[BioC] error in plotKEGGGraph
Pierre Neuvial
pierre at stat.berkeley.edu
Thu Sep 23 19:20:41 CEST 2010
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/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 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/
>
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