[BioC] Rgraphviz: Edge attributes not displaying
Li.Long at isb-sib.ch
Li.Long at isb-sib.ch
Fri Feb 2 10:43:42 CET 2007
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.
> I can confirm the problem. I'll have a look at the source code today or
(more likely) tomorrow.
> 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:
>> V <- letters[1:10]
>> M <- 1:4
>> g1 <- randomGraph(V, M, 0.2)
>> nAttrs <- list()
>> eAttrs <- list()
>> z <- strsplit(packageDescription("Rgraphviz")$Description, " ")[] z
>> names(z) = nodes(g1)
>> nAttrs$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
>> 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 Byrnes
>> Population Biology Graduate Group, UC Davis
>> Bodega Marine Lab
>> [[alternative HTML version deleted]]
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