Question: Rgraphviz edge attributes can't be changed on Mac
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gravatar for Luo Weijun
11.9 years ago by
Luo Weijun1.5k
United States
Luo Weijun1.5k wrote:
Hello everybody, I used Rgraphviz to plot some signaling pathway. It did work well in many aspects, including node attributes. However, when I tried to customize the edge attributes, it did really work. I can't change any of these attributes, including arrowhead, style (e.g. line style, dashed, solid etc), labelfontsize. I did see the edge labels but their size was too big and I couldn't change it. I doubt other attributes would all work well. I noticed that other people reported something similar on Mac early this year in a thread titled "Rgraphviz: Edge attributes not displaying", but they couldn't even see the labels. I would appreciate it much if anybody can give me a little help on this. Thank you! Weijun These is the codes I used to layout and plot the graph: tgf=agopen(kg1, name='kg', attrs = attrs, nodeAttrs=nAttr, edgeAttrs=eAttr, subGList=subGList) loc=getNodeXY(tgf) pdf('kg.pdf') plot(tgf) text(loc, label = labType[1,ni], cex = 0.4) dev.off() Not that I have to use agopen, because I need to retrieve locations of the nodes and add other things after plot(). I tried toFile() function to output as PS file, didn't work at all (I can't even open the file). Actually toFile doesn't allow me add anything later even if it works. My operating system is Mac OS X 10.4.9, and this is my session information > sessionInfo() R version 2.5.1 (2007-06-27) powerpc-apple-darwin8.9.1 locale: C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: Rgraphviz geneplotter lattice annotate Biobase graph "1.14.1" "1.14.0" "0.15-11" "1.14.1" "1.14.0" "1.14.2" XML "1.9-0"
geneplotter rgraphviz • 493 views
ADD COMMENTlink modified 11.9 years ago by Hervé Pagès ♦♦ 14k • written 11.9 years ago by Luo Weijun1.5k
Answer: Rgraphviz edge attributes can't be changed on Mac
0
gravatar for Hervé Pagès
11.9 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:
Hi Luo, Please update your R + Bioconductor installation to the current release (R 2.6.0 and BioC 2.1) and see if this solves your problem. Past releases of BioC are not supported. FYI the current release version of Rgraphviz is 1.16.0 and that's the version you should get if you use biocLite() from R 2.6.0: http://bioconductor.org/docs/install-howto.html Thanks! H. Luo Weijun wrote: > Hello everybody, > > I used Rgraphviz to plot some signaling pathway. It > did work well in many aspects, including node > attributes. However, when I tried to customize the > edge attributes, it did really work. I can't change > any of these attributes, including arrowhead, style > (e.g. line style, dashed, solid etc), labelfontsize. I > did see the edge labels but their size was too big and > I couldn't change it. I doubt other attributes would > all work well. I noticed that other people reported > something similar on Mac early this year in a thread > titled "Rgraphviz: Edge attributes not displaying", > but they couldn't even see the labels. I would > appreciate it much if anybody can give me a little > help on this. Thank you! > Weijun > > These is the codes I used to layout and plot the > graph: > > tgf=agopen(kg1, name='kg', attrs = attrs, > nodeAttrs=nAttr, edgeAttrs=eAttr, subGList=subGList) > loc=getNodeXY(tgf) > pdf('kg.pdf') > plot(tgf) > text(loc, label = labType[1,ni], cex = 0.4) > dev.off() > > Not that I have to use agopen, because I need to > retrieve locations of the nodes and add other things > after plot(). I tried toFile() function to output as > PS file, didn't work at all (I can't even open the > file). Actually toFile doesn't allow me add anything > later even if it works. > > My operating system is Mac OS X 10.4.9, and this is my > session information > >> sessionInfo() > R version 2.5.1 (2007-06-27) > powerpc-apple-darwin8.9.1 > > locale: > C > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" > "utils" "datasets" > [7] "methods" "base" > > other attached packages: > Rgraphviz geneplotter lattice annotate > Biobase graph > "1.14.1" "1.14.0" "0.15-11" "1.14.1" > "1.14.0" "1.14.2" > XML > "1.9-0" > > _______________________________________________ > 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
ADD COMMENTlink written 11.9 years ago by Hervé Pagès ♦♦ 14k
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