Hi,

i updated the R version to 2.9.0 and indeed it solved all my problems.

thanks so much!

Yaniv



2009/6/24 Deepayan Sarkar <deepayan.sarkar@gmail.com>

> On Wed, Jun 24, 2009 at 3:30 AM, Yaniv Semel<ys1276@gmail.com> wrote:
> > here is my session info after i updated the Rgraphviz package. its 1.20.4
> > (whereas yours is 1.22).
> > the manual page for layoutGraph is still the same as i had before the
> > update.
>
> You need to use R 2.9.x and the associated version of Rgraphviz. The
> manual page there shows you how to change the layout algorithm, and
> also how to use custom arrowheads.
>
> -Deepayan
>
> >
> >
> > R version 2.8.1 (2008-12-22)
> > i386-pc-mingw32
> >
> > locale:
> > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> > States.1252;LC_MONETARY=English_United
> > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> >
> > attached base packages:
> > [1] grid      stats     graphics  grDevices utils     datasets  methods
> > [8] base
> >
> > other attached packages:
> > [1] Rgraphviz_1.20.4 graph_1.20.0
> >
> > loaded via a namespace (and not attached):
> > [1] cluster_1.12.0 tools_2.8.1
> >
> >
> > Yaniv
> >
> >
> >
> >
> >
> > 2009/6/24 Robert Gentleman <rgentlem@fhcrc.org>
> >
> >> 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  Perhaps your R  or Rgraphviz are out of date?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;LC_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]]
> >
> > _______________________________________________
> > 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
> >
>

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