R/dplyr_methods.R

In tidySummarizedExperiment: Brings SummarizedExperiment to the Tidyverse

#' Efficiently bind multiple data frames by row and column
#'
#' This is an efficient implementation of the common pattern of
#' `do.call(rbind, dfs)` or `do.call(cbind, dfs)` for binding many
#' data frames into one.
#'
#' The output of `bind_rows()` will contain a column if that column
#' appears in any of the inputs.
#'
#' @param ... Data frames to combine.
#'
#'   Each argument can either be a data frame, a list that could be a data
#'   frame, or a list of data frames.
#'
#'   When row-binding, columns are matched by name, and any missing
#'   columns will be filled with NA.
#'
#'   When column-binding, rows are matched by position, so all data
#'   frames must have the same number of rows. To match by value, not
#'   position, see [mutate-joins].
#' @param .id Data frame identifier.
#'
#'   When `.id` is supplied, a new column of identifiers is
#'   created to link each row to its original data frame. The labels
#'   are taken from the named arguments to `bind_rows()`. When a
#'   list of data frames is supplied, the labels are taken from the
#'   names of the list. If no names are found a numeric sequence is
#'   used instead.
#' @param add.cell.ids from SummarizedExperiment 3.0 A character vector of
#'   length(x=c(x, y)). Appends the corresponding values to the start of each
#'   objects' cell names.
#'
#' @return `bind_rows()` and `bind_cols()` return the same type as
#'   the first input, either a data frame, `tbl_df`, or `grouped_df`.
#' @examples
#' `%>%` <- magrittr::`%>%`
#' library(tibble)
#' tt <- tidySummarizedExperiment::pasilla %>% tidy()
#' bind_rows(tt, tt)
#'
#' num_rows <- nrow(tidySummarizedExperiment::as_tibble(tt))
#' tt %>% bind_cols(tibble(a=0, num_rows))
#' @name bind
NULL

#' @rdname dplyr-methods
#'
#' @inheritParams bind
#'
#' @export
#'
bind_rows <- function(..., .id=NULL, add.cell.ids=NULL) {
    UseMethod("bind_rows")
}

#' @export
bind_rows.default <- function(..., .id=NULL, add.cell.ids=NULL) {
    dplyr::bind_rows(..., .id=.id)
}

#' @importFrom rlang dots_values
#' @importFrom rlang flatten_if
#' @importFrom rlang is_spliced
#'
#' @export
#'
bind_rows.tidySummarizedExperiment <- function(..., .id=NULL, add.cell.ids=NULL) {
    tts <- flatten_if(dots_values(...), is_spliced)

    new_obj <- cbind(tts[[1]], tts[[2]]) %>% tidy()

    # If duplicated cell names
    if (new_obj %>% colnames() %>% duplicated() %>% which() %>% length() %>% gt(0)) {
        warning("tidySummarizedExperiment says: you have duplicated sample names, they will be made unique.")
    }
    unique_colnames <- make.unique(colnames(new_obj), sep="_")

    colnames(new_obj) <- unique_colnames

    # Change also all assays colnames
    assays(new_obj)@listData <- assays(new_obj)@listData %>% map(~ {
        colnames(.x) <- unique_colnames
        .x
    })

    new_obj
}

#' @export
#'
#' @inheritParams bind
#'
#' @rdname dplyr-methods
bind_cols <- function(..., .id=NULL) {
    UseMethod("bind_cols")
}

#' @export
bind_cols.default <- function(..., .id=NULL) {
    dplyr::bind_cols(..., .id=.id)
}

bind_cols_ = function(..., .id=NULL) {
    tts <- tts <- flatten_if(dots_values(...), is_spliced)

    tts[[1]] %>%
        as_tibble() %>%
        dplyr::bind_cols(tts[[2]], .id=.id) %>%
        when(

            # If the column added are not sample-wise or transcript-wise return tibble
            (colnames(tts[[2]]) %in% c(
                get_subset_columns(., sample),
                get_subset_columns(., transcript)
            )
            ) %>% all() ~ update_SE_from_tibble(., tts[[1]]),

            # Return tiblle
            ~ {
                warning("tidySummarizedExperiment says: The new columns do not include pure sample-wise or transcript-wise. A data frame is returned for independent data analysis.")
                (.)
            }
        )
}

#' @importFrom rlang dots_values
#' @importFrom rlang flatten_if
#' @importFrom rlang is_spliced
#'
#' @export
#'
bind_cols.tidySummarizedExperiment <- bind_cols_

#' distinct
#'
#'
#' @param .data A tbl. (See dplyr)
#' @param ... Data frames to combine (See dplyr)
#' @param .keep_all If TRUE, keep all variables in .data. If a combination
#'   of ... is not distinct, this keeps the first row of values. (See dplyr)
#'
#' @return A tidySummarizedExperiment object
#'
#' @importFrom dplyr distinct
#'
#' @rdname dplyr-methods
#' @name distinct
#'
#' @examples
#'
#' `%>%` <- magrittr::`%>%`
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     distinct(sample)
#' @export
NULL

#' @inheritParams distinct
#' @export
distinct.tidySummarizedExperiment <- function(.data, ..., .keep_all=FALSE) {
    message(data_frame_returned_message)

    .data %>%
        as_tibble() %>%
        dplyr::distinct(..., .keep_all=.keep_all)
}


#' Subset rows using column values
#'
#' `filter()` retains the rows where the conditions you provide a `TRUE`. Note
#' that, unlike base subsetting with `[`, rows where the condition evaluates
#' to `NA` are dropped.
#'
#' dplyr is not yet smart enough to optimise filtering optimisation
#' on grouped datasets that don't need grouped calculations. For this reason,
#' filtering is often considerably faster on [ungroup()]ed data.
#'
#' @importFrom dplyr filter
#'
#' @section Useful filter functions:
#'
#' * [`==`], [`>`], [`>=`] etc
#' * [`&`], [`|`], [`!`], [xor()]
#' * [is.na()]
#' * [between()], [near()]
#'
#' @section Grouped tibbles:
#'
#' Because filtering expressions are computed within groups, they may
#' yield different results on grouped tibbles. This will be the case
#' as soon as an aggregating, lagging, or ranking function is
#' involved. Compare this ungrouped filtering:
#'
#'
#' The former keeps rows with `mass` greater than the global average
#' whereas the latter keeps rows with `mass` greater than the gender
#'
#' average.
#' @family single table verbs
#' @inheritParams arrange
#' @param .data A tidySummarizedExperiment object or any data frame
#' @param ... <[`tidy-eval`][dplyr_tidy_eval]> Logical predicates defined in
#'   terms of the variables in `.data`.
#'   Multiple conditions are combined with `&`. Only rows where the
#'   condition evaluates to `TRUE` are kept.
#' @param .preserve when `FALSE` (the default), the grouping structure
#'   is recalculated based on the resulting data, otherwise it is kept as is.
#' @return
#' An object of the same type as `.data`.
#'
#' * Rows are a subset of the input, but appear in the same order.
#' * Columns are not modified.
#' * The number of groups may be reduced (if `.preserve` is not `TRUE`).
#' * Data frame attributes are preserved.
#' @section Methods:
#' This function is a **generic**, which means that packages can provide
#' implementations (methods) for other classes. See the documentation of
#' individual methods for extra arguments and differences in behaviour.
#'
#' The following methods are currently available in loaded packages:
#' @seealso [filter_all()], [filter_if()] and [filter_at()].
#'
#' @rdname dplyr-methods
#' @name filter
#'
#' @export
#' @examples
#'
#' `%>%` <- magrittr::`%>%`
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     filter(sample == "untrt1")
#'
#' # Learn more in ?dplyr_tidy_eval
#' @export
NULL

#' @inheritParams filter
#' @export
filter.tidySummarizedExperiment <- function(.data, ..., .preserve=FALSE) {
    new_meta <- .data %>%
        as_tibble() %>%
        dplyr::filter(..., .preserve=.preserve) # %>% update_SE_from_tibble(.data)

    new_meta %>%

        when(

            # If rectangular
            is_rectangular(.) ~ .data[
                unique(.$transcript),
                unique(.$sample)
            ],

            # If not rectangular return just tibble
            ~ {
                message("tidySummarizedExperiment says: The resulting data frame is not rectangular (all genes for all samples), a tibble is returned for independent data analysis.")
                (.)
            }
        )
}


#' Group by one or more variables
#'
#' @importFrom dplyr group_by_drop_default
#' @importFrom dplyr group_by
#'
#' @description
#' Most data operations are done on groups defined by variables.
#' `group_by()` takes an existing tbl and converts it into a grouped tbl
#' where operations are performed "by group". `ungroup()` removes grouping.
#'
#' @family grouping functions
#' @inheritParams arrange
#' @param .data A tidySummarizedExperiment object or any data frame
#' @param ... In `group_by()`, variables or computations to group by.
#'   In `ungroup()`, variables to remove from the grouping.
#' @param .add When `FALSE`, the default, `group_by()` will
#'   override existing groups. To add to the existing groups, use
#'   `.add=TRUE`.
#'
#'   This argument was previously called `add`, but that prevented
#'   creating a new grouping variable called `add`, and conflicts with
#'   our naming conventions.
#' @param .drop When `.drop=TRUE`, empty groups are dropped. See
#'   [group_by_drop_default()] for what the default value is for this argument.
#' @return A [grouped data frame][grouped_df()], unless the combination of
#'   `...` and `add` yields a non empty set of grouping columns, a
#'   regular (ungrouped) data frame otherwise.
#' @section Methods:
#' These function are **generic**s, which means that packages can provide
#' implementations (methods) for other classes. See the documentation of
#' individual methods for extra arguments and differences in behaviour.
#'
#' Methods available in currently loaded packages:
#'
#' @rdname dplyr-methods
#' @name group_by
#'
#' @export
#' @examples
#' `%>%` <- magrittr::`%>%`
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     group_by(sample)
#' @export
NULL

#' @export
group_by.tidySummarizedExperiment <- function(.data, ..., .add=FALSE, .drop=group_by_drop_default(.data)) {
    message(data_frame_returned_message)

    .data %>%
        as_tibble() %>%
        dplyr::group_by(..., .add=.add, .drop=.drop)
}


#' Summarise each group to fewer rows
#'
#' @importFrom dplyr summarise
#'
#' @description
#' `summarise()` creates a new data frame. It will have one (or more) rows for
#' each combination of grouping variables; if there are no grouping variables,
#' the output will have a single row summarising all observations in the input.
#' It will contain one column for each grouping variable and one column
#' for each of the summary statistics that you have specified.
#'
#' `summarise()` and `summarize()` are synonyms.
#'
#' @section Useful functions:
#'
#' * Center: [mean()], [median()]
#' * Spread: [sd()], [IQR()], [mad()]
#' * Range: [min()], [max()], [quantile()]
#' * Position: [first()], [last()], [nth()],
#' * Count: [n()], [n_distinct()]
#' * Logical: [any()], [all()]
#'
#' @section Backend variations:
#'
#' The data frame backend supports creating a variable and using it in the
#' same summary. This means that previously created summary variables can be
#' further transformed or combined within the summary, as in [mutate()].
#' However, it also means that summary variables with the same names as previous
#' variables overwrite them, making those variables unavailable to later summary
#' variables.
#'
#' This behaviour may not be supported in other backends. To avoid unexpected
#' results, consider using new names for your summary variables, especially when
#' creating multiple summaries.
#'
#' @param .data A tidySummarizedExperiment object or any data frame
#'
#' @rdname dplyr-methods
#' @name summarise
#'
#' @export
#' @inheritParams arrange
#' @param ... <[`tidy-eval`][dplyr_tidy_eval]> Name-value pairs of summary
#'   functions. The name will be the name of the variable in the result.
#'
#'   The value can be:
#'
#'   * A vector of length 1, e.g. `min(x)`, `n()`, or `sum(is.na(y))`.
#'   * A vector of length `n`, e.g. `quantile()`.
#'   * A data frame, to add multiple columns from a single expression.
#' @family single table verbs
#' @return
#' An object _usually_ of the same type as `.data`.
#'
#' * The rows come from the underlying `group_keys()`.
#' * The columns are a combination of the grouping keys and the summary
#'   expressions that you provide.
#' * If `x` is grouped by more than one variable, the output will be another
#'   [grouped_df] with the right-most group removed.
#' * If `x` is grouped by one variable, or is not grouped, the output will
#'   be a [tibble].
#' * Data frame attributes are **not** preserved, because `summarise()`
#'   fundamentally creates a new data frame.
#' @section Methods:
#' This function is a **generic**, which means that packages can provide
#' implementations (methods) for other classes. See the documentation of
#' individual methods for extra arguments and differences in behaviour.
#'
#' The following methods are currently available in loaded packages:
#' @examples
#' `%>%` <- magrittr::`%>%`
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     summarise(mean(counts))
#' @export
NULL

#' @export
summarise.tidySummarizedExperiment <- function(.data, ...) {
    message(data_frame_returned_message)


    .data %>%
        as_tibble() %>%
        dplyr::summarise(...)
}


#' Create, modify, and delete columns
#'
#' `mutate()` adds new variables and preserves existing ones;
#' `transmute()` adds new variables and drops existing ones.
#' New variables overwrite existing variables of the same name.
#' Variables can be removed by setting their value to `NULL`.
#'
#' @importFrom dplyr mutate
#'
#' @section Useful mutate functions:
#'
#' * [`+`], [`-`], [log()], etc., for their usual mathematical meanings
#'
#' * [lead()], [lag()]
#'
#' * [dense_rank()], [min_rank()], [percent_rank()], [row_number()],
#'   [cume_dist()], [ntile()]
#'
#' * [cumsum()], [cummean()], [cummin()], [cummax()], [cumany()], [cumall()]
#'
#' * [na_if()], [coalesce()]
#'
#' * [if_else()], [recode()], [case_when()]
#'
#' @section Grouped tibbles:
#'
#' Because mutating expressions are computed within groups, they may
#' yield different results on grouped tibbles. This will be the case
#' as soon as an aggregating, lagging, or ranking function is
#' involved. Compare this ungrouped mutate:
#'
#' @param .data A tidySummarizedExperiment object or any data frame
#'
#' With the grouped equivalent:
#'
#' The former normalises `mass` by the global average whereas the
#' latter normalises by the averages within gender levels.
#'
#' @export
#' @inheritParams arrange
#' @param ... <[`tidy-eval`][dplyr_tidy_eval]> Name-value pairs.
#'   The name gives the name of the column in the output.
#'
#'   The value can be:
#'
#'   * A vector of length 1, which will be recycled to the correct length.
#'   * A vector the same length as the current group (or the whole data frame
#'     if ungrouped).
#'   * `NULL`, to remove the column.
#'   * A data frame or tibble, to create multiple columns in the output.
#'
#' @family single table verbs
#' @return
#' An object of the same type as `.data`.
#'
#' For `mutate()`:
#'
#' * Rows are not affected.
#' * Existing columns will be preserved unless explicitly modified.
#' * New columns will be added to the right of existing columns.
#' * Columns given value `NULL` will be removed
#' * Groups will be recomputed if a grouping variable is mutated.
#' * Data frame attributes are preserved.
#'
#' For `transmute()`:
#'
#' * Rows are not affected.
#' * Apart from grouping variables, existing columns will be remove unless
#'   explicitly kept.
#' * Column order matches order of expressions.
#' * Groups will be recomputed if a grouping variable is mutated.
#' * Data frame attributes are preserved.
#' @section Methods:
#' These function are **generic**s, which means that packages can provide
#' implementations (methods) for other classes. See the documentation of
#' individual methods for extra arguments and differences in behaviour.
#'
#' Methods available in currently loaded packages:
#'
#' @examples
#' `%>%` <- magrittr::`%>%`
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     mutate(logcounts=log2(counts))
#'
#' @rdname dplyr-methods
#' @name mutate
#'
#' @export
NULL

#' @importFrom dplyr mutate
#' @importFrom rlang enquos
#'
#' @export
mutate.tidySummarizedExperiment <- function(.data, ...) {

    # Check that we are not modifying a key column
    cols <- enquos(...) %>% names()

    tst =
        intersect(
            cols,
            get_special_columns(.data) %>% c(get_needed_columns())
        ) %>%
        length() %>%
        gt(0)


    if (tst) {
        columns =
            get_special_columns(.data) %>%
            c(get_needed_columns()) %>%
            paste(collapse=", ")
        stop(
            "tidySummarizedExperiment says: you are trying to rename a column that is view only",
            columns,
            "(it is not present in the colData). If you want to mutate a view-only column, make a copy and mutate that one."
        )
    }

    .data %>%
        as_tibble() %>%
        dplyr::mutate(...) %>%
        update_SE_from_tibble(.data)
}



#' Rename columns
#'
#' Rename individual variables using `new_name=old_name` syntax.
#'
#' @importFrom dplyr rename
#'
#' @section Scoped selection and renaming:
#'
#' Use the three scoped variants ([rename_all()], [rename_if()], [rename_at()])
#' to renaming a set of variables with a function.
#'
#' @inheritParams arrange
#'
#' @param .data A tidySummarizedExperiment object or any data frame
#' @param ... <[`tidy-select`][dplyr_tidy_select]> Use `new_name=old_name`
#'   to rename selected variables.
#' @return
#' An object of the same type as `.data`.
#' * Rows are not affected.
#' * Column names are changed; column order is preserved
#' * Data frame attributes are preserved.
#' * Groups are updated to reflect new names.
#' @section Methods:
#' This function is a **generic**, which means that packages can provide
#' implementations (methods) for other classes. See the documentation of
#' individual methods for extra arguments and differences in behaviour.
#'
#' The following methods are currently available in loaded packages:
#' @family single table verbs
#'
#' @rdname dplyr-methods
#' @name rename
#'
#' @export
#' @examples
#' `%>%` <- magrittr::`%>%`
#' # tidySummarizedExperiment::pasilla %>%
#' #     tidy() %>%
#' #     rename(cond=condition)
#' @export
NULL

#' @importFrom tidyselect eval_select
#' @export
rename.tidySummarizedExperiment <- function(.data, ...) {

    # Check that we are not modifying a key column
    cols <- tidyselect::eval_select(expr(c(...)), colData(.data) %>% as.data.frame())

    tst =
        intersect(
            cols %>% names(),
            get_special_columns(.data) %>% c(get_needed_columns())
        ) %>%
        length() %>%
        gt(0)


    if (tst) {
        columns =
            get_special_columns(.data) %>%
            c(get_needed_columns()) %>%
            paste(collapse=", ")
        stop(
            "tidySummarizedExperiment says: you are trying to rename a column that is view only",
            columns,
            "(it is not present in the colData). If you want to mutate a view-only column, make a copy and mutate that one."
        )
    }

    colData(.data) <- dplyr::rename(colData(.data) %>% as.data.frame(), ...) %>% DataFrame()

    .data
}


#' Group input by rows
#'
#'
#' See [this repository](https://github.com/jennybc/row-oriented-workflows)
#' for alternative ways to perform row-wise operations.
#'
#' `rowwise()` is used for the results of [do()] when you
#' create list-variables. It is also useful to support arbitrary
#' complex operations that need to be applied to each row.
#'
#' Currently, rowwise grouping only works with data frames. Its
#' main impact is to allow you to work with list-variables in
#' [summarise()] and [mutate()] without having to
#' use \code{[[1]]}. This makes `summarise()` on a rowwise tbl
#' effectively equivalent to [plyr::ldply()].
#'
#' @importFrom dplyr rowwise
#'
#' @param data Input data frame.
#' @param ... See dplyr::rowwise
#'
#' @return A `tbl`
#'
#'   A `tbl`
#'
#' @rdname dplyr-methods
#' @name rowwise
#'
#' @export
#' @examples
#' `%>%` <- magrittr::`%>%`
#' @export
NULL

#' @export
rowwise.tidySummarizedExperiment <- function(data, ...) {
    message(data_frame_returned_message)

    data %>%
        as_tibble() %>%
        dplyr::rowwise()
}


#' Left join datasets
#'
#' @importFrom dplyr count
#' @importFrom dplyr left_join
#'
#' @param x tbls to join. (See dplyr)
#' @param y tbls to join. (See dplyr)
#' @param by A character vector of variables to join by. (See dplyr)
#' @param copy If x and y are not from the same data source, and copy is TRUE,
#'   then y will be copied into the same src as x. (See dplyr)
#' @param suffix If there are non-joined duplicate variables in x and y, these
#'   suffixes will be added to the output to disambiguate them. Should be a
#'   character vector of length 2. (See dplyr)
#' @param ... Data frames to combine (See dplyr)
#'
#' @return A tidySummarizedExperiment object
#'
#' @rdname dplyr-methods
#' @name left_join
#'
#' @export
#'
#' @examples
#' `%>%` <- magrittr::`%>%`
#'
#' tt <- tidySummarizedExperiment::pasilla %>% tidy()
#' tt %>% left_join(tt %>% distinct(condition) %>% mutate(new_column=1:2))
NULL

#' @export
left_join.tidySummarizedExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c(".x", ".y"),
    ...) {
    x %>%
        as_tibble() %>%
        dplyr::left_join(y, by=by, copy=copy, suffix=suffix, ...) %>%
        when(

            # If duplicated sample-transcript pair returns tibble
            !is_not_duplicated(.) ~ {
                message(duplicated_cell_names)
                (.)
            },

            # Otherwise return updated tidySummarizedExperiment
            ~ update_SE_from_tibble(., x)
        )
}

#' Inner join datasets
#'
#' @importFrom dplyr pull
#' @importFrom dplyr inner_join
#'
#' @param x tbls to join. (See dplyr)
#' @param y tbls to join. (See dplyr)
#' @param by A character vector of variables to join by. (See dplyr)
#' @param copy If x and y are not from the same data source, and copy is TRUE, then y will be copied into the same src as x. (See dplyr)
#' @param suffix If there are non-joined duplicate variables in x and y, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2. (See dplyr)
#' @param ... Data frames to combine (See dplyr)
#'
#' @return A tidySummarizedExperiment object
#'
#' @examples
#' `%>%` <- magrittr::`%>%`
#'
#' tt <- tidySummarizedExperiment::pasilla %>% tidy()
#' tt %>% inner_join(tt %>% distinct(condition) %>% mutate(new_column=1:2) %>% slice(1))
#'
#' @rdname dplyr-methods
#' @name inner_join
#'
#' @export
NULL

#' @export
inner_join.tidySummarizedExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c(".x", ".y"), ...) {
    x %>%
        as_tibble() %>%
        dplyr::inner_join(y, by=by, copy=copy, suffix=suffix, ...) %>%
        when(

            # If duplicated sample-transcript pair returns tibble

            !is_not_duplicated(.) | !is_rectangular(.) ~ {
                message(duplicated_cell_names)
                (.)
            },

            # Otherwise return updated tidySummarizedExperiment
            ~ update_SE_from_tibble(., x)
        )
}

#' Right join datasets
#'
#' @importFrom dplyr pull
#' @importFrom dplyr right_join
#'
#' @param x tbls to join. (See dplyr)
#' @param y tbls to join. (See dplyr)
#' @param by A character vector of variables to join by. (See dplyr)
#' @param copy If x and y are not from the same data source, and copy is TRUE,
#'   then y will be copied into the same src as x. (See dplyr)
#' @param suffix If there are non-joined duplicate variables in x and y, these
#'   suffixes will be added to the output to disambiguate them. Should be a
#'   character vector of length 2. (See dplyr)
#' @param ... Data frames to combine (See dplyr)
#'
#' @return A tidySummarizedExperiment object
#'
#' @examples
#' `%>%` <- magrittr::`%>%`
#'
#' tt <- tidySummarizedExperiment::pasilla %>% tidy()
#' tt %>% right_join(tt %>% distinct(condition) %>% mutate(new_column=1:2) %>% slice(1))
#'
#' @rdname dplyr-methods
#' @name right_join
#'
#' @export
NULL

#' @export
right_join.tidySummarizedExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c(".x", ".y"),
    ...) {
    x %>%
        as_tibble() %>%
        dplyr::right_join(y, by=by, copy=copy, suffix=suffix, ...) %>%
        when(

            # If duplicated sample-transcript pair returns tibble
            !is_not_duplicated(.) | !is_rectangular(.) ~ {
                message(duplicated_cell_names)
                (.)
            },

            # Otherwise return updated tidySummarizedExperiment
            ~ update_SE_from_tibble(., x)
        )
}


#' Full join datasets
#'
#' @importFrom dplyr pull
#' @importFrom dplyr full_join
#'
#' @param x tbls to join. (See dplyr)
#' @param y tbls to join. (See dplyr)
#' @param by A character vector of variables to join by. (See dplyr)
#' @param copy If x and y are not from the same data source, and copy is TRUE,
#'   then y will be copied into the same src as x. (See dplyr)
#' @param suffix If there are non-joined duplicate variables in x and y, these
#'   suffixes will be added to the output to disambiguate them. Should be a
#'   character vector of length 2. (See dplyr)
#' @param ... Data frames to combine (See dplyr)
#'
#' @return A tidySummarizedExperiment object
#'
#' @examples
#' `%>%` <- magrittr::`%>%`
#'
#' tt <- tidySummarizedExperiment::pasilla %>% tidy()
#' tt %>% full_join(tibble::tibble(condition="treated", dose=10))
#'
#' @rdname dplyr-methods
#' @name full_join
#'
#' @export
NULL

#' @export
full_join.tidySummarizedExperiment <- function(x, y, by=NULL, copy=FALSE, suffix=c(".x", ".y"),
    ...) {
    x %>%
        as_tibble() %>%
        dplyr::full_join(y, by=by, copy=copy, suffix=suffix, ...) %>%
        when(

            # If duplicated sample-transcript pair returns tibble
            !is_not_duplicated(.) | !is_rectangular(.) ~ {
                message(duplicated_cell_names)
                (.)
            },

            # Otherwise return updated tidySummarizedExperiment
            ~ update_SE_from_tibble(., x)
        )
}

#' Subset rows using their positions
#'
#' @description
#' `slice()` lets you index rows by their (integer) locations. It allows you
#' to select, remove, and duplicate rows. It is accompanied by a number of
#' helpers for common use cases:
#'
#' * `slice_head()` and `slice_tail()` select the first or last rows.
#' * `slice_sample()` randomly selects rows.
#' * `slice_min()` and `slice_max()` select rows with highest or lowest values
#'   of a variable.
#'
#' If `.data` is a [grouped_df], the operation will be performed on each group,
#' so that (e.g.) `slice_head(df, n=5)` will select the first five rows in
#' each group.
#'
#' @importFrom dplyr slice
#'
#' @details
#' Slice does not work with relational databases because they have no
#' intrinsic notion of row order. If you want to perform the equivalent
#' operation, use [filter()] and [row_number()].
#'
#' @family single table verbs
#' @inheritParams arrange
#' @inheritParams filter
#'
#' @param .data A tidySummarizedExperiment object or any data frame
#' @param ... For `slice()`: <[`data-masking`][dplyr_data_masking]> Integer row
#'   values.
#'
#'   Provide either positive values to keep, or negative values to drop.
#'   The values provided must be either all positive or all negative.
#'   Indices beyond the number of rows in the input are silently ignored.
#'
#'   For `slice_helpers()`, these arguments are passed on to methods.
#'
#'
#'   If `n` is greater than the number of rows in the group (or `prop > 1`),
#'   the result will be silently truncated to the group size. If the
#'   `prop`ortion of a group size is not an integer, it is rounded down.
#' @return
#' An object of the same type as `.data`. The output has the following
#' properties:
#'
#' * Each row may appear 0, 1, or many times in the output.
#' * Columns are not modified.
#' * Groups are not modified.
#' * Data frame attributes are preserved.
#' @section Methods:
#' These function are **generic**s, which means that packages can provide
#' implementations (methods) for other classes. See the documentation of
#' individual methods for extra arguments and differences in behaviour.
#'
#' Methods available in currently loaded packages:
#'
#' * `slice()`: \Sexpr[stage=render,results=rd]{dplyr:::methods_rd("slice")}.
#' * `slice_head()`: \Sexpr[stage=render,results=rd]{dplyr:::methods_rd("slice_head")}.
#' * `slice_tail()`: \Sexpr[stage=render,results=rd]{dplyr:::methods_rd("slice_tail")}.
#' * `slice_min()`: \Sexpr[stage=render,results=rd]{dplyr:::methods_rd("slice_min")}.
#' * `slice_max()`: \Sexpr[stage=render,results=rd]{dplyr:::methods_rd("slice_max")}.
#' * `slice_sample()`: \Sexpr[stage=render,results=rd]{dplyr:::methods_rd("slice_sample")}.
#'
#' @rdname dplyr-methods
#' @name slice
#'
#' @export
#' @examples
#'
#' `%>%` <- magrittr::`%>%`
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     slice(1)
NULL

#' @export
slice.tidySummarizedExperiment <- function(.data, ..., .preserve=FALSE) {
    .data %>%
        as_tibble() %>%
        dplyr::slice(..., .preserve=.preserve) %>%
        when(

            # If duplicated sample-transcript pair returns tibble
            !is_not_duplicated(.) | !is_rectangular(.) ~ {
                message(duplicated_cell_names)
                (.)
            },

            # Otherwise return updated tidySummarizedExperiment
            ~ update_SE_from_tibble(., .data)
        )
}

#' Subset columns using their names and types
#'
#' @description
#'
#' Select (and optionally rename) variables in a data frame, using a concise
#' mini-language that makes it easy to refer to variables based on their name
#' (e.g. `a:f` selects all columns from `a` on the left to `f` on the
#' right). You can also use predicate functions like [is.numeric] to select
#' variables based on their properties.
#'
#'
#' ## Overview of selection features
#'
#' ```{r, child="man/rmd/overview.Rmd"}
#' ```
#'
#' @importFrom dplyr select
#'
#' @inheritParams arrange
#'
#' @param .data A tidySummarizedExperiment object or any data frame
#' @param ... <[`tidy-select`][dplyr_tidy_select]> One or more unquoted
#'   expressions separated by commas. Variable names can be used as if they
#'   were positions in the data frame, so expressions like `x:y` can
#'   be used to select a range of variables.
#' @return
#' An object of the same type as `.data`. The output has the following
#' properties:
#'
#' * Rows are not affected.
#' * Output columns are a subset of input columns, potentially with a different
#'   order. Columns will be renamed if `new_name=old_name` form is used.
#' * Data frame attributes are preserved.
#' * Groups are maintained; you can't select off grouping variables.
#'
#' @section Methods:
#' This function is a **generic**, which means that packages can provide
#' implementations (methods) for other classes. See the documentation of
#' individual methods for extra arguments and differences in behaviour.
#'
#' The following methods are currently available in loaded packages:
#' \Sexpr[stage=render,results=rd]{dplyr:::methods_rd("select")}.
#'
#' @examples
#'
#' `%>%` <- magrittr::`%>%`
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     select(sample, transcript, counts)
#' @family single table verbs
#'
#' @rdname dplyr-methods
#' @name select
#'
#' @export
NULL

#' @export
select.tidySummarizedExperiment <- function(.data, ...) {
    .data %>%
        as_tibble() %>%
        select_helper(...) %>%
        when(

            # If key columns are missing
            (get_special_columns(.data) %>% c(get_needed_columns()) %in% colnames(.)) %>%
                all() %>%
                `!`() ~ {
                message("tidySummarizedExperiment says: Key columns are missing. A data frame is returned for independent data analysis.")
                (.)
            },

            # If valid SummarizedExperiment meta data
            ~ update_SE_from_tibble(., .data)
        )
}


#' Sample n rows from a table
#'
#' @description
#' \Sexpr[results=rd, stage=render]{lifecycle::badge("superseded")}
#' `sample_n()` and `sample_frac()` have been superseded in favour of
#' [slice_sample()]. While they will not be deprecated in the near future,
#' retirement means that we will only perform critical bug fixes, so we recommend
#' moving to the newer alternative.
#'
#' These functions were superseded because we realised it was more convenient to
#' have two mutually exclusive arguments to one function, rather than two
#' separate functions. This also made it to clean up a few other smaller
#' design issues with `sample_n()`/`sample_frac`:
#'
#' * The connection to `slice()` was not obvious.
#' * The name of the first argument, `tbl`, is inconsistent with other
#'   single table verbs which use `.data`.
#' * The `size` argument uses tidy evaluation, which is surprising and
#'   undocumented.
#' * It was easier to remove the deprecated `.env` argument.
#' * `...` was in a suboptimal position.
#'
#' @importFrom dplyr sample_n
#'
#' @keywords internal
#' @param tbl A data.frame.
#' @param size <[`tidy-select`][dplyr_tidy_select]>
#'   For `sample_n()`, the number of rows to select.
#'   For `sample_frac()`, the fraction of rows to select.
#'   If `tbl` is grouped, `size` applies to each group.
#' @param replace Sample with or without replacement?
#' @param weight <[`tidy-select`][dplyr_tidy_select]> Sampling weights.
#'   This must evaluate to a vector of non-negative numbers the same length as
#'   the input. Weights are automatically standardised to sum to 1.
#' @param .env DEPRECATED.
#' @param ... ignored
#' @examples
#'
#' `%>%` <- magrittr::`%>%`
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     sample_n(50)
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     sample_frac(0.1)
#' @return A tidySummarizedExperiment object
#'
#' @rdname dplyr-methods
#' @name sample_n
#'
#' @export
NULL

#' @export
sample_n.tidySummarizedExperiment <- function(tbl, size, replace=FALSE,
    weight=NULL, .env=NULL, ...) {
    lifecycle::signal_superseded("1.0.0", "sample_n()", "slice_sample()")

    message(data_frame_returned_message)

    tbl %>%
        as_tibble() %>%
        dplyr::sample_n(size, replace=replace, weight=weight, .env=.env, ...)
}

#' @importFrom dplyr sample_frac
#'
#' @rdname dplyr-methods
#' @name sample_frac
#'
#' @export
NULL

#' @export
sample_frac.tidySummarizedExperiment <- function(tbl, size=1, replace=FALSE,
    weight=NULL, .env=NULL, ...) {
    lifecycle::signal_superseded("1.0.0", "sample_frac()", "slice_sample()")

    message(data_frame_returned_message)

    tbl %>%
        as_tibble() %>%
        dplyr::sample_frac(size, replace=replace, weight=weight, .env=.env, ...)
}


#' Count observations by group
#'
#' @description
#' `count()` lets you quickly count the unique values of one or more variables:
#' `df %>% count(a, b)` is roughly equivalent to
#' `df %>% group_by(a, b) %>% summarise(n=n())`.
#' `count()` is paired with `tally()`, a lower-level helper that is equivalent
#' to `df %>% summarise(n=n())`. Supply `wt` to perform weighted counts,
#' switching the summary from `n=n()` to `n=sum(wt)`.
#'
#' `add_count()` are `add_tally()` are equivalents to `count()` and `tally()`
#' but use `mutate()` instead of `summarise()` so that they add a new column
#' with group-wise counts.
#'
#' @param x A data frame, data frame extension (e.g. a tibble), or a
#'   lazy data frame (e.g. from dbplyr or dtplyr).
#' @param ... <[`data-masking`][dplyr_data_masking]> Variables to group by.
#' @param wt <[`data-masking`][dplyr_data_masking]> Frequency weights.
#'   Can be `NULL` or a variable:
#'
#'   * If `NULL` (the default), counts the number of rows in each group.
#'   * If a variable, computes `sum(wt)` for each group.
#' @param sort If `TRUE`, will show the largest groups at the top.
#' @param name The name of the new column in the output.
#'
#'   If omitted, it will default to `n`. If there's already a column called `n`,
#'   it will error, and require you to specify the name.
#' @param .drop For `count()`: if `FALSE` will include counts for empty groups
#'   (i.e. for levels of factors that don't exist in the data). Deprecated in
#'   `add_count()` since it didn't actually affect the output.
#' @return
#' An object of the same type as `.data`. `count()` and `add_count()`
#' group transiently, so the output has the same groups as the input.
#' @export
#' @examples
#'
#' `%>%` <- magrittr::`%>%`
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     count(sample)
count <- function(x, ..., wt=NULL, sort=FALSE, name=NULL, .drop=group_by_drop_default(x)) {
    UseMethod("count")
}

#' @export
count.default <- function(x, ..., wt=NULL, sort=FALSE, name=NULL, .drop=group_by_drop_default(x)) {
    if (!missing(...)) {
        out <- dplyr::group_by(x, ..., .add=TRUE, .drop=.drop)
    }
    else {
        out <- x
    }
    out <- dplyr::tally(out, wt=!!enquo(wt), sort=sort, name=name)
    if (is.data.frame(x)) {
        out <- dplyr::dplyr_reconstruct(out, x)
    }
    out
}
#' @export
count.tidySummarizedExperiment <- function(x, ..., wt=NULL, sort=FALSE, name=NULL, .drop=group_by_drop_default(x)) {
    message(data_frame_returned_message)

    x %>%
        as_tibble() %>%
        dplyr::count(..., wt=!!enquo(wt), sort=sort, name=name, .drop=.drop)
}



#' Extract a single column
#'
#' `pull()` is similar to `$`. It's mostly useful because it looks a little
#' nicer in pipes, it also works with remote data frames, and it can optionally
#' name the output.
#'
#' @importFrom ellipsis check_dots_used
#' @importFrom dplyr pull
#'
#' @inheritParams arrange
#' @inheritParams tidyselect::vars_pull
#'
#' @param .data A tidySummarizedExperiment object or any data frame
#' @param name An optional parameter that specifies the column to be used
#'   as names for a named vector. Specified in a similar manner as \code{var}.
#' @param ... For use by methods.
#' @return A vector the same size as `.data`.
#' @section Methods:
#' This function is a **generic**, which means that packages can provide
#' implementations (methods) for other classes. See the documentation of
#' individual methods for extra arguments and differences in behaviour.
#'
#' The following methods are currently available in loaded packages:
#' \Sexpr[stage=render,results=rd]{dplyr:::methods_rd("pull")}.
#'
#' @rdname dplyr-methods
#' @name pull
#'
#' @export
#' @examples
#'
#' `%>%` <- magrittr::`%>%`
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     pull(transcript)
NULL

#' @export
pull.tidySummarizedExperiment <- function(.data, var=-1, name=NULL, ...) {
    var <- enquo(var)
    name <- enquo(name)

    .data %>%
        as_tibble() %>%
        dplyr::pull(var=!!var, name=!!name, ...)
}