Hi Yaniv,
Perhaps your R or Rgraphviz are out of date? Please follow the
posting
guide, and provide the output of sessionInfo. The example I see on
this man
page is much longer and answers your question (my sessionInfo is
below)
> sessionInfo()
R version 2.9.1 RC (2009-06-22 r48824)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C
;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;L
C_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Rgraphviz_1.22.1 graph_1.22.2
loaded via a namespace (and not attached):
[1] tools_2.9.1
On Wed, Jun 24, 2009 at 2:38 AM, Yaniv Semel <ys1276@gmail.com> wrote:
> Thanks, Robert
>
> this is the example in layoutGraph:
>
> library(graph)
> set.seed(123)
> V <- letters[1:10]
> M <- 1:4
> g1 <- randomGraph(V, M, 0.8)
> x <- layoutGraph(g1)
>
>
> now, if i do
> renderGraph(x)
>
> it draws it as "dot" layout by default. how can i change it to
"neato" or
> "twopi"?
>
>
> Thanks,
> Yaniv
>
>
>
>
> 2009/6/23 Robert Gentleman <rgentlem@fhcrc.org>
>
>> Hi Yaniv,
>> Let me direct you to the examples on the manual page for
>> layoutGraph.
>> best wishes
>> Robert
>>
>> On Tue, Jun 23, 2009 at 9:30 AM, Yaniv Semel <ys1276@gmail.com>
wrote:
>>
>>> >
>>> > regarding the arrowhead issue, its written in the documentation
of the
>>> > ?GraphvizAttributes that the arrowhead is very limited in R
compared to
>>> the
>>> > Graphviz library and it can only be of "open" or "none" shape,
but not
>>> any
>>> > of the "box", "diamnod" shapes that are contained in the
Graphviz
>>> library.
>>> > so i guess (correct me if i wrong) that i just cant do any
shaped
>>> > arrowhead.
>>> >
>>> > when following the instructions of newRgraphvizInterface
vignette, how
>>> can
>>> > i set the layout of a graph to be "neato"?
>>> > the default is "dot" and i dont know how to change it.
>>> > in the old interface i just did:
>>> >
>>> > plot(g, "neato") # neato layout
>>> >
>>> > or:
>>> >
>>> > plot(g, "dot") # dot layout
>>> >
>>> > but now, the code doesnt use plot at all. instead it uses
layoutGraph:
>>> >
>>> > library("Rgraphviz")
>>> > set.seed(123)
>>> > V <- letters[1:10]
>>> > M <- 1:4
>>> > g1 <- randomGraph(V, M, 0.2)
>>> > g1 <- layoutGraph(g1)
>>> > renderGraph(g1)
>>> >
>>> > how do i change it to be of neato layout?
>>> >
>>> > Thanks,
>>> > Yaniv
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > 2009/6/18 Deepayan Sarkar <deepayan.sarkar@gmail.com>
>>> >
>>> >> On Wed, Jun 17, 2009 at 3:00 PM, Yaniv Semel<ys1276@gmail.com>
wrote:
>>> >>
>>> >> > Hi all,
>>> >> >
>>> >> >
>>> >> > i'm using the package Rgraphviz to draw graphs, and its
really
>>> awesome.
>>> >> > there is only one thing that i cant accomplish no matter what
i try:
>>> to
>>> >> draw
>>> >> > arrowhead (on edges) that are different than the normal.
>>> >> > i'm trying to change the arrowhead property to be "box" or
"diamond"
>>> or
>>> >> > anything else according to the instructions here:
>>> >> >
>>> >> >
http://www.graphviz.org/pub/scm/graphviz2/doc/info/attrs.html
>>> >> >
>>> >> > but it doesnt have any effect. i always get the normal
arrowhead.
>>> >> >
>>> >> > what am i missing here?
>>> >> > can somebody please show me a working code that produce a
simple
>>> graph
>>> >> with
>>> >> > not normal arrowheads (for example box or diamonds) ?
>>> >> >
>>> >> > here is a simple code that shows that i can manage to control
the
>>> edge
>>> >> color
>>> >> > (red), but not the arrowhead:
>>> >> >
>>> >> >
>>> >> > nodes <- c(n1="a", n2="b", n3="c")
>>> >> > edges <- list(a=list(edges=c("b", "c")),
b=list(edges=c("c")),
>>> >> > c=list(edges=c()))
>>> >> > g <- new("graphNEL", nodes=nodes, edgeL=edges,
edgemode="directed")
>>> >> > plot(g, attrs=list(edge=list(color="red", arrowhead="box",
>>> >> > dir="forward")))
>>> >>
>>> >> Try the new layoutGraph/renderGraph interface, described in the
"A New
>>> >> Interface to Plot Graphs Using Rgraphviz" vignette:
>>> >>
>>> >>
>>> >>
>>>
http://bioconductor.org/packages/2.4/bioc/vignettes/Rgraphviz/inst
/doc/newRgraphvizInterface.pdf
>>> >>
>>> >> -Deepayan
>>> >>
>>> >
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@stat.math.ethz.ch
>>>
https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>
>>
>> --
>> Robert Gentleman, PhD
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M2-B876
>> PO Box 19024
>> Seattle, Washington 98109-1024
>> 206-667-7700
>> rgentlem@fhcrc.org
>>
>>
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem@fhcrc.org
[[alternative HTML version deleted]]
