KEGGgraph help
1
0
Entering edit mode
Yan Jiao ▴ 140
@yan-jiao-4354
Last seen 10.3 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}}
graph graph • 1.7k views
ADD COMMENT
0
Entering edit mode
@jitao-david-zhang-3188
Last seen 7.9 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]]
ADD COMMENT
0
Entering edit mode
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}}
ADD REPLY
0
Entering edit mode
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}}
ADD REPLY
0
Entering edit mode
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}}
ADD REPLY
0
Entering edit mode
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]]
ADD REPLY
0
Entering edit mode
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
ADD REPLY

Login before adding your answer.

Traffic: 834 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6