Rgraphviz - arrowhead
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Yaniv Semel ▴ 60
@yaniv-semel-3512
Last seen 7.8 years ago
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"))) any assistance will be highly appreciated, Yaniv [[alternative HTML version deleted]]
Rgraphviz Rgraphviz • 1.3k views
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@deepayan-sarkar-1436
Last seen 7.8 years ago
On Wed, Jun 17, 2009 at 3:00 PM, Yaniv Semel<ys1276 at="" 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
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Yaniv Semel ▴ 60
@yaniv-semel-3512
Last seen 7.8 years ago
> > 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]]
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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/d oc/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 [[alternative HTML version deleted]]
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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 > > [[alternative HTML version deleted]]
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 7.2 years ago
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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]]
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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. 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/ins t/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]]
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On Wed, Jun 24, 2009 at 3:30 AM, Yaniv Semel<ys1276 at="" 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 at="" 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_MONETAR Y=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 at="" 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 at="" 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 at="" 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 at="" gmail.com=""> >>>>> > >>>>> >> On Wed, Jun 17, 2009 at 3:00 PM, Yaniv Semel<ys1276 at="" 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/in st/doc/newRgraphvizInterface.pdf >>>>> >> >>>>> >> -Deepayan >>>>> >> >>>>> > >>>>> >>>>> ? ? ? ? [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at 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 at 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 at fhcrc.org >> >> > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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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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/d oc/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 > > > [[alternative HTML version deleted]]
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