KEGGgraph help
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Yan Jiao ▴ 140
@yan-jiao-4354
Last seen 8.1 years ago
Dear all, I managed reading in a kegg graph A graphNEL graph with directed edges Number of Nodes = 70 Number of Edges = 109 but when I do plotKEGGgraph, R crashed, my R version is 2.12.0 , how can I see the graph? Many thanks yan ********************************************************************** This email and any files transmitted with it are confide...{{dropped:10}}
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@jitao-david-zhang-3188
Last seen 5.6 years ago
please report sessionInfo() results. Currently I have no clue. It might be caused by corrupt graphviz, but I am not sure. Best wishes, David 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> > Dear all, > > > > I managed reading in a kegg graph > > > > A graphNEL graph with directed edges > > Number of Nodes = 70 > > Number of Edges = 109 > > > > but when I do plotKEGGgraph, R crashed, my R version is 2.12.0 , how can > I see the graph? > > > > Many thanks > > > > yan > > > > > ********************************************************************** > This email and any files transmitted with it are confide...{{dropped:10}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jitao David Zhang Pre-doc staff of Computational Biology and Biostatistics Division of Molecular Genome Analysis DKFZ, Heidelberg D-69120, Germany http://www.NextBioMotif.com/ [[alternative HTML version deleted]]
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sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] KEGGgraph_1.6.0 XML_3.2-0.2 Rgraphviz_1.28.0 graph_1.28.0 loaded via a namespace (and not attached): [1] tools_2.12.0 From: Jitao David Zhang [mailto:davidvonpku@gmail.com] Sent: 29 November 2010 16:40 To: Yan Jiao Cc: bioconductor@r-project.org Subject: Re: [BioC] KEGGgraph help please report sessionInfo() results. Currently I have no clue. It might be caused by corrupt graphviz, but I am not sure. Best wishes, David 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> Dear all, I managed reading in a kegg graph A graphNEL graph with directed edges Number of Nodes = 70 Number of Edges = 109 but when I do plotKEGGgraph, R crashed, my R version is 2.12.0 , how can I see the graph? Many thanks yan ********************************************************************** This email and any files transmitted with it are confide...{{dropped:10}} _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Jitao David Zhang Pre-doc staff of Computational Biology and Biostatistics Division of Molecular Genome Analysis DKFZ, Heidelberg D-69120, Germany http://www.NextBioMotif.com/ ********************************************************************** This email and any files transmitted with it are confide...{{dropped:10}}
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Hi dear Yan, Maybe give a try to draw a toy network V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, 0.2) plot(g1) Is is okay? Cheers, David 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> > sessionInfo() > > R version 2.12.0 (2010-10-15) > > Platform: i386-pc-mingw32/i386 (32-bit) > > > > locale: > > [1] LC_COLLATE=English_United Kingdom.1252 > > [2] LC_CTYPE=English_United Kingdom.1252 > > [3] LC_MONETARY=English_United Kingdom.1252 > > [4] LC_NUMERIC=C > > [5] LC_TIME=English_United Kingdom.1252 > > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] KEGGgraph_1.6.0 XML_3.2-0.2 Rgraphviz_1.28.0 graph_1.28.0 > > > > loaded via a namespace (and not attached): > > [1] tools_2.12.0 > > > > *From:* Jitao David Zhang [mailto:davidvonpku@gmail.com] > *Sent:* 29 November 2010 16:40 > *To:* Yan Jiao > *Cc:* bioconductor@r-project.org > *Subject:* Re: [BioC] KEGGgraph help > > > > > please report sessionInfo() results. Currently I have no clue. It might be > caused by corrupt graphviz, but I am not sure. > > > Best wishes, > David > > 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> > > Dear all, > > > > I managed reading in a kegg graph > > > > A graphNEL graph with directed edges > > Number of Nodes = 70 > > Number of Edges = 109 > > > > but when I do plotKEGGgraph, R crashed, my R version is 2.12.0 , how can > I see the graph? > > > > Many thanks > > > > yan > > > > > ********************************************************************** > This email and any files transmitted with it are confide...{{dropped:10}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Jitao David Zhang > Pre-doc staff of Computational Biology and Biostatistics > Division of Molecular Genome Analysis > DKFZ, Heidelberg D-69120, Germany > > http://www.NextBioMotif.com/ > > ********************************************************************** > > This email and any files transmitted with it are confi...{{dropped:26}}
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No, it crashed From: Jitao David Zhang [mailto:davidvonpku@gmail.com] Sent: 29 November 2010 16:48 To: Yan Jiao Cc: bioconductor@r-project.org Subject: Re: [BioC] KEGGgraph help Hi dear Yan, Maybe give a try to draw a toy network V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M, 0.2) plot(g1) Is is okay? Cheers, David 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] KEGGgraph_1.6.0 XML_3.2-0.2 Rgraphviz_1.28.0 graph_1.28.0 loaded via a namespace (and not attached): [1] tools_2.12.0 From: Jitao David Zhang [mailto:davidvonpku@gmail.com] Sent: 29 November 2010 16:40 To: Yan Jiao Cc: bioconductor@r-project.org Subject: Re: [BioC] KEGGgraph help please report sessionInfo() results. Currently I have no clue. It might be caused by corrupt graphviz, but I am not sure. Best wishes, David 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> Dear all, I managed reading in a kegg graph A graphNEL graph with directed edges Number of Nodes = 70 Number of Edges = 109 but when I do plotKEGGgraph, R crashed, my R version is 2.12.0 , how can I see the graph? Many thanks yan ********************************************************************** This email and any files transmitted with it are confide...{{dropped:10}} _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Jitao David Zhang Pre-doc staff of Computational Biology and Biostatistics Division of Molecular Genome Analysis DKFZ, Heidelberg D-69120, Germany http://www.NextBioMotif.com/ ********************************************************************** This email and any files transmitted with it are confide...{{dropped:27}}
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Hi dear Yan Jiao, Well, then it must be the problem of Rgraphviz. You may have to turn to the maintainers of Rgraphviz (help(package=Rgraphviz)). Before that, check out the installation of Rgraphviz as well as the documentation of the package. In case the question still exists, please tell me. Paul Shannon and I are working on an alternative approach, which might be in beta-phase soon and might help. Best wishes, David 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> > No, it crashed > > > > > > *From:* Jitao David Zhang [mailto:davidvonpku@gmail.com] > *Sent:* 29 November 2010 16:48 > > *To:* Yan Jiao > *Cc:* bioconductor@r-project.org > *Subject:* Re: [BioC] KEGGgraph help > > > > Hi dear Yan, > > Maybe give a try to draw a toy network > > V <- letters[1:10] > M <- 1:4 > g1 <- randomGraph(V, M, 0.2) > plot(g1) > > Is is okay? > > Cheers, David > > 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> > > sessionInfo() > > R version 2.12.0 (2010-10-15) > > Platform: i386-pc-mingw32/i386 (32-bit) > > > > locale: > > [1] LC_COLLATE=English_United Kingdom.1252 > > [2] LC_CTYPE=English_United Kingdom.1252 > > [3] LC_MONETARY=English_United Kingdom.1252 > > [4] LC_NUMERIC=C > > [5] LC_TIME=English_United Kingdom.1252 > > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] KEGGgraph_1.6.0 XML_3.2-0.2 Rgraphviz_1.28.0 graph_1.28.0 > > > > loaded via a namespace (and not attached): > > [1] tools_2.12.0 > > > > *From:* Jitao David Zhang [mailto:davidvonpku@gmail.com] > *Sent:* 29 November 2010 16:40 > *To:* Yan Jiao > *Cc:* bioconductor@r-project.org > *Subject:* Re: [BioC] KEGGgraph help > > > > > please report sessionInfo() results. Currently I have no clue. It might be > caused by corrupt graphviz, but I am not sure. > > > Best wishes, > David > > 2010/11/29 Yan Jiao <y.jiao@ucl.ac.uk> > > Dear all, > > > > I managed reading in a kegg graph > > > > A graphNEL graph with directed edges > > Number of Nodes = 70 > > Number of Edges = 109 > > > > but when I do plotKEGGgraph, R crashed, my R version is 2.12.0 , how can > I see the graph? > > > > Many thanks > > > > yan > > > > > ********************************************************************** > This email and any files transmitted with it are confide...{{dropped:10}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Jitao David Zhang > Pre-doc staff of Computational Biology and Biostatistics > Division of Molecular Genome Analysis > DKFZ, Heidelberg D-69120, Germany > > http://www.NextBioMotif.com/ > > ********************************************************************** > > This email and any files transmitted with it are confidential and > > intended solely for the use of the individual or entity to whom they > > are addressed. If you have received this email in error please notify > > the system manager (it.support@cancer.ucl.ac.uk). > > ********************************************************************** > > > > > > > -- > Jitao David Zhang > Pre-doc staff of Computational Biology and Biostatistics > Division of Molecular Genome Analysis > DKFZ, Heidelberg D-69120, Germany > > http://www.NextBioMotif.com/ > -- Jitao David Zhang Pre-doc staff of Computational Biology and Biostatistics Division of Molecular Genome Analysis DKFZ, Heidelberg D-69120, Germany http://www.NextBioMotif.com/ [[alternative HTML version deleted]]
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On 11/29/2010 09:01 AM, Jitao David Zhang wrote: > Hi dear Yan Jiao, > > Well, then it must be the problem of Rgraphviz. You may have to turn to the > maintainers of Rgraphviz (help(package=Rgraphviz)). Before that, check out > the installation of Rgraphviz as well as the documentation of the package. > > In case the question still exists, please tell me. Paul Shannon and I are > working on an alternative approach, which might be in beta-phase soon and > might help. > > Best wishes, > David > > 2010/11/29 Yan Jiao <y.jiao at="" ucl.ac.uk=""> > >> No, it crashed Can you be more specific? Martin >> >> >> >> >> >> *From:* Jitao David Zhang [mailto:davidvonpku at gmail.com] >> *Sent:* 29 November 2010 16:48 >> >> *To:* Yan Jiao >> *Cc:* bioconductor at r-project.org >> *Subject:* Re: [BioC] KEGGgraph help >> >> >> >> Hi dear Yan, >> >> Maybe give a try to draw a toy network >> >> V <- letters[1:10] >> M <- 1:4 >> g1 <- randomGraph(V, M, 0.2) >> plot(g1) >> >> Is is okay? >> >> Cheers, David >> >> 2010/11/29 Yan Jiao <y.jiao at="" ucl.ac.uk=""> >> >> sessionInfo() >> >> R version 2.12.0 (2010-10-15) >> >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> >> >> locale: >> >> [1] LC_COLLATE=English_United Kingdom.1252 >> >> [2] LC_CTYPE=English_United Kingdom.1252 >> >> [3] LC_MONETARY=English_United Kingdom.1252 >> >> [4] LC_NUMERIC=C >> >> [5] LC_TIME=English_United Kingdom.1252 >> >> >> >> attached base packages: >> >> [1] grid stats graphics grDevices utils datasets methods >> >> [8] base >> >> >> >> other attached packages: >> >> [1] KEGGgraph_1.6.0 XML_3.2-0.2 Rgraphviz_1.28.0 graph_1.28.0 >> >> >> >> loaded via a namespace (and not attached): >> >> [1] tools_2.12.0 >> >> >> >> *From:* Jitao David Zhang [mailto:davidvonpku at gmail.com] >> *Sent:* 29 November 2010 16:40 >> *To:* Yan Jiao >> *Cc:* bioconductor at r-project.org >> *Subject:* Re: [BioC] KEGGgraph help >> >> >> >> >> please report sessionInfo() results. Currently I have no clue. It might be >> caused by corrupt graphviz, but I am not sure. >> >> >> Best wishes, >> David >> >> 2010/11/29 Yan Jiao <y.jiao at="" ucl.ac.uk=""> >> >> Dear all, >> >> >> >> I managed reading in a kegg graph >> >> >> >> A graphNEL graph with directed edges >> >> Number of Nodes = 70 >> >> Number of Edges = 109 >> >> >> >> but when I do plotKEGGgraph, R crashed, my R version is 2.12.0 , how can >> I see the graph? >> >> >> >> Many thanks >> >> >> >> yan >> >> >> >> >> ********************************************************************** >> This email and any files transmitted with it are confide...{{dropped:10}} >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> >> -- >> Jitao David Zhang >> Pre-doc staff of Computational Biology and Biostatistics >> Division of Molecular Genome Analysis >> DKFZ, Heidelberg D-69120, Germany >> >> http://www.NextBioMotif.com/ >> >> ********************************************************************** >> >> This email and any files transmitted with it are confidential and >> >> intended solely for the use of the individual or entity to whom they >> >> are addressed. If you have received this email in error please notify >> >> the system manager (it.support at cancer.ucl.ac.uk). >> >> ********************************************************************** >> >> >> >> >> >> >> -- >> Jitao David Zhang >> Pre-doc staff of Computational Biology and Biostatistics >> Division of Molecular Genome Analysis >> DKFZ, Heidelberg D-69120, Germany >> >> http://www.NextBioMotif.com/ >> > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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