[Bioc-devel] SetMethod to dispatch on class in unattached package
Pages, Herve
hp@ge@ @end|ng |rom |redhutch@org
Wed Jan 30 23:31:21 CET 2019
Hi Michael,
So IIUC this upfront class registration wouldn't do much beside making
the "no definition for class 'seurat'" message issued by setMethod
disappear. Maybe that's not enough to justify adding more bloat to the
methods package?
My 2 cents,
H.
On 1/30/19 13:35, Michael Lawrence via Bioc-devel wrote:
> Unrelated to the specific question, a generic function introduces more
> vocabulary into the ecosystem. Since SingleCellExperiment defines the
> standard interface, why not make a new method on logcounts()?
>
> Back on topic, what if the methods package were to support forward
> class declarations? For example,
>
> setExternalClass("seurat", package="seurat")
>
> I have no idea how to implement that, but perhaps we could at least
> agree on the API. Honestly, it may be that just some dummy class would
> work for method registration. But it's nice to be explicit and to list
> the source package, even if nothing is formally checked.
>
> Michael
>
>
>
> On Wed, Jan 30, 2019 at 12:41 PM Brendan Innes
> <brendan.innes using mail.utoronto.ca> wrote:
>> Thanks Martin!
>>
>>
>> The fun strategy (zzz.R .onLoad setHook trick) worked well, except for setting this particular method:
>>
>>
>> setMethod(scClustViz::getDR,"SingleCellExperiment",function(x,DRtype) {
>> if (any(grepl(DRtype,SingleCellExperiment::reducedDimNames(x),ignore.case=T))) {
>> SingleCellExperiment::reducedDim(x,grep(DRtype,
>> SingleCellExperiment::reducedDimNames(x),
>> ignore.case=T,value=T))
>> } else {
>> stop(paste(paste0("DRtype '",DRtype,"' not found."),
>> "The following cell embeddings are available in this object:",
>> paste0(SingleCellExperiment::reducedDimNames(x),collapse=", "),
>> sep="\n "))
>> }
>> },
>> where=.GlobalEnv)
>>
>>
>> which gives the following error when SingleCellExperiment is loaded:
>>
>> Error in as.vector(x, "character") :
>> cannot coerce type 'closure' to vector of type 'character'
>>
>>
>> But if I just run that code, it doesn't give the error. I thought this might be due to where in the order of loading and attaching namespaces the hook is running, but changing the packageEvent event to "attach" makes no difference.
>>
>>
>> Anyway, suppressing the message works, so I'm happy. Just wanted to report back on the partial success of doing it the cool way, in case anyone was interested.
>>
>>
>> Thanks again!
>>
>> Brendan
>>
>>
>> www.baderlab.org/BrendanInnes<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.baderlab.org_BrendanInnes&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=HwMn126h-7G4XmAqvYBr8lGjzQbgLqGq4-KkAOUH9r0&s=OIIsBqppQCVjbRlE5mpw0XnWEc-hiPwpjOCLNdiu4Mg&e=>
>>
>> ________________________________
>> From: Martin Morgan <mtmorgan.bioc using gmail.com>
>> Sent: Wednesday, January 30, 2019 12:16:20 PM
>> To: Brendan Innes; bioc-devel using r-project.org
>> Subject: Re: [Bioc-devel] SetMethod to dispatch on class in unattached package
>>
>> A simple approach is to suppress the message (I think this is pragmatic, rather than dumb __) about unknown class (along with DESCRIPTION Suggests: Seurat)
>>
>> setGeneric("getGE", function(x) standardGeneric("getGE"))
>>
>> suppressMessages({
>> setMethod("getGE", "seurat", function(x) Seurat::GetAssayData(x))
>> })
>>
>> One fun thing to try is use hooks for package load; I would say that this is rarely used so may have surprising issues... Note the need to specify the location of the generic `PkgA::getGE` and that the method is defined in the global environment, rather than in the package environment, so would not have access to non-exported functions. The DESCRIPTION file has Suggests: Seurat
>>
>> Something along the lines of
>>
>> setGeneric("getGE", function(x) standardGeneric("getGE"))
>>
>> .onLoad <-
>> function(...)
>> {
>> if ("Seurat" %in% loadedNamespaces()) {
>> setMethod(
>> getGE, "seurat",
>> function(x) Seurat::GetAssayData(x)
>> )
>> } else {
>> setHook(
>> packageEvent("Seurat", "onLoad"),
>> function(...) {
>> setMethod(
>> PkgA::getGE, "seurat",
>> function(x) Seurat::GetAssayData(x),
>> where = .GlobalEnv
>> )
>> }
>> )
>> }
>> }
>>
>> Martin
>>
>> On 1/29/19, 9:27 PM, "Bioc-devel on behalf of Brendan Innes" <bioc-devel-bounces using r-project.org on behalf of brendan.innes using mail.utoronto.ca> wrote:
>>
>> Hi friendly Bioc gang! I'm struggling with what seems like a silly problem. I'm trying to write a simple wrapper S4 generic that accesses the data slot of various S4 objects (seurat and SingleCellExperiment objects). So the generic is:
>>
>> setGeneric("getGE",function(x) standardGeneric("getGE"))
>>
>>
>> And the methods are:
>>
>> setMethod("getGE","seurat",
>> function(x) Seurat::GetAssayData(x))
>> setMethod("getGE","SingleCellExperiment",
>> function(x) SingleCellExperiment::logcounts(x))
>>
>>
>> Problem is that when I install the package, I get the warning
>>
>> > in method for �getGE� with signature �"seurat"�: no definition for class �seurat�
>>
>>
>> This isn't surprising, since Seurat isn't imported, but I don't want the user to have to import it if their data is in a SingleCellExperiment object. The function still seems to work fine if I attach Seurat and load a seurat object, so I'm tempted to just suppress the error (but darned if I know how to do that either). Before I do something so rash, does anyone have a suggestion for a less dumb way to do this?
>>
>> Thanks so much!
>> Brendan
>>
>>
>>
>> www.baderlab.org/BrendanInnes<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.baderlab.org_BrendanInnes&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=HwMn126h-7G4XmAqvYBr8lGjzQbgLqGq4-KkAOUH9r0&s=OIIsBqppQCVjbRlE5mpw0XnWEc-hiPwpjOCLNdiu4Mg&e=<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.baderlab.org_BrendanInnes&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=HwMn126h-7G4XmAqvYBr8lGjzQbgLqGq4-KkAOUH9r0&s=OIIsBqppQCVjbRlE5mpw0XnWEc-hiPwpjOCLNdiu4Mg&e=<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.baderlab.org_BrendanInnes&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=HwMn126h-7G4XmAqvYBr8lGjzQbgLqGq4-KkAOUH9r0&s=OIIsBqppQCVjbRlE5mpw0XnWEc-hiPwpjOCLNdiu4Mg&e=>>
>>
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>>
>>
>>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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