Dear Stuart,
The uniqueReaction option has been deleted in the latest release.
Could you tell which graph was NULL from AllGraphs? And the KGML
file of
that? If so I can have a deeper look into the issue.
Best,
David
On Wed, Oct 16, 2013 at 9:50 AM, Stuart Bradley
<stuy.bradley@gmail.com>wrote:
> Right final email before I go to sleep. Probably should've kept
these
> together. Apologies!
>
> After removing uniqueReaction = FALSE, the: FinalGraph <-
> mergeKEGGgraphs(AllGraphs, edgemode = "directed") ; line throws the
> following error:
>
> Error in (function (classes, fdef, mtable) :
> unable to find an inherited method for function âgetNameâ for
signature
> â"NULL"â
>
> Is that likely to be related? Or something else entirely?
>
> Cheers,
> Stuart
>
>
> On Wed, Oct 16, 2013 at 8:27 PM, Stuart Bradley
<stuy.bradley@gmail.com>wrote:
>
>> Ok found the actual culprit. It appears UniqueReaction = FALSE is
an
>> unused argument in KEGGpathway2reactionGraph. Did this change? Or
is
>> something funny going on? I've used it previously.
>>
>> Stuart
>>
>>
>> On Wed, Oct 16, 2013 at 8:18 PM, Stuart Bradley
<stuy.bradley@gmail.com>wrote:
>>
>>> Correction; Error hasn't disappeared; KEGGpathway2reactionGraph is
>>> returning all NULL entries.
>>>
>>>
>>> On Wed, Oct 16, 2013 at 7:53 PM, Stuart Bradley
<stuy.bradley@gmail.com>wrote:
>>>
>>>> Hi David,
>>>>
>>>> Appears to be working as normal on my laptop now. Not sure why,
haven't
>>>> changed anything. But the error has dissappeared. Will use exact
files from
>>>> laptop on the workstation on Monday to confirm it's a non-issue.
>>>>
>>>> Cheers,
>>>> Stuart
>>>>
>>>>
>>>> On Tue, Oct 15, 2013 at 9:47 PM, Zhang, Jitao David <
>>>> jitao_david.zhang@roche.com> wrote:
>>>>
>>>>> Dear Stuart, do you have an idea which file broke the code?
>>>>>
>>>>> Best, David
>>>>>
>>>>>
>>>>> On Mon, Oct 14, 2013 at 6:48 PM, Stuart Bradley <
>>>>> stuy.bradley@gmail.com> wrote:
>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> 1.19.0 appears to break our code (tried it on my laptop this
morning)
>>>>>> see: for code and
>>>>>> Session Info.
>>>>>>
>>>>>> Cheers,
>>>>>> Stuart
>>>>>>
>>>>>>
>>>>>> On Mon, Oct 14, 2013 at 7:21 PM, Stuart Bradley <
>>>>>> stuy.bradley@gmail.com> wrote:
>>>>>>
>>>>>>> Hi folks,
>>>>>>>
>>>>>>> Finally got hold of our KEGG data to test, and it works!
>>>>>>>
>>>>>>> Well, only on my laptop - and not the workstation, but that's
a
>>>>>>> problem for tomorrow.
>>>>>>>
>>>>>>> I believe it's a setup issue, since I'm running 1.17.0 fine on
my
>>>>>>> end, and Paul says 1.19.0 (the workstation version) is
working.
>>>>>>>
>>>>>>> If it appears to be related I'll let everyone know.
>>>>>>>
>>>>>>> Otherwise, thank you all for your help! Our department is
quite
>>>>>>> excited to get KEGG into Cytoscape!
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Stuart Bradley
>>>>>>>
>>>>>>>
>>>>>>> On Fri, Oct 11, 2013 at 7:50 AM, Paul Shannon <
>>>>>>> paul.thurmond.shannon@gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi David,
>>>>>>>>
>>>>>>>> I tried out the new code (KEGGgraph v 1.19.0), and it works
great.
>>>>>>>> Thanks!
>>>>>>>>
>>>>>>>> I took the liberty (I hope you don't mind) of adding a
unitTest to
>>>>>>>> your package which
>>>>>>>>
>>>>>>>> 1) fails with the old version, demonstrating Stuart's
problem
>>>>>>>> 2) succeeds with the new
>>>>>>>>
>>>>>>>> The file is inst/unitTests/test_KEGGgraph.R
>>>>>>>>
>>>>>>>> - Paul
>>>>>>>>
>>>>>>>> On Oct 7, 2013, at 11:35 PM, Zhang, Jitao David wrote:
>>>>>>>>
>>>>>>>> > Dear both,
>>>>>>>> >
>>>>>>>> > I have updated KEGGgraph to version 1.18.0 (subversion
>>>>>>>> revision: 81275) in the devel branch of bioconductor. The
>>>>>>>> KEGGpathway2reactionGraph function now returns a reaction
graph that can be
>>>>>>>> merged with other KEGG pathway/reaction graphs.
>>>>>>>> >
>>>>>>>> > The updated function is given below.
>>>>>>>> >
>>>>>>>> > KEGGpathway2reactionGraph <- function(pathway) {
>>>>>>>> > reactions <- getReactions(pathway)
>>>>>>>> > if(length(reactions)==0) {
>>>>>>>> > stop("The pathway contains no chemical reactions!\n")
>>>>>>>> > }
>>>>>>>> > subs <- sapply(reactions, getSubstrate)
>>>>>>>> > prods <- sapply(reactions, getProduct)
>>>>>>>> > types <- sapply(reactions, getType)
>>>>>>>> > gridlist <- lapply(seq(along=reactions),
>>>>>>>> > function(i)
>>>>>>>> > expand.grid(subs[[i]], prods[[i]],
>>>>>>>> stringsAsFactors=FALSE))
>>>>>>>> > grid <- as.matrix(do.call(rbind, gridlist))
>>>>>>>> > isRepGrid <- duplicated(grid)
>>>>>>>> > uniqGrid <- grid[!isRepGrid,,drop=FALSE]
>>>>>>>> > gridTypes <- rep(types, sapply(gridlist, nrow))
>>>>>>>> > uniqGridTypes <- gridTypes[!isRepGrid]
>>>>>>>> >
>>>>>>>> > cg <- ftM2graphNEL(uniqGrid)
>>>>>>>> > allNodes <- nodes(pathway)
>>>>>>>> > allNodeNames <- sapply(allNodes, function(x)
paste(getName(x),
>>>>>>>> collapse=","))
>>>>>>>> > cgNodes <- allNodes[match(nodes(cg), allNodeNames)]
>>>>>>>> >
>>>>>>>> > cgEdges <- sapply(1:nrow(uniqGrid),
>>>>>>>> > function(x)
>>>>>>>> > new("KEGGEdge",
>>>>>>>> > entry1ID=uniqGrid[x,1],
>>>>>>>> > entry2ID=uniqGrid[x,2],
>>>>>>>> > type=uniqGridTypes[x],
>>>>>>>> > subtype=list()))
>>>>>>>> >
>>>>>>>> > ## set node and edge data - as KEGGNode and KEGGEdge
>>>>>>>> > ## attention: KEGGEdges may be more than graph edges, due
to
>>>>>>>> non-genes
>>>>>>>> > names(cgEdges) <- apply(uniqGrid,1L, paste, collapse="~")
>>>>>>>> > env.node <- new.env()
>>>>>>>> > env.edge <- new.env()
>>>>>>>> > assign("nodes", cgNodes, envir=env.node)
>>>>>>>> > assign("edges", cgEdges, envir=env.edge)
>>>>>>>> >
>>>>>>>> > nodeDataDefaults(cg, "KEGGNode") <- env.node
>>>>>>>> > edgeDataDefaults(cg, "KEGGEdge") <- env.edge
>>>>>>>> >
>>>>>>>> > return(cg)
>>>>>>>> > }
>>>>>>>> >
>>>>>>>> > Try it out and please let me know if you encounter any
problem.
>>>>>>>> >
>>>>>>>> > Best wishes,
>>>>>>>> > David
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > On Tue, Sep 3, 2013 at 9:47 PM, Paul Shannon <
>>>>>>>> paul.thurmond.shannon@gmail.com> wrote:
>>>>>>>> > Hi Stuart,
>>>>>>>> >
>>>>>>>> > I have included Jitao David Zhang here as well, the package
>>>>>>>> author and maintainer.
>>>>>>>> >
>>>>>>>> > I think I can reduce your problem report to these steps:
>>>>>>>> >
>>>>>>>> > library(KEGGgraph)
>>>>>>>> > filename <- "hsa00260.kgml"
>>>>>>>> > retrieveKGML("00260", organism="hsa", destfile=filename,
method =
>>>>>>>> "internal")
>>>>>>>> > pathway <- parseKGML(filename)
>>>>>>>> >
>>>>>>>> > g.reaction <- KEGGpathway2reactionGraph(pathway,
uniqueReaction =
>>>>>>>> FALSE)
>>>>>>>> > g.pathway <- KEGGpathway2Graph(pathway, genesOnly=FALSE)
>>>>>>>> >
>>>>>>>> > names(nodeDataDefaults(g.reaction)) # NULL
>>>>>>>> > names(nodeDataDefaults(g.pathway)) # KEGGNode
>>>>>>>> >
>>>>>>>> > mergeKEGGgraphs (in KEGGgraph/R/graph.R) requires that
there be
>>>>>>>> an edge attribute "KEGGEdge" and a node attribute "KEGGNode",
and fails
>>>>>>>> with the error you saw.
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > So the reaction graph does not have the two attributes
required
>>>>>>>> by mergeKEGGgraphs. I am not sure whether this is by design,
or whether it
>>>>>>>> is an oversight.
>>>>>>>> > Once David clarifies that, we can devise some possible next
steps
>>>>>>>> for you.
>>>>>>>> >
>>>>>>>> > - Paul
>>>>>>>> >
>>>>>>>> > P.S For future posts, please include (as I have tried to
do
>>>>>>>> here) a smallish, self-contained and reproducible example,
along with your
>>>>>>>> sessionInfo:
>>>>>>>> >
>>>>>>>> > R version 3.0.1 Patched (2013-05-26 r62815)
>>>>>>>> > Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>>>>>>> >
>>>>>>>> > locale:
>>>>>>>> > [1] C
>>>>>>>> >
>>>>>>>> > attached base packages:
>>>>>>>> > [1] stats graphics grDevices utils datasets
methods
>>>>>>>> base
>>>>>>>> >
>>>>>>>> > other attached packages:
>>>>>>>> > [1] KEGGgraph_1.17.0 graph_1.39.3 XML_3.95-0.2
>>>>>>>> >
>>>>>>>> > loaded via a namespace (and not attached):
>>>>>>>> > [1] BiocGenerics_0.7.4 parallel_3.0.1 stats4_3.0.1
>>>>>>>> tools_3.0.1
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > On Sep 2, 2013, at 2:51 PM, Stuart Bradley wrote:
>>>>>>>> >
>>>>>>>> > > Hello all,
>>>>>>>> > >
>>>>>>>> > > I'm trying to build unified compound pathway maps, and
have
>>>>>>>> been successful
>>>>>>>> > > using this method:
>>>>>>>> > >
>>>>>>>> > > library(graph)
>>>>>>>> > > library(KEGGgraph)
>>>>>>>> > >
>>>>>>>> > > KEGGList <- list.files(path = "C:/Users/Castor
>>>>>>>> > > Castle/Documents/kgml/metabolic/ko/subset/", full.names =
TRUE)
>>>>>>>> > >
>>>>>>>> > > AllGraphs <- lapply(KEGGList, function(x) {
>>>>>>>> > > pathway <- parseKGML(x)
>>>>>>>> > > pathway <- KEGGpathway2reactionGraph(pathway,
uniqueReaction =
>>>>>>>> FALSE)
>>>>>>>> > > })
>>>>>>>> > >
>>>>>>>> > > FinalGraph <- mergeGraphs(AllGraphs, edgemode =
"directed")
>>>>>>>> > >
>>>>>>>> > > However, I'd like to be able to use mergeKEGGgraphs as it
>>>>>>>> retains more
>>>>>>>> > > information. The problem is that when I replace
mergeGraphs
>>>>>>>> with
>>>>>>>> > > mergeKEGGgraphs
>>>>>>>> > > I get the following error (regardless of whether it's my
own
>>>>>>>> files, or the
>>>>>>>> > > example ones provided):
>>>>>>>> > >
>>>>>>>> > > Error in .verifyAttrName(attr, names(self@defaults)):
>>>>>>>> > > unknown attribute name: ÅKEGGNodeâ
>>>>>>>> > >
>>>>>>>> > > Has anyone found a work around for this? I was fiddling
with
>>>>>>>> > > setKEGGnodeData/setKEGGEdgeData in conjunction with
>>>>>>>> mergeGraphs, but I
>>>>>>>> > > can't get it to work.
>>>>>>>> > >
>>>>>>>> > > Any help would be greatly appreciated.
>>>>>>>> > >
>>>>>>>> > > Cheers,
>>>>>>>> > > Stuart Bradley
>>>>>>>> > >
>>>>>>>> > > [[alternative HTML version deleted]]
>>>>>>>> > >
>>>>>>>> > > _______________________________________________
>>>>>>>> > > Bioconductor mailing list
>>>>>>>> > > Bioconductor@r-project.org
>>>>>>>> > >
https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>> > > Search the archives:
>>>>>>>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> >
>>>>>>>> > --
>>>>>>>> >
>>>>>>>> > Jitao David Zhang | å¼ ç»§æ¶ | Computational Biology and
>>>>>>>> Bioinformatics | Pharmaceutical Divison | F. Hoffmann-La-
Roche AG | CH-4070
>>>>>>>> Basel | Switzerland
>>>>>>>> >
>>>>>>>> > Tel +41 61 688 62 51
>>>>>>>> >
>>>>>>>> > Confidentiality Note: This message is intended only for the
use
>>>>>>>> of the named recipient(s) and may contain confidential and/or
privileged
>>>>>>>> information. If you are not the intended recipient, please
contact the
>>>>>>>> sender and delete this message. Any unauthorized use of the
information
>>>>>>>> contained in this message is prohibited.
>>>>>>>> >
>>>>>>>> > Please inform me immediately in case attached documents are
>>>>>>>> missing!
>>>>>>>> >
>>>>>>>> >
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> *Jitao David Zhang | **å¼ ç»§æ¶** | Computational Biology and
>>>>> Bioinformatics | Pharmaceutical Divison | F. Hoffmann-La-Roche
AG | CH-4070
>>>>> Basel | Switzerland*****
>>>>>
>>>>> *Tel +41 61 688 62 51 *
>>>>>
>>>>> Confidentiality Note: This message is intended only for the use
of the
>>>>> named recipient(s) and may contain confidential and/or
privileged
>>>>> information. If you are not the intended recipient, please
contact the
>>>>> sender and delete this message. Any unauthorized use of the
information
>>>>> contained in this message is prohibited.****
>>>>>
>>>>> *Please inform me immediately in case attached documents are
missing!*
>>>>>
>>>>>
>>>>
>>>
>>
>
--
*Jitao David Zhang | **å¼ ç»§æ¶** | Computational Biology and
Bioinformatics |
Pharmaceutical Divison | F. Hoffmann-La-Roche AG | CH-4070 Basel |
Switzerland*****
*Tel +41 61 688 62 51 *
Confidentiality Note: This message is intended only for
...{{dropped:11}}
