[Bioc-devel] Possible to export coerce2() from S4Vectors?

Michael Lawrence l@wrence@mich@el @ending from gene@com
Wed Nov 14 21:58:54 CET 2018 

The only reliable way to implement cbind() is through cbind2(). Perhaps we
should drop cbind,DataFrame. The only downside would be poorer performance
due to additional dispatch.

We could try to more fully define dots dispatch, but how should it behave
in this case? Intuitively, I would expect all arguments in "..." to be
IndexedDataFrames for cbind,IndexedDataFrame to be called. But there are
other possibilities.

Michael

On Wed, Nov 14, 2018 at 9:57 AM Bemis, Kylie <k.bemis using northeastern.edu>
wrote:

> Yes, I will make sure my cbind() implementation coerces to the correct
> subclass.
>
> That could solve my error as well, but the warnings about S4 dispatch on
> “...” are still a problem.
>
> -Kylie
>
> On Nov 14, 2018, at 12:38 PM, Michael Lawrence <lawrence.michael using gene.com>
> wrote:
>
> The use of c() in the implementation of [[<- is problematic, since [[<-
> has the semantic of insertion, preserving the overall structure of x, while
> c() is a combination of two or more peer data structures, and it is
> difficult to define the correct logic through dispatch.
>
> The dispatch on ... is not well documented. I will try to improve that, as
> soon as I understand it myself. But no matter what, your cbind() method
> will need to uplift ordinary DataFrames to IndexedDataFrame.
>
> Michael
>
> On Wed, Nov 14, 2018 at 7:52 AM Bemis, Kylie <k.bemis using northeastern.edu>
> wrote:
>
>> Hi Michael,
>>
>> Here is a simple example of what I’m trying to do:
>>
>> setClass("IndexedDataFrame",
>> contains="DataFrame",
>> slots=c(ids="numeric"))
>>
>> # track additional ID metadata w/ special rules
>> IndexedDataFrame <- function(ids, ...) {
>> x <- DataFrame(...)
>> new("IndexedDataFrame",
>> ids=ids,
>> rownames=rownames(x),
>> nrows=nrow(x),
>> listData=x using listData,
>> elementMetadata=mcols(x))
>> }
>>
>> # check for matching IDs before cbind-ing
>> setMethod("cbind", "IndexedDataFrame",
>> function(...) {
>> args <- list(...)
>> ids <- args[[1L]]@ids
>> ok <- vapply(args, function(a) {
>> # check for compatible IDs
>> identical(a using ids, ids)
>> }, logical(1))
>> if ( !all(ok) )
>> stop("ids must match")
>> x <- callNextMethod(...)
>> new(class(args[[1L]]),
>> ids=ids,
>> rownames=rownames(x),
>> nrows=nrow(x),
>> listData=x using listData,
>> elementMetadata=mcols(x))
>> })
>>
>> set.seed(1)
>> idf <- IndexedDataFrame(ids=runif(10), a=1:10, b=11:20)
>> idf$c <- 21:30
>>
>> Error in identical(a using ids, ids) :
>>   no slot of name "ids" for this object of class "DataFrame"
>> In addition: Warning message:
>> In methods:::.selectDotsMethod(classes, .MTable, .AllMTable) :
>>   multiple direct matches: "IndexedDataFrame", "DataFrame"; using the
>> first of these
>>
>> Specific examples where I use this pattern are new MassDataFrame and
>> PositionDataFrame classes in Cardinal, which require associated m/z-values
>> and pixel coordinates as additional metadata. Current source code is here:
>>
>>
>> https://github.com/kuwisdelu/Cardinal/blob/master/R/methods2-MassDataFrame.R
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fkuwisdelu%2FCardinal%2Fblob%2Fmaster%2FR%2Fmethods2-MassDataFrame.R&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=VZC1bED%2BMesUG3%2FYmjm2NarP3rH3wpwsI3Xmqlnv6AU%3D&reserved=0>
>>
>> https://github.com/kuwisdelu/Cardinal/blob/master/R/methods2-PositionDataFrame.R
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fkuwisdelu%2FCardinal%2Fblob%2Fmaster%2FR%2Fmethods2-PositionDataFrame.R&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=FqUMv0fDdgEe3H0yKV%2BhfKl%2BtCml5pgwR%2FyQBoSnWwk%3D&reserved=0>
>>
>> In older versions of Cardinal, similar versions of these classes extended
>> AnnotatedDataFrame and used regular columns for this metadata, while
>> requiring those columns to follow a specific naming scheme. This proved
>> fragile, difficult to maintain, and easily broken, so I am now using slots
>> to contain this metadata so they can be validated independently of whatever
>> user-supplied columns exist.
>>
>> Kylie
>>
>> ~~~
>> Kylie Ariel Bemis
>> College of Computer and Information Science
>> Northeastern University
>> kuwisdelu.github.io
>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fkuwisdelu.github.io&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=gu3BTRG0wUSpYQtG%2F6Vy605LkJvKqZWlsyUt1LHmqRk%3D&reserved=0>
>>
>>
>>
>>
>>
>> On Nov 14, 2018, at 10:12 AM, Michael Lawrence <lawrence.michael using gene.com>
>> wrote:
>>
>> I don't want to derail this thread, but why is coerce2() necessary? Would
>> it be possible to fold its logic into as() without breaking too much?
>>
>> Kylie,
>>
>> It would help to see your code, with some pointers to where things break.
>>
>> Michael
>>
>> On Wed, Nov 14, 2018 at 5:36 AM Bemis, Kylie <k.bemis using northeastern.edu>
>> wrote:
>>
>>> Hi Herve,
>>>
>>> Thanks for the detailed reply. Using as() makes sense. Unfortunately my
>>> use case makes it a little more complicated.
>>>
>>> The issue comes from a combination of factors:
>>>
>>> - My DataFrame subclasses track additional metadata for each row,
>>> separate from the typical user-defined columns
>>> - This metadata is checked to decide how to do cbind(...) or if
>>> cbind(...) makes sense for those objects
>>> - cbind(...) ends up being called internally by some inherited
>>> assignment methods like [[<-
>>> - Coercing to my subclass with as() results in incompatible metadata,
>>> causing cbind(...) to fail
>>>
>>> I see a few solutions:
>>>
>>> 1. Using coerce2() works where as() doesn’t, because it takes an example
>>> of the “to” object rather than just the class, so compatible metadata can
>>> be copied directly from the “to” object, allowing cbind(…) to work as
>>> intended.
>>>
>>> 2. Create an exception to my class logic that allows the metadata to be
>>> missing, and change my cbind(…) implementation to ignore the metadata in
>>> the case that it is missing.
>>>
>>> 3. Supply my own version of methods like [[<-. I don’t like this one,
>>> since it should be unnecessary.
>>>
>>> I can do (2), but I would need to rethink some of my other methods that
>>> expect that metadata to exist, so I wanted to check on the plans for
>>> coerce2() before making those changes.
>>>
>>> What are your thoughts?
>>>
>>> Thanks!
>>> Kylie
>>>
>>> ~~~
>>> Kylie Ariel Bemis
>>> College of Computer and Information Science
>>> Northeastern University
>>> kuwisdelu.github.io
>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fkuwisdelu.github.io&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=gb8odSGF5K9LUohcpSKAxHK4RZu948LKGWoRImihcZQ%3D&reserved=0>
>>> <https://kuwisdelu.github.io
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fkuwisdelu.github.io&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=gu3BTRG0wUSpYQtG%2F6Vy605LkJvKqZWlsyUt1LHmqRk%3D&reserved=0>
>>> >
>>>
>>>
>>>
>>>
>>>
>>> On Nov 13, 2018, at 8:55 PM, Pages, Herve <hpages using fredhutch.org<mailto:
>>> hpages using fredhutch.org>> wrote:
>>>
>>>
>>> Hi Kylie,
>>>
>>> I've modified coerce2() in S4Vectors 0.21.5 so that `coerce2(from, to)`
>>> should now do the right thing when 'to' is a DataFrame derivative:
>>>
>>>
>>> https://github.com/Bioconductor/S4Vectors/commit/48e11dd2c8d474c63e09a69ee7d2d2ec35d7307a
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FS4Vectors%2Fcommit%2F48e11dd2c8d474c63e09a69ee7d2d2ec35d7307a&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=QyzrJNfFWBBin44CKQSIcZ4tfZEUT9evK3EVOOeOClI%3D&reserved=0>
>>> <
>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FS4Vectors%2Fcommit%2F48e11dd2c8d474c63e09a69ee7d2d2ec35d7307a&data=02%7C01%7Ck.bemis%40northeastern.edu%7Cd1ed8517bd164aeed6be08d649d441d6%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636777573332495470&sdata=6QqZsJmrVuB1fQ0FcBCvSIZT3Uyt3CBmhlsE7YzZNiw%3D&reserved=0
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FBioconductor%2FS4Vectors%2Fcommit%2F48e11dd2c8d474c63e09a69ee7d2d2ec35d7307a&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=QyzrJNfFWBBin44CKQSIcZ4tfZEUT9evK3EVOOeOClI%3D&reserved=0>
>>> >
>>>
>>> With the following gotcha: this will work only if coercion (with as())
>>> from DataFrame to the DataFrame derivative does the right thing. So I'm
>>> assuming that this coercion makes sense and can be supported. There are 2
>>> possible situations:
>>>
>>> 1) The automatic coercion method from DataFrame to your DataFrame
>>> derivative (i.e. the coercion method automatically defined by the methods
>>> package) does the right thing. In this case coerce2() (and therefore [[<-)
>>> will also do the right thing on your DataFrame derivatives. For example:
>>>
>>>   library(S4Vectors)
>>>   setClass("MyDataFrameExtension", contains="DataFrame")
>>>
>>>   ## WARNING: Don't trust selectMethod() here!
>>>   selectMethod("coerce", c("DataFrame", "MyDataFrameExtension"))
>>>   # Error in selectMethod("coerce", c("DataFrame",
>>> "MyDataFrameExtension")) :
>>>   #  no method found for signature DataFrame, MyDataFrameExtension
>>>
>>>   as(DataFrame(), "MyDataFrameExtension")
>>>   # MyDataFrameExtension with 0 rows and 0 columns
>>>
>>>   ## The automatic coercion method is only created the 1st time it's
>>> used!
>>>   ## So now selectMethod() shows it:
>>>   selectMethod("coerce", c("DataFrame", "MyDataFrameExtension"))
>>>   # Method Definition:
>>>   #
>>>   # function (from, to = "MyDataFrameExtension", strict = TRUE)
>>>   # {
>>>   #     obj <- new("MyDataFrameExtension")
>>>   #     as(obj, "DataFrame") <- from
>>>   #     obj
>>>   # }
>>>   # <environment: namespace:S4Vectors>
>>>   #
>>>   # Signatures:
>>>   #         from        to
>>>   # target  "DataFrame" "MyDataFrameExtension"
>>>   # defined "DataFrame" "MyDataFrameExtension"
>>>
>>>
>>>   MDF <- new("MyDataFrameExtension")
>>>   S4Vectors:::coerce2(list(aa=1:3, bb=21:23), MDF)
>>>   # MyDataFrameExtension with 3 rows and 2 columns
>>>   #          aa        bb
>>>   #   <integer> <integer>
>>>   # 1         1        21
>>>   # 2         2        22
>>>   # 3         3        23
>>>
>>>
>>> 2) The automatic coercion method from DataFrame to your DataFrame
>>> derivative doesn't do the right thing (e.g. it returns an invalid object).
>>> In this case you need to define this coercion (with a setAs() statement).
>>> This will allow coerce2() (and therefore [[<-) to do the right thing on
>>> your DataFrame derivatives.
>>>
>>> There is no plan at the moment to export coerce2() because this should
>>> not be needed. The idea is that developers should not need to define
>>> "coerce2" methods but instead make it work via the addition of the
>>> appropriate coercion methods. The only purpose of coerce2() is to support
>>> things like [[<- and endoapply(). Once coerce2() works properly, these
>>> things work out-of-the-box.
>>>
>>> So to summarize: just make sure that a DataFrame can be coerced to your
>>> DataFrame derivative and [[<- and endoapply() will work out-of-the-box. It
>>> could be however that this coercion doesn't make sense and cannot be
>>> supported, in which case, we'll need to do something different. Let me know
>>> if that's the case.
>>>
>>> H.
>>>
>>>
>>> On 11/13/18 12:45, Bemis, Kylie wrote:
>>>
>>> Dear all,
>>>
>>> Are there any plans to export coerce2() from the S4Vectors namespace,
>>> like other exported internal utilities such as showAsCell() and
>>> setListElement()?
>>>
>>> I have a couple classes that inherit from DataFrame, and some inherited
>>> methods (like [[<-) break in certain situations due to calls to coerce2()
>>> that coerce arguments to a regular DataFrame (instead of my subclass). This
>>> could be fixed if I were able to implement a coerce2() method for my
>>> subclass.
>>>
>>> Any suggestions on how to approach problems like this when inheriting
>>> from DataFrame and other Vector derivatives?
>>>
>>> Many thanks,
>>> Kylie
>>>
>>> ~~~
>>> Kylie Ariel Bemis
>>> College of Computer and Information Science
>>> Northeastern University
>>> kuwisdelu.github.io
>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fkuwisdelu.github.io&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=gb8odSGF5K9LUohcpSKAxHK4RZu948LKGWoRImihcZQ%3D&reserved=0>
>>> <http://kuwisdelu.github.io
>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fkuwisdelu.github.io&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=gb8odSGF5K9LUohcpSKAxHK4RZu948LKGWoRImihcZQ%3D&reserved=0>
>>> ><
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__kuwisdelu.github.io&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=YnUxTakT9DhxLeLzGGXceB1HxJFEr0ZVHagTMe0vAWw&s=HNW2_h6JRKnX1LQZ2SSqiL_QW6jpN_tkMhrFIREkk7Y&e=
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__kuwisdelu.github.io%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DYnUxTakT9DhxLeLzGGXceB1HxJFEr0ZVHagTMe0vAWw%26s%3DHNW2_h6JRKnX1LQZ2SSqiL_QW6jpN_tkMhrFIREkk7Y%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=ZvJ%2FcmTbRv6Y%2BREBEzyoekFBSL6D7txjzBWne1KM9wU%3D&reserved=0>
>>> ><
>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__kuwisdelu.github.io%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DYnUxTakT9DhxLeLzGGXceB1HxJFEr0ZVHagTMe0vAWw%26s%3DHNW2_h6JRKnX1LQZ2SSqiL_QW6jpN_tkMhrFIREkk7Y%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Cd1ed8517bd164aeed6be08d649d441d6%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636777573332505479&sdata=uPTxySms1gmD4n6y3msY32Wbk%2FnJ%2FypXQFHxb3bITIQ%3D&reserved=0
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__kuwisdelu.github.io%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DYnUxTakT9DhxLeLzGGXceB1HxJFEr0ZVHagTMe0vAWw%26s%3DHNW2_h6JRKnX1LQZ2SSqiL_QW6jpN_tkMhrFIREkk7Y%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=ZvJ%2FcmTbRv6Y%2BREBEzyoekFBSL6D7txjzBWne1KM9wU%3D&reserved=0>
>>> >
>>>
>>>
>>>
>>>
>>>
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=YnUxTakT9DhxLeLzGGXceB1HxJFEr0ZVHagTMe0vAWw&s=dHF-9Xq_n_5IQLQOG3zZ9agK2zTSyNmaRq1M8N29Flc&e=
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DYnUxTakT9DhxLeLzGGXceB1HxJFEr0ZVHagTMe0vAWw%26s%3DdHF-9Xq_n_5IQLQOG3zZ9agK2zTSyNmaRq1M8N29Flc%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=%2FVEWv7TksaRiSCNVtvK9HRQOBAfOgzOu%2BJ%2FSL4P4C%2Fg%3D&reserved=0>
>>> <
>>> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DYnUxTakT9DhxLeLzGGXceB1HxJFEr0ZVHagTMe0vAWw%26s%3DdHF-9Xq_n_5IQLQOG3zZ9agK2zTSyNmaRq1M8N29Flc%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7Cd1ed8517bd164aeed6be08d649d441d6%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636777573332515491&sdata=Rjm40EluXANLI2LAdgoGr8Xxi%2FfvvcbWU2cwBuhl7zU%3D&reserved=0
>>> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel%26d%3DDwICAg%26c%3DeRAMFD45gAfqt84VtBcfhQ%26r%3DBK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA%26m%3DYnUxTakT9DhxLeLzGGXceB1HxJFEr0ZVHagTMe0vAWw%26s%3DdHF-9Xq_n_5IQLQOG3zZ9agK2zTSyNmaRq1M8N29Flc%26e%3D&data=02%7C01%7Ck.bemis%40northeastern.edu%7C081784ec8f744e4f53ea08d64a57fbe3%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636778139103458490&sdata=%2FVEWv7TksaRiSCNVtvK9HRQOBAfOgzOu%2BJ%2FSL4P4C%2Fg%3D&reserved=0>
>>> >
>>>
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
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>>>
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>>>
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