error in plotKEGGGraph
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@robert-m-flight-4158
Last seen 2.0 years ago
United States
Hi All, I'm playing around with KEGGGraph to examine some pathways, and I am running into some errors. When I try to plot some pathways, I get the error: "Error in .subtypeDisplay(object) : Given subtype 'missing interaction' is not found!" Here is an example with one pathway that gives the error and another that does not: library(KEGGgraph) # this one gives the error keggID <- "05213" tmpXML <- "testKGML1.xml" retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, method="wget") tmpGraph1 <- parseKGML2Graph(tmpXML, genesOnly=FALSE) plotKEGGgraph(tmpGraph1) # this one does not give an error, and spits out a very complicated graph keggID <- "04810" tmpXML <- "testKGML2.xml" retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, method="wget") tmpGraph2 <- parseKGML2Graph(tmpXML, genesOnly=FALSE) plotKEGGgraph(tmpGraph2) Any help on why this error is cropping up would be appreciated. R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] KEGGgraph_1.4.0 Rgraphviz_1.26.0 graph_1.26.0 XML_3.1-0 loaded via a namespace (and not attached): [1] tools_2.11.1 Thanks in advance, -Robert Robert M. Flight, Ph.D. Bioinformatics and Biomedical Computing Laboratory University of Louisville Louisville, KY PH 502-852-0467 EM robert.flight at louisville.edu EM rflight79 at gmail.com Williams and Holland's Law: If enough data is collected, anything may be proven by statistical methods.
Pathways KEGGgraph Pathways KEGGgraph • 749 views
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@jitao-david-zhang-3188
Last seen 5.7 years ago
Hi dear Robert, Thanks for reporting! Would you please send the file you used? I will try to figure out what went wrong. Best wishes, David 2010/7/7 Robert M. Flight <rflight79@gmail.com> > Hi All, > > I'm playing around with KEGGGraph to examine some pathways, and I am > running into some errors. > > When I try to plot some pathways, I get the error: "Error in > .subtypeDisplay(object) : Given subtype 'missing interaction' is not > found!" > > Here is an example with one pathway that gives the error and another > that does not: > > library(KEGGgraph) > > # this one gives the error > keggID <- "05213" > tmpXML <- "testKGML1.xml" > retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, > method="wget") > tmpGraph1 <- parseKGML2Graph(tmpXML, genesOnly=FALSE) > plotKEGGgraph(tmpGraph1) > > # this one does not give an error, and spits out a very complicated graph > keggID <- "04810" > tmpXML <- "testKGML2.xml" > retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, > method="wget") > tmpGraph2 <- parseKGML2Graph(tmpXML, genesOnly=FALSE) > plotKEGGgraph(tmpGraph2) > > Any help on why this error is cropping up would be appreciated. > > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] KEGGgraph_1.4.0 Rgraphviz_1.26.0 graph_1.26.0 XML_3.1-0 > > loaded via a namespace (and not attached): > [1] tools_2.11.1 > > Thanks in advance, > > -Robert > > Robert M. Flight, Ph.D. > Bioinformatics and Biomedical Computing Laboratory > University of Louisville > Louisville, KY > > PH 502-852-0467 > EM robert.flight@louisville.edu > EM rflight79@gmail.com > > Williams and Holland's Law: > If enough data is collected, anything may be proven by > statistical methods. > > _______________________________________________ > 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 > -- 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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