Thanks ! Pierre On Thu, Sep 23, 2010 at 12:44 AM, Jitao David Zhang <davidvonpku at="" gmail.com=""> wrote: > Hello dear All, > ?? A fix has been submitted to KEGGgraph package at bioc-svn (revision > 49560), which hopefully fix this issue. Thanks to the suggestion of Pierre, > I have added an backup subtype 'others' which will be bumped in case no > subtype could be matched. It is presented as a black dash line with question > mark (?) in the plot. > ??Thanks to Robert and Pierre again. > ??Best wishes, > David > > 2010/9/21 Pierre Neuvial <pierre at="" stat.berkeley.edu=""> >> >> Hi David, >> >> Has there been any follow-up on this ? I bumped into the same error as >> Robert. >> >> You asked for the file he used. ?If you run the code sent by Robert, >> you will get >> >> > keggID <- "05213" >> > tmpXML <- "testKGML1.xml" >> > retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, >> > method="wget") >> --2010-09-21 12:23:04-- >> >> ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- metabolic/organisms/mmu/mmu05213.xml >> ? ? ? ? ?=> >> `/var/folders/R7/R7TMUh6WGeSJE0LtxqwHWk+++TI/-Tmp-//RtmpmGNCWB/file 1eaf6b0f' >> Resolving ftp.genome.jp... 133.103.100.184 >> Connecting to ftp.genome.jp|133.103.100.184|:21... connected. >> Logging in as anonymous ... Logged in! >> ==> SYST ... done. ? ?==> PWD ... done. >> ==> TYPE I ... done. ?==> CWD >> /pub/kegg/xml/kgml/non-metabolic/organisms/mmu ... done. >> ==> SIZE mmu05213.xml ... 16729 >> ==> PASV ... done. ? ?==> RETR mmu05213.xml ... done. >> Length: 16729 (16K) >> >> 100%[======================================>] 16,729 ? ? ?38.4K/s ? in >> 0.4s >> >> 2010-09-21 12:23:07 (38.4 KB/s) - >> >> `/var/folders/R7/R7TMUh6WGeSJE0LtxqwHWk+++TI/-Tmp-//RtmpmGNCWB/file 1eaf6b0f' >> saved [16729] >> >> --2010-09-21 12:23:07-- >> >> ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- metabolic/organisms/mmu/mmu05213.xml >> ? ? ? ? ?=> `testKGML1.xml' >> Resolving ftp.genome.jp... 133.103.100.184 >> Connecting to ftp.genome.jp|133.103.100.184|:21... connected. >> Logging in as anonymous ... Logged in! >> ==> SYST ... done. ? ?==> PWD ... done. >> ==> TYPE I ... done. ?==> CWD >> /pub/kegg/xml/kgml/non-metabolic/organisms/mmu ... done. >> ==> SIZE mmu05213.xml ... 16729 >> ==> PASV ... done. ? ?==> RETR mmu05213.xml ... done. >> Length: 16729 (16K) >> >> 100%[======================================>] 16,729 ? ? ?44.2K/s ? in >> 0.4s >> >> 2010-09-21 12:23:09 (44.2 KB/s) - `testKGML1.xml' saved [16729] >> >> That should be enough for you to reproduce the error. ?If not, the file is >> here: >> >> >> ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- metabolic/organisms/mmu/mmu05213.xml >> >> I've investigated this issue a bit more. The problem comes from the >> fact that this KEGG pathway (as well as a fair proportion of KEGG >> pathways) has at least one edge whose label is not understood by >> KEGGgraph, in this case (quoted from the above KGML file): >> >> ? <relation entry1="20" entry2="25" type="PCrel"> >> ? ? ? <subtype name="missing interaction" value="-/-"/> >> ? </relation> >> >> The types of interaction known by KEGGgraph are retrieved from a data >> object from the package: >> >> > data(KEGGEdgeSubtype, package="KEGGgraph") >> > as.character(KEGGEdgeSubtype[["name"]]) >> ?[1] "compound" ? ? ? ? ? ?"hidden compound" ? ? "activation" >> ?[4] "inhibition" ? ? ? ? ?"expression" ? ? ? ? ?"repression" >> ?[7] "indirect" ? ? ? ? ? ?"indirect effect" ? ? "state change" >> [10] "binding/association" "dissociation" ? ? ? ?"phosphorylation" >> [13] "dephosphorylation" ? "glycosylation" ? ? ? "ubiquitination" >> [16] "methylation" >> >> Because "missing interaction" is not known, the above error occurs. >> An easy fix for this problem is to add a line with name=="missing >> interaction" to this data.frame, and re-build the package. >> >> I've also encountered another instance of the same problem: >> >> > keggID <- "05213" >> > tmpXML <- "testKGML2.xml" >> > retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, >> > method="wget") >> --2010-09-21 13:56:37-- >> >> ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- metabolic/organisms/mmu/mmu05213.xml >> ? ? ? ? ?=> >> `/var/folders/R7/R7TMUh6WGeSJE0LtxqwHWk+++TI/-Tmp-//RtmpmGNCWB/file 13f877e9' >> Resolving ftp.genome.jp... 133.103.100.184 >> Connecting to ftp.genome.jp|133.103.100.184|:21... connected. >> Logging in as anonymous ... Logged in! >> ==> SYST ... done. ? ?==> PWD ... done. >> ==> TYPE I ... done. ?==> CWD >> /pub/kegg/xml/kgml/non-metabolic/organisms/mmu ... done. >> ==> SIZE mmu05213.xml ... 16729 >> ==> PASV ... done. ? ?==> RETR mmu05213.xml ... done. >> Length: 16729 (16K) >> >> 100%[======================================>] 16,729 ? ? ?41.4K/s ? in >> 0.4s >> >> 2010-09-21 13:56:39 (41.4 KB/s) - >> >> `/var/folders/R7/R7TMUh6WGeSJE0LtxqwHWk+++TI/-Tmp-//RtmpmGNCWB/file 13f877e9' >> saved [16729] >> >> --2010-09-21 13:56:39-- >> >> ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- metabolic/organisms/mmu/mmu05213.xml >> ? ? ? ? ?=> `testKGML2.xml' >> Resolving ftp.genome.jp... 133.103.100.184 >> Connecting to ftp.genome.jp|133.103.100.184|:21... connected. >> Logging in as anonymous ... Logged in! >> ==> SYST ... done. ? ?==> PWD ... done. >> ==> TYPE I ... done. ?==> CWD >> /pub/kegg/xml/kgml/non-metabolic/organisms/mmu ... done. >> ==> SIZE mmu05213.xml ... 16729 >> ==> PASV ... done. ? ?==> RETR mmu05213.xml ... done. >> Length: 16729 (16K) >> >> 100%[======================================>] 16,729 ? ? ?58.8K/s ? in >> 0.3s >> >> 2010-09-21 13:56:42 (58.8 KB/s) - `testKGML2.xml' saved [16729] >> >> > tmpGraph2 <- parseKGML2Graph(tmpXML, genesOnly=FALSE) >> > plotKEGGgraph(tmpGraph2) >> Error in .subtypeDisplay(object) : >> ?Given subtype 'ubiquination' is not found! >> >> This actually comes from a typo in KEGG entries: ubiquitination has >> been misspelled as "ubiquination" in >> >> ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- metabolic/organisms/mmu/mmu05213.xml >> (and a bunch of other KEGG files too). >> >> Again, this can be fixed by adding a line with name=="ubiquination" to >> KEGGEdgeSubtype. >> I've done this locally: edited the file >> KEGGgraph/data/KEGGEdgeSubtype.csv, recompiled the KEGGgraph package, >> and it works with no error. >> >> David, could you do this kind of fix ? >> >> More generally, it would of course be much better if the >> .subtypeDisplay function did not throw an *error* but a *warning* when >> encountering unknown interaction names. >> >> Hope this helps, >> >> Pierre >> >> R version 2.11.1 Patched (2010-09-16 r52946) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] grid ? ? ?stats ? ? graphics ?grDevices datasets ?utils ? ? methods >> [8] base >> >> other attached packages: >> [1] KEGGgraph_1.5.0 Rgraphviz_1.26.0 ?graph_1.26.0 ? ? ?XML_2.8-1 >> [5] R.utils_1.5.2 ? ? R.oo_1.7.3 ? ? ? ?R.methodsS3_1.2.0 fortunes_1.3-7 >> >> loaded via a namespace (and not attached): >> [1] tools_2.11.1 >> >> On Wed, Jul 21, 2010 at 2:31 PM, Jitao David Zhang >> <davidvonpku at="" gmail.com=""> wrote: >> > 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 at="" 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 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. >> >> >> >> _______________________________________________ >> >> 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 >> >> >> > >> > >> > >> > -- >> > 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]] >> > >> > _______________________________________________ >> > 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 >> > > > > > -- > 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/ >