Wow, I don't know how I didn't see these replies. After a bunch of poking around, I ended up doing the same as Pierre, and just modified my local copy of the subtypes file. Glad to hear the next version will be updated. Cheers, -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. On Thu, Sep 23, 2010 at 13:20, Pierre Neuvial <pierre@stat.berkeley.edu>wrote: > Thanks ! > > Pierre > > On Thu, Sep 23, 2010 at 12:44 AM, Jitao David Zhang > <davidvonpku@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@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/file1 eaf6b0f' > >> 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/file1 eaf6b0f' > >> 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/file1 3f877e9' > >> 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/file1 3f877e9' > >> 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@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@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]] > >> > > >> > _______________________________________________ > >> > 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]]