[Bioc-devel] Recent issue with plot method dispatch

[Martin Morgan]

On 03/13/2013 12:32 PM, Martin Morgan wrote:
> On 03/13/2013 04:02 AM, Joern Toedling wrote:
>> Hello,
>>
>> I have encountered a strange issue with the plotting function in my package
>> "girafe" that I need some help with. I haven't changed anything in the plot
>> methods or the NAMESPACE of the package recently, and it worked before, yet I
>> observe the following error now.
>>
>> When calling the "plot" method for objects of the class
>> "AlignedGenomeIntervals", rather than using the appropriate S4 method and
>> calling another function (plotAligned), R falls back to the S3 method
>> "plot.Intervals_full" (Intervals_full is the class that AlignedGenomeIntervals
>> indirectly inherits from). Please see below for the sessionInfo() output.
>>
>> Has anybody encountered the same behaviour or any insights what might be going
>> on? I'm grateful for any suggestions what I could fix in the method definition
>> and/or the NAMESPACE. I guess as a workaround I could add an S3 plot method for
>> the "AlignedGenomeIntervals" calls but that would be rather ugly.

Actually, from

?Methods

in the section 'Methods for S3 Generic Functions' the recommendation is to do 
just this -- define both an S3 and S4 methods. It is not too ugly

   plot.AlignedGenomeIntervals = function(x, ...) { ... }
   setMethod(plot, "AlignedGenomeIntervals", plot.AlignedGenomeIntervals)

and

   S3method(plot, A)
   exportMethods(plot)

in NAMESPACE. This 'works' in my toy package, though I'd be hard-pressed to 
explain why.

Martin

>
> I think this is a bug in S4, triggered by complex relations between the
> intervals and girafe package. I'll pursue this on R-devel.
>
> I can reproduce this with a PkgA that has DESCRIPTION with
>
> Depends: intervals
> Imports: graphics
>
> NAMESPACE:
>
> importFrom(graphics, "plot")
> export("plot")
> exportMethods("plot")
>
> R/tmp.R
>
> setClass("A")
> setMethod("plot", "A", function(x, y, ...) {})
>
>
> and then
>
>  > library(PkgA)
> Loading required package: intervals
>  > plot
> function (x, y, ...)
> UseMethod("plot")
> <environment: namespace:graphics>
>
> notice that 'plot' is reported as an S3 generic, but should be an S4 generic.
>
> Removing Depends: intervals or changing to importsFrom(intervals, "plot")
> recovers S4 export
>
>  > library(PkgA)
> Loading required package: intervals
>  > plot
> standardGeneric for "plot" defined from package "graphics"
>
> function (x, y, ...)
> standardGeneric("plot")
> <environment: 0x60aea90>
> Methods may be defined for arguments: x, y
> Use  showMethods("plot")  for currently available ones.
>
>
> The 'intervals' package Depends: on methods but nothing else. It defines S3 and
> S4 methods on plot, creating an implicit S4 generic in the process. It's
> NAMESPACE has
>
> S3method( "plot", "Intervals" )
> S3method( "plot", "Intervals_full" )
> exportMethods("plot")
>
> and we have
>
>  > library(intervals)
>  > plot
> standardGeneric for "plot" defined from package "graphics"
>
> function (x, y, ...)
> standardGeneric("plot")
> <environment: 0x68cdc78>
> Methods may be defined for arguments: x, y
> Use  showMethods("plot")  for currently available ones.
>
>
>
>>
>> Thanks in advance,
>> Joern
>>
>>
>>  > sessionInfo()
>> R Under development (unstable) (2013-03-12 r62224)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> ...
>> other attached packages:
>>   [1] org.Mm.eg.db_2.9.0     RSQLite_0.11.2 DBI_0.2-5
>>   [4] AnnotationDbi_1.21.13  Biobase_2.19.3 girafe_1.11.2
>>   [7] genomeIntervals_1.15.1 intervals_0.14.0 ShortRead_1.17.10
>> [10] latticeExtra_0.6-24    RColorBrewer_1.0-5 lattice_0.20-13
>> [13] Rsamtools_1.11.21      Biostrings_2.27.11 GenomicRanges_1.11.36
>> [16] IRanges_1.17.37        BiocGenerics_0.5.6 BiocInstaller_1.9.7
>>
>> loaded via a namespace (and not attached):
>> [1] bitops_1.0-5    BSgenome_1.27.1 hwriter_1.3     stats4_3.1.0
>> [5] tcltk_3.1.0     tools_3.1.0     zlibbioc_1.5.0
>>
>>
>> Example producing the error:
>>
>> library("girafe")
>> example("plotAligned")
>>
>>
>>
>>
>
>


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