[BioC] Rgraphviz: Edge attributes not displaying

[Jarrett Byrnes]

I see.  So, lty (aka style in the Rgraphviz documentataion - or  
should one use $lty) just doesn't work yet?  That still does not  
explain why labels are not showing up.

On Feb 2, 2007, at 1:43 AM, Li.Long at isb-sib.ch wrote:

> Hi,
>
> Some attributes affect layout, while others don't.  For edges,
> "label"-attribute does affect layout, as documented by graphviz.   
> That's
> why you see the edges are plotted differently after adding labels.
>
> The attribute for line type, "lty" in Ragraph-class, is not  
> retrieved from
> graphviz at present, so it does not have any effect.
>
> Some newly added functions (in devel branch) allow you to see a nicely
> rendered graph by using "toFile" function to output the graph to a  
> file
> (.svg, .ps, etc.).  This function invokes the renderer from  
> graphviz and
> honors many more attributes nicely.
>
> The work is underway to render the graphs (laid out by graphviz)  
> better:
> to honor more attributes, to honor them better.
>
> Li
>
>
>> I can confirm the problem. I'll have a look at the source code  
>> today or
> (more likely) tomorrow.
>>
>> Kasper
>>
>> On Feb 1, 2007, at 11:36 AM, Jarrett Byrnes wrote:
>>
>>> Hey, all.  I'm working on some methods with Rgraphviz to plot sem
> objects (structrual equation models from the sem library) and have run
> into a problem.  It would seem that Rgraphviz is not dealing with edge
> properties correctly.  I've tried the following sample code:
> set.seed(123)
>>> V <- letters[1:10]
>>> M <- 1:4
>>> g1 <- randomGraph(V, M, 0.2)
>>> nAttrs <- list()
>>> eAttrs <- list()
>>> z <- strsplit(packageDescription("Rgraphviz")$Description, " ") 
>>> [[1]] z
> <- z[1:numNodes(g1)]
>>> names(z) = nodes(g1)
>>> nAttrs$label <- z
>>> eAttrs$label <- c("a~h" = "Label 1", "c~h" = "Label 2")
>>> attrs <- list(node = list(shape = "ellipse", fixedsize = FALSE))
> plot(g1, nodeAttrs = nAttrs, edgeAttrs = eAttrs, attrs = attrs) And
> instead of labeling the edges, they become more angled/straight and
> less curved.  I've had similar problems with my own functions that I'm
> coding.  Similarly, when I specify "solid" or "dashed" nothing  
> happens.
>  I'd be happy to send a picture, if you would like. Although making
> solid or dashed a label instead of a style tends to again straighten
> the edges.
>>> FYI, I'm running R 2.4.1 and Rgraphviz 1.12.3 (the most current) and
> the proper version of xgvis that's needed to install this version of
> Rgraphviz.  All of this is on a mac running OSX 10.4.8.
>>> Any clue why this might be happening/is there a fix?
>>> -Jarrett
>>> ----------------------------------------
>>> Jarrett Byrnes
>>> Population Biology Graduate Group, UC Davis
>>> Bodega Marine Lab
>>> 707-875-1969
>>> http://www-eve.ucdavis.edu/stachowicz/byrnes.shtml
>>> 	[[alternative HTML version deleted]]
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>
>