g)

I get: http://doyenne.com/personal/files/Levins2.png

So I would like to edit the various parameters according to Rgraphviz, BUT, I
get the following errors with the following commands:

edgemode(g) <- "directed"
Error in function (classes, fdef, mtable)  :
 unable to find an inherited method for function ‘edgemode<-’ for
signature ‘"Ragraph", "character"’


edgeRenderInfo(g) <- list(arrowhead=c("R~R"="dot", "R~H"="normal",
"H~R"="dot", "H~x"="normal", "H~y"="normal", "x~H"="dot", "y~H"="dot",
"y~y"="dot"), arrowtail="open")
Error in function (classes, fdef, mtable)  :
 unable to find an inherited method for function ‘isDirected’ for
signature ‘"Ragraph"’


Can you help?

Thank you!

Alexis


Here's the content of Levins.dot:


digraph G {
graph [bgcolor = "transparent", size = "18!,18!", nodesep="1", ranksep="1",
rankdir="LR"];
node [fixedsize=true, fontname="Sans", fontsize="70.85", shape=circle,
height="2", width="2", style="setlinewidth(5)"];
edge [style="setlinewidth(4)", arrowsize=3];
        "R" [color="#8000BF"];
                "R" -> "R" [color="#8000BF", arrowhead=dot];
                "R" -> "H" [color="#8000BF"];
        "H" [color="#0000BF"];
                "H" -> "R" [color="#0000BF", arrowhead=dot];
                "H" -> "x" [color="#0000BF"];
                "H" -> "y" [color="#0000BF"];
        "x" [color="#00BF00"];
                "x" -> "H" [color="#00BF00", arrowhead=dot];
        "y" [color="#BF0000"];
                "y" -> "H" [color="#BF0000", arrowhead=dot];
                "y" -> "y" [color="#BF0000", arrowhead=dot];
}