[BioC] Rgraphviz: Edge attributes not displaying

Jarrett Byrnes jebyrnes at ucdavis.edu
Mon Feb 5 17:53:16 CET 2007 

Nope, I get something very different

 > AgEdge(g2)[[5]]@txtLabel at labelText
character(0)
 > AgEdge(g2)[[10]]@txtLabel at labelText
character(0)

Given what I saw looking at the edgeAttrs of the Ragraph object  
itself, (namely, Null), I'm guessing that the problem is there.  This  
may also be why edge style (solid v. dashed) wasn't getting picked  
up.  Why it is different on linux instead of a mac, I am uncertain,  
unless there are different binaries in the Bioconductor archive.

But I could be wrong about that, as I don't know the code.

On Feb 5, 2007, at 8:21 AM, Li.Long at isb-sib.ch wrote:

>
> Hi,
>
> Here's what I got on my Linux:
>
>> g2 <- plot(g1, nodeAttrs = nAttrs, edgeAttrs = eAttrs, attrs = attrs)
>> AgEdge(g2)[[5]]@txtLabel at labelText
> [1] "Label 1"
>> AgEdge(g2)[[10]]@txtLabel at labelText
> [1] "Label 2"
>
> Index 5/10 are the two edges you set labels on.  For me, they are  
> "Label
> 1" and "Label 2" as you set.  I would double check on Mac to see if  
> they
> are
> like that.
>
> If you do see these label texts, then the problem has more to do with
> rendering.  Various things could go wrong: (just my speculation) a  
> wrong
> color could make text invisible, function "lines" could have trouble
> dealing with labels, function "plot" might have problem on Mac, etc.
>
> If you don't see these label texts, we need to look further into  
> how these
> labels are handled in Rgraphviz/graphviz on Mac.
>
> Li
>
>
>> I'm unclear as to what you mean by object g.  I'm assuming that you
>> mean the Ragraph object generated by plot.  So, I did the following,
>> after running the previous code from my first post:
>>
>>> g2<-plot(g1, nodeAttrs = nAttrs, edgeAttrs = eAttrs, attrs = attrs)
>>>
>>> g<-layoutGraph(g2)
>>> AgEdge(g)
>> [[1]]
>> An edge between e and b with 1 BezierCurve objects:
>> 257,706 223,656 121,506 87,456
>>
>> [[2]]
>> An edge between f and b with 1 BezierCurve objects:
>> 268,704 268,653 268,508 268,457
>>
>> [[3]]
>> An edge between j and b with 1 BezierCurve objects:
>> 272,704 293,618 382,247 407,141
>>
>> [[4]]
>> An edge between j and e with 1 BezierCurve objects:
>> 91,423 147,370 328,196 391,135
>>
>> [[5]]
>> An edge between j and i with 1 BezierCurve objects:
>> 539,421 517,367 451,205 425,140
>>
>>
>> Note, however, the following
>>
>>> g2$edgeAttrs
>> NULL
>>
>>
>>
>>
>> On Feb 5, 2007, at 2:13 AM, Li.Long at isb-sib.ch wrote:
>>
>>>
>>> On my linux (R2.4 + graphviz 2.8/2.12), the edge labels DO show  
>>> up...
>>>
>>> I don't have Mac on hand...  On the other hand, I don't see any
>>> codes that
>>> are Mac-ed or Apple-ed in either Rgraphviz or graphviz.
>>>
>>> You can do (in R):  g1 <- layoutGraph(g), then look at g1's AgEdge
>>> info to
>>> see if the label info are available.  If they are, then the  
>>> problem is
>>> likely to be in rendering on Mac, other wise, it's more to do with
>>> retrieving label info.
>>>
>>> In case of the latter, I would try to change the following line (in
>>> doLayout.c) from
>>>         if ( edge->u.label != NULL )
>>> to
>>>         if ( agget(edge, "label") )
>>> just to see what happens...
>>>
>>> Li
>>>
>>>
>>>
>>>
>>>> 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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