help with large Rgraphviz output
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@kimpel-mark-w-727
Last seen 6.9 years ago
I am generating some complex graph output using Rgraphviz: plot(graphNEL object) and it is too cluttered to easily decipher on screen. Saving the screen output to postscript does not help. What seems like it might work would be outputting directly to a .ps file after setting options(papersize=customLargeSize). Can this be accomplished. If so, how? If not, is there a better option to accomplish what I need to do? Thanks, Mark Mark W. Kimpel MD ? Official Business Address: ? Department of Psychiatry Indiana University School of Medicine Biotechnology, Research, & Training Center 1345 W. 16th Street Indianapolis, IN ?46202 ? Preferred Mailing Address: ? 15032 Hunter Court Westfield, IN? 46074 ? (317) 490-5129 Home, Work, & Mobile 1-(317)-536-2730 FAX
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 6.9 years ago
Hi Mark, "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > I am generating some complex graph output using Rgraphviz: > plot(graphNEL object) and it is too cluttered to easily decipher on > screen. Saving the screen output to postscript does not help. What > seems like it might work would be outputting directly to a .ps file > after setting options(papersize=customLargeSize). > > Can this be accomplished. If so, how? It looks like the postscript device accepts paper="special" in which case the paper size can be defined using widght and height. I haven't tried this, but it sounds like what you want. > If not, is there a better option to accomplish what I need to do? It depends on what you need to do :-) Laying out large graphs in a readable fashion is difficult. If there is a part of the graph that you want to emphasize, you may be able to improve the display by varying the node sizes. You can also take a look at the subgraph plotting in Rgraphviz. This essentially gives a hint to the layout algorithms that a subgraph is important. Hope that helps some. + seth
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 6.9 years ago
"Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > Seth, > > I am a novice at manipulating options in R and working with output > devices. > > Assuming I want to set my postscript paper size as Width= 15" and > Height= 15", what code would set the option for this? > > Also, how to I get the plot method for Rgraphviz to output to postscript > instead of screen? Warning: untested code ahead I think it would look something like this: ## a graphNEL instance you want to plot g ## setup the postscript device. All plot commands will be ## sent to this device until you call dev.off(). postscript(file="bigGraphPlot.ps", paper="special", width=15, height=15) ## do the plot, you should not see anything on screen plot(g) ## close the graphics device dev.off() You might also want to try the pdf() device.
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On Tue, 2006-06-06 at 14:00 -0700, Seth Falcon wrote: > "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > > > Seth, > > > > I am a novice at manipulating options in R and working with output > > devices. > > > > Assuming I want to set my postscript paper size as Width= 15" and > > Height= 15", what code would set the option for this? > > > > Also, how to I get the plot method for Rgraphviz to output to postscript > > instead of screen? > > Warning: untested code ahead > > I think it would look something like this: > > ## a graphNEL instance you want to plot > g > > ## setup the postscript device. All plot commands will be > ## sent to this device until you call dev.off(). > postscript(file="bigGraphPlot.ps", paper="special", > width=15, height=15) > ## do the plot, you should not see anything on screen > plot(g) > ## close the graphics device > dev.off() > > > You might also want to try the pdf() device. I've personally had success with: pdf("foo.pdf", width=24, height=36) ### width/height whatever you want plot(g) dev.off() for large networks of genes (also a graphNEL object). Even if you don't print it out, the layout is much easier to read when opened on-screen. --Jake
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@kimpel-mark-w-727
Last seen 6.9 years ago
Seth, I am a novice at manipulating options in R and working with output devices. Assuming I want to set my postscript paper size as Width= 15" and Height= 15", what code would set the option for this? Also, how to I get the plot method for Rgraphviz to output to postscript instead of screen? Mark Mark W. Kimpel MD (317) 490-5129 Home, Work, & Mobile 1-(317)-536-2730 FAX -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon Sent: Tuesday, June 06, 2006 4:03 PM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] help with large Rgraphviz output Hi Mark, "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > I am generating some complex graph output using Rgraphviz: > plot(graphNEL object) and it is too cluttered to easily decipher on > screen. Saving the screen output to postscript does not help. What > seems like it might work would be outputting directly to a .ps file > after setting options(papersize=customLargeSize). > > Can this be accomplished. If so, how? It looks like the postscript device accepts paper="special" in which case the paper size can be defined using widght and height. I haven't tried this, but it sounds like what you want. > If not, is there a better option to accomplish what I need to do? It depends on what you need to do :-) Laying out large graphs in a readable fashion is difficult. If there is a part of the graph that you want to emphasize, you may be able to improve the display by varying the node sizes. You can also take a look at the subgraph plotting in Rgraphviz. This essentially gives a hint to the layout algorithms that a subgraph is important. Hope that helps some. + seth _______________________________________________ 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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