[Rd] How to use `[` without evaluating the arguments.
Hugh Parsonage
hugh@p@r@on@ge @end|ng |rom gm@||@com
Fri Sep 25 14:18:09 CEST 2020
This works as expected:
"[.foo" <- function(x, i, j) {
sx <- substitute(x)
si <- substitute(i)
sj <- substitute(j)
100 * length(sx) + 10 * length(si) + length(sj)
}
x <- 1:10
class(x) <- "foo"
x[y == z, a(x)]
#> [1] 132
Note in your implementation you ask the function evaluate the
expression. You may have been intending to recompose the calls from
the substituted values of x, i, j and evaluate this new call.
On Fri, 25 Sep 2020 at 20:02, Eeles, Christopher
<Christopher.Eeles using uhnresearch.ca> wrote:
>
> Hello R-devel,
>
> I am currently attempting to implement an API similar to data.table wherein single bracket subsetting can accept an unquoted expression to be evaluated in the context of my object.
>
> A simple example from the data.table package looks like this:
>
>
> DT <- data.table(col1 = c('a', 'b', 'c'), col2 = c('x', 'y', 'z'))
> DT[col1 == 'a']
>
> Where the expression i in DT[i, j] is captured with substitute then evaluated inside the DT object.
>
> Reviewing the source code from data.table, it seems that they implemented this feature simple by defining a new S3 method on `[` called `[.data.table`. I tried to replicate this API as follows.
>
> I have defined an S4 which contains an S3 class as follows:
>
>
> #' Define an S3 Class
> #'
> #' Allows use of S3 methods with new S4 class. This is required to overcome
> #' limitations of the `[` S4 method.
> #'
> setOldClass('long.table')
>
> #' LongTable class definition
> #'
> #' Define a private constructor method to be used to build a `LongTable` object.
> #'
> #' @param drugs [`data.table`]
> #' @param cells [`data.table`]
> #' @param assays [`list`]
> #' @param metadata [`list`]
> #'
> #'
> #' @return [`LongTable`] object containing the assay data from a
> #'
> #' @import data.table
> #' @keywords internal
> .LongTable <- setClass("LongTable",
> slots=list(rowData='data.table',
> colData='data.table',
> assays='list',
> metadata='list',
> .intern='environment'),
> contains='long.table')
>
> #' LongTable constructor method
> #'
> #' @param rowData [`data.table`, `data.frame`, `matrix`] A table like object
> #' coercible to a `data.table` containing the a unique `rowID` column which
> #' is used to key assays, as well as additional row metadata to subset on.
> #' @param rowIDs [`character`, `integer`] A vector specifying
> #' the names or integer indexes of the row data identifier columns. These
> #' columns will be pasted together to make up the row.names of the
> #' `LongTable` object.
> #' @param colData [`data.table`, `data.frame`, `matrix`] A table like object
> #' coercible to a `data.table` containing the a unique `colID` column which
> #' is used to key assays, as well as additional column metadata to subset on.
> #' @param colIDs [`character`, `integer`] A vector specifying
> #' the names or integer indexes of the col data identifier columns. These
> #' columns will be pasted together to make up the col.names of the
> #' `LongTable` object.
> #' @param assays A [`list`] containing one or more objects coercible to a
> #' `data.table`, and keyed by rowID and colID corresponding to the rowID and
> #' colID columns in colData and rowData.
> #' @param metadata A [`list`] of metadata associated with the `LongTable`
> #' object being constructed
> #' @param keep.rownames [`logical` or `character`] Logical: whether rownames
> #' should be added as a column if coercing to a `data.table`, default is FALSE.
> #' If TRUE, rownames are added to the column 'rn'. Character: specify a custom
> #' column name to store the rownames in.
> #'
> #' @return [`LongTable`] object
> #'
> #' @import data.table
> #' @export
> LongTable <- function(rowData, rowIDs, colData, colIDs, assays,
> metadata=list(), keep.rownames=FALSE) {
>
> ## TODO:: Handle missing parameters
>
> if (!is(colData, 'data.table')) {
> colData <- data.table(colData, keep.rownames=keep.rownames)
> }
>
> if (!is(rowData, 'data.table')) {
> rowData <- data.table(rowData, keep.rownames=keep.rownames)
> }
>
> if (!all(vapply(assays, FUN=is.data.table, FUN.VALUE=logical(1)))) {
> tryCatch({
> assays <- lapply(assays, FUN=data.table, keep.rownames=keep.rownames)
> }, warning = function(w) {
> warning(w)
> }, error = function(e, assays) {
> message(e)
> types <- lapply(assays, typeof)
> stop(paste0('List items are types: ',
> paste0(types, collapse=', '),
> '\nPlease ensure all items in the assays list are
> coerced to data.tables!'))
> })
> }
>
> # Initialize the .internals object to store private metadata for a LongTable
> internals <- new.env()
>
> ## TODO:: Implement error handling
> internals$rowIDs <-
> if (is.numeric(rowIDs) && max(rowIDs) < ncol(rowData))
> rowIDs
> else
> which(colnames(rowData) %in% rowIDs)
> lockBinding('rowIDs', internals)
>
> internals$colIDs <-
> if (is.numeric(colIDs) && max(colIDs) < ncol(colData))
> colIDs
> else
> which(colnames(colData) %in% colIDs)
> lockBinding('colIDs', internals)
>
> # Assemble the pseudo row and column names for the LongTable
> .pasteColons <- function(...) paste(..., collapse=':')
> rowData[, `:=`(.rownames=mapply(.pasteColons, transpose(.SD))), .SDcols=internals$rowIDs]
> colData[, `:=`(.colnames=mapply(.pasteColons, transpose(.SD))), .SDcols=internals$colIDs]
>
> return(.LongTable(rowData=rowData, colData=colData,
> assays=assays, metadata=metadata,
> .intern=internals))
> }
>
> I have also defined a subset method as an S3 and S4 generic:
>
>
> #' Subset method for a LongTable object.
> #'
> #' Allows use of the colData and rowData `data.table` objects to query based on
> #' rowID and colID, which is then used to subset all value data.tables stored
> #' in the dataList slot.
> #'
> #' This function is endomorphic, it always returns a LongTable object.
> #'
> #' @param x [`LongTable`] The object to subset.
> #' @param rowQuery [`character`, `numeric`, `logical` or `expression`]
> #' Character: pass in a character vector of drug names, which will subset the
> #' object on all row id columns matching the vector.
> #'
> #' Numeric or Logical: these select based on the rowKey from the `rowData`
> #' method for the `LongTable`.
> #'
> #' Expression: Accepts valid query statements to the `data.table` i parameter,
> #' this can be used to make complex queries using the `data.table` API
> #' for the `rowData` data.table.
> #'
> #' @param columnQuery [`character`, `numeric`, `logical` or `expression`]
> #' Character: pass in a character vector of drug names, which will subset the
> #' object on all drug id columns matching the vector.
> #'
> #' Numeric or Logical: these select base don the rowID from the `rowData`
> #' method for the `LongTable`.
> #'
> #' Expression: Accepts valid query statements to the `data.table` i parameter,
> #' this can be used to make complex queries using the `data.table` API
> #' for the `rowData` data.table.
> #'
> #' @param values [`character`, `numeric` or `logical`] Optional list of value
> #' names to subset. Can be used to subset the dataList column further,
> #' returning only the selected items in the new LongTable.
> #'
> #' @return [`LongTable`] A new `LongTable` object subset based on the specified
> #' parameters.
> #'
> #' @importMethodsFrom BiocGenerics subset
> #' @import data.table
> #' @export
> subset.long.table <- function(x, rowQuery, columnQuery, assays) {
>
> longTable <- x
> rm(x)
>
> if (!missing(rowQuery)) {
> if (tryCatch(is.character(rowQuery), error=function(e) FALSE)) {
> select <- grep('^cellLine[:digit:]*', colnames(rowData(longTable)), value=TRUE)
> rowQueryString <- paste0(paste0(select, ' %in% ', .variableToCodeString(rowQuery)), collapse=' | ')
> rowQuery <- str2lang(rowQueryString)
> } else {
> rowQuery <- substitute(rowQuery)
> }
> rowDataSubset <- rowData(longTable)[eval(rowQuery), ]
> } else {
> rowDataSubset <- rowData(longTable)
> }
>
> if (!missing(columnQuery)) {
> if (tryCatch(is.character(columnQuery), error=function(e) FALSE)) {
> select <- grep('^drug[:digit:]*', colnames(colData(longTable)), value=TRUE)
> columnQueryString <- paste0(paste0(select, ' %in% ', .variableToCodeString(columnQuery)), collapse=' | ')
> columnQuery <- str2lang(columnQueryString)
> } else {
> columnQuery <- substitute(columnQuery)
> }
> colDataSubset <- colData(longTable)[eval(columnQuery), ]
> } else {
> colDataSubset <- colData(longTable)
> }
>
> rowKeys <- rowDataSubset$rowKey
> colKeys <- colDataSubset$colKey
>
> if (missing(assays)) { assays <- assayNames(longTable) }
> keepAssays <- assayNames(longTable) %in% assays
>
> assayData <- lapply(assays(longTable)[keepAssays],
> FUN=.filterLongDataTable,
> indexList=list(rowKeys, colKeys))
>
> return(LongTable(colData=colDataSubset, colIDs=longTable using .intern$colIDs ,
> rowData=rowDataSubset, rowIDs=longTable using .intern$rowIDs,
> assays=assayData, metadata=metadata(longTable)))
> }
>
> setMethod('subset', 'LongTable', subset.long.table)
>
> Everything behaves as I expect when calling the subset function. For example
>
> subset(longTable, cellLine1 == 'VCAP)
>
> Successfully returns while also working with character, integer or boolean based indexing.
>
> The issue arises when I try to implement the '[' method. I have tried a number of different approaches, but none of them has been successful. My current approach is as follows:
>
>
> `[.long.table` <- function(x, i, j) eval(substitute(subset(x, i, j)))
>
> This function works as expected in most cases, for example.
>
>
> longTable[c(1,2,3), c(1,2,3,]
> `[.long.table`(longTable, cellLine1 == 'VCAP')
>
> Both work normally.
>
> However, when I try using `[` like an operator:
>
> longTable[cellLine1 == 'VCAP', ]
>
> I get the error 'Error: object 'cellLine1' not found'.
>
> This suggests to me that instead of passing the expression into the function `[`, it is trying to evaluate the expression before dispatching a method.
>
> Given that similar syntax works fine with data.table, and I believe also in the tibble tidyverse package, I am quite confused.
>
> If you have any recommendations on how I can prevent evaluation prior to method dispatch, or of a work around that would produce the same API using a different approach, it would be appreciated.
>
> Thanks for your assistance.
>
>
> Best,
>
> ---
> Christopher Eeles
> Software Developer
> BHK Laboratory<http://www.bhklab.ca/>
> Princess Margaret Cancer Centre<https://www.pmgenomics.ca/pmgenomics/>
> University Health Network<http://www.uhn.ca/>
>
>
>
>
> This e-mail may contain confidential and/or privileged i...{{dropped:22}}
>
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