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

[Martin Morgan]

On 12/20/2012 03:07 PM, Kasper Daniel Hansen wrote:
> The issue is that agread() returns an object of class Ragraph and not
> a standard graph.  Ragraph is really an internal class.
> Unfortunately, you cannot convert from Ragraph to a standard graph
> (which is quite unfortunately).
>
> What you are doing, is using the
>    edgeRenderInfo()
> paradigm as described in the vignette "newRgraphvizInterface".  This
> works on graph objects, but not Ragraph.
>
> Instead, you need to use the old style layout functions, like
>    plot( , nodeAttrs = list(), edgeAttrs = list())

I played around with this just a little this morning and found toFile() to be 
useful, e.g.,

   toFile(g, filename="/tmp/foo.svg", fileType="svg")

to recreate the output from graphviz (fileType from 
graphvizCapabilities()$deviceType), and things like

 > edgeData(g, "R", "R", "arrowhead")
   R~R
"dot"
 > edgeData(g, "R", "R", "arrowhead") <- "normal"

(as documented on ?Ragraph) to manipulate.

Martin


>
> Let me end by saying that your request is completely reasonable and it
> is unfortunate that it is not easy to do.  Recently, I spent a lot of
> time fixing up the C code for Rgraphviz and the next step is cleaning
> up the R code.  However, due to other commitments, this may take a
> while to materialize.
>
> Best,
> Kasper
>
> On Wed, Dec 19, 2012 at 4:32 PM, Alexis Dinno <alexis.dinno at pdx.edu> wrote:
>> 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];
>> }
>>
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>
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