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/file1eaf6b0f'
> >> 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/file1eaf6b0f'
> >> 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/file13f877e9'
> >> 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/file13f877e9'
> >> 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]]

