Hi,
On Sun, Mar 24, 2013 at 1:01 PM, Thomas Barnum <[email protected]> wrote:
> Dear All,
> I am trying to export a Pajek file and a graphml file to be opened in
> gephi. However, when I open the file in gephi, all the graph attributes
> (vertex names, vertex colors, and edge colors) are not recognized by gephi.
> I dropped the graphml file into Firefox and Firefox states that there does
> not appear to be style information associated with the file (for example,
> nodes are listed as 'n1' instead of by letters).
I am not sure why you expect Firefox to be able to interpret graphml files.
It cannot do that.
> Here is some workable code that reproduces the problem:
>
> ### I want to export two different colored edges in the final graph so
> this code uses two colors for the edges
>
> foo<-graph.ring(10)
> E(foo)$color[1:5]<-"blue"
> E(foo)$color[6:10]<-"green"
> V(foo)$name <- LETTERS[1:10]
>
> plot(foo, vertex.label=V(foo)$name)
>
> write.graph(foo, format="pajek", file="test.net")
>
See ?read.graph for the attributes that are used in Pajek exports.
(Referenced from ?write.graph.) The 'color' edge attribute is fine. Instead
of 'name' use 'id', and that is saved.
> write.graph(foo, format="graphml", file="test.graphml")
>
I can see all the attributes in the file.
I guess the problem is, different programs set different attributes, so
even if both can read and write graphml files, they just cannot interpret
the attribute data. I understand that this is annoying, and something
should be done about it.
As for your specific problem, I am not sure what attributes gephi
interprets in graphml files, but maybe you can just check this in the gephi
documentation and then make sure to use those.
I feel like I am missing something really obvious here, particularly in
> regards to the Pajek format, but I can't figure it out. I have tried
> including some attributes when I write the Pajek file. For example:
>
> write.graph(foo, format="pajek", file="test.net",
> foo$color("blue","green"))
>
> or
>
> write.graph(foo, format="pajek", file="test.net", foo$c("blue","green"))
>
> but I get this error message:
>
> Error in write.graph.pajek(graph, file, ...) : attempt to apply
> non-function
>
I agree the error message is cryptic, but why do you think write.graph
works this way? It does not, actually I am not even sure what
foo$color("blue", "green") means, I guess it is a syntax error, because
foo$color is NULL.
Gabor
> Any ideas/help/suggestions will be greatly appreciated.
> All the best,
> Tom
>
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>
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