[BioC] Rgraphviz: Edge attributes not displaying

[Jarrett Byrnes]

graphvizVersion gives me graphvizVersion()

I am on  PPC G4 Powerbook.

Sorry that this is such a pickle - and if line style ends up being  
fixed as well, that would be ever so wonderful.  I'd like to use this  
method (the plot.sem I'm whipping up) in a seminar tutorial on R and  
SEM later in the week, but I understand if that's not possible.

Thanks so much!

-Jarrett

On Feb 3, 2007, at 11:31 PM, Kasper Daniel Hansen wrote:

> As Jarrett says, this does not explain why the labels don't show up.
>
> Jarrett: could you do a
> R> graphvizVersion()
> for me. And are you on an Intel or PPC machine?
>
> I have spent some time in GDB and I am stuck for the moment.
>
> Notes for Li and me:
>   R> library(Rgraphviz)
>   gdb> break getEdgeLocs
> run Jarrett's example
>   gdb> break 124
>   gdb> cont
> (continue 5 times I think). Now we should be at the first edge with  
> a label, it has the attribute set correctly:
>
> (gdb) p agget(edge, "label")
> $19 = 0x2113cac "Label 1"
>
> But the label is not reflected in the laidout structure, instead of  
> a textlabel we get a pointer to NULL:
>
> (gdb) p edge->u.label
> $20 = (textlabel_t *) 0x0
>
> I am at a loss here, running Graphviz 2.12 on Mac PPC. Do you see  
> the same Li? Perhaps there have been some changes in how to read  
> the labels? Anyway, bedtime.
>
> Kasper
>
>
>
>
>
> On Feb 2, 2007, at 11:52 AM, Jarrett Byrnes wrote:
>
>> 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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>>
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