R/dplyr_methods.R

In tidyseurat: Brings Seurat to the Tidyverse

#' @name arrange
#' @rdname arrange
#' @inherit dplyr::arrange
#' @family single table verbs
#'
#' @examples
#' data(pbmc_small)
#' pbmc_small |>
#'     arrange(nFeature_RNA)
#' 
#' @importFrom tibble as_tibble
#' @importFrom dplyr arrange
#' @export
arrange.Seurat <- function(.data, ..., .by_group=FALSE) {
    .data@meta.data <-
        .data %>%
        as_tibble() %>%
        dplyr::arrange(  ..., .by_group=.by_group  ) %>%
        as_meta_data(.data)

    .data
}

#' @name bind_rows
#' @rdname bind_rows
#' @inherit ttservice::bind_rows
#'
#' @examples
#' data(pbmc_small)
#' tt <- pbmc_small
#' ttservice::bind_rows(tt, tt)
#'
#' tt_bind <- tt |> select(nCount_RNA ,nFeature_RNA)
#' tt |> ttservice::bind_cols(tt_bind)
#' 
#' @importFrom rlang dots_values
#' @importFrom rlang flatten_if
#' @importFrom rlang is_spliced
#' @importFrom ttservice bind_rows
#' @export
bind_rows.Seurat <- function(..., .id=NULL,  add.cell.ids=NULL)
{
    tts <- flatten_if(dots_values(...), is_spliced)

    # Strange error for Seurat merge
    # GetResidualSCTModel
    # close to a line as such
    # slot(object=object[[assay]], name="SCTModel.list")
    # So I have to delete any sample of size 1 if I have calculated SCT
    # if()
    # GetAssayData(object, slot='SCTModel.list', assay="SCT") %>%
    #     map(~ .x@cell.attributes %>% nrow)

    # Check if cell with same name
    merge(tts[[1]], y=tts[[2]], add.cell.ids=add.cell.ids)
}

#' @importFrom rlang flatten_if
#' @importFrom rlang is_spliced
#' @importFrom rlang dots_values
#' @importFrom ttservice bind_cols
bind_cols_ <- function(..., .id=NULL){

    tts <- flatten_if(dots_values(...), is_spliced)

    tts[[1]]@meta.data <- bind_cols(tts[[1]][[]], tts[[2]], .id=.id)

    tts[[1]]
}

#' @rdname bind_rows
#' @aliases bind_cols
#' @export
bind_cols.Seurat <- bind_cols_

#' @name distinct
#' @rdname distinct
#' @inherit dplyr::distinct
#'
#' @examples
#' data("pbmc_small")
#' pbmc_small |> distinct(groups)
#'
#' @importFrom dplyr distinct
#' @export
distinct.Seurat <- function (.data, ..., .keep_all=FALSE)
{
    message(data_frame_returned_message)

    distinct_columns <-
        (enquos(..., .ignore_empty="all") %>% map(~ quo_name(.x)) %>% unlist)

    # Deprecation of special column names
    if(is_sample_feature_deprecated_used(.data, distinct_columns)){
        .data= ping_old_special_column_into_metadata(.data)
    }

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

}

#' @name filter
#' @rdname filter
#' @inherit dplyr::filter
#' 
#' @examples
#' data("pbmc_small")
#' pbmc_small |>  filter(groups == "g1")
#'
#' # Learn more in ?dplyr_eval
#' 
#' @importFrom purrr map
#' @importFrom dplyr filter
#' @export
filter.Seurat <- function (.data, ..., .preserve=FALSE)
{

    # Deprecation of special column names
    if(is_sample_feature_deprecated_used(
        .data,
        (enquos(..., .ignore_empty="all") %>% map(~ quo_name(.x)) %>% unlist)
    )){
        .data= ping_old_special_column_into_metadata(.data)
    }

    new_meta <- .data %>%
        as_tibble() %>%
        dplyr::filter( ..., .preserve=.preserve) %>%
        as_meta_data(.data)

    # Error if size == 0
    if(nrow(new_meta) == 0) stop("tidyseurat says: the resulting data",
        " container is empty. Seurat does not allow for empty containers.")

    new_obj <-
        subset(.data, cells=rownames(new_meta)) %>%

    # Clean empty slots
    clean_seurat_object()

    new_obj

}

#' @name group_by
#' @rdname group_by
#' @inherit dplyr::group_by
#' 
#' @examples
#' data("pbmc_small")
#' pbmc_small |>  group_by(groups)
#'
#' @importFrom dplyr group_by_drop_default
#' @importFrom dplyr group_by
#' @export
group_by.Seurat <- function (.data, ..., .add=FALSE,
    .drop=group_by_drop_default(.data))
{
    message(data_frame_returned_message)

    # Deprecation of special column names
    if(is_sample_feature_deprecated_used(
        .data,
        (enquos(..., .ignore_empty="all") %>% map(~ quo_name(.x)) %>% unlist)
    )){
        .data <- ping_old_special_column_into_metadata(.data)
    }

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

}

#' @name summarise
#' @aliases summarize
#' @inherit dplyr::summarise
#' @family single table verbs
#' 
#' @examples
#' data(pbmc_small)
#' pbmc_small |> summarise(mean(nCount_RNA))
#'
#' @importFrom dplyr summarise
#' @importFrom purrr map
#' @export
summarise.Seurat <- function (.data, ...) {
    message(data_frame_returned_message)

    # Deprecation of special column names
    if(is_sample_feature_deprecated_used(
        .data,
        (enquos(..., .ignore_empty="all") %>% map(~ quo_name(.x)) %>% unlist)
    )){
        .data= ping_old_special_column_into_metadata(.data)
    }

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

}

#' @name summarise
#' @rdname summarise
#' @importFrom dplyr summarize
#' @export
summarize.Seurat <- summarise.Seurat

#' @name mutate
#' @rdname mutate
#' @inherit dplyr::mutate
#' @family single table verbs
#'
#' @examples
#' data(pbmc_small)
#' pbmc_small |> mutate(nFeature_RNA=1)
#'
#' @importFrom rlang enquos
#' @importFrom dplyr mutate
#' @importFrom purrr map
#' @export
mutate.Seurat <- function(.data, ...) {

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

    # Deprecation of special column names
    .cols <- enquos(..., .ignore_empty="all") %>% 
        map(~ quo_name(.x)) %>% unlist()
    if (is_sample_feature_deprecated_used(.data, .cols)) {
        .data <- ping_old_special_column_into_metadata(.data)
    }

    .view_only_cols <- c(
        get_special_columns(.data),
        get_needed_columns(.data))
    
    .test <- cols |>
        intersect(.view_only_cols) |>
        length()

    if (.test) {
        stop("tidyseurat says:",
            " you are trying to mutate a column that is view only",
            " ", paste(.view_only_cols, collapse=", "),
            " (it is not present in the colData).",
            " If you want to mutate a view-only column, make a copy",
            " (e.g. mutate(new_column=", cols[1], ")) and mutate that one.")
    }

    .data@meta.data <-
        .data %>%
        as_tibble %>%
        dplyr::mutate( ...)  %>%
        as_meta_data(.data)

    .data
}

#' @name rename
#' @rdname rename
#' @inherit dplyr::rename
#' @family single table verbs
#'
#' @examples
#' data(pbmc_small)
#' pbmc_small |> rename(s_score=nFeature_RNA)
#'
#' @importFrom tidyselect eval_select
#' @importFrom dplyr rename
#' @export
rename.Seurat <- function(.data, ...)
{

    # Check that we are not modifying a key column
    read_only_columns <- c(
        get_needed_columns(.data),
        get_special_columns(.data))

    # Small df to be more efficient
    df <- .data[1, 1] |> as_tibble() 
    
    # What columns we are going to create
    cols_from <- tidyselect::eval_select(expr(c(...)), df) |> names()
    
    # What are the columns before renaming
    original_columns <- df |> colnames()
    
    # What the column after renaming would be
    new_colums <- df |> rename(...) |> colnames()
    
    # What column you are impacting
    changed_columns <- original_columns |> setdiff(new_colums)
    
    # Check that you are not impacting any read-only columns
    if (any(changed_columns %in% read_only_columns)) {
        stop("tidyseurat says:",
            " you are trying to rename a column that is view only",
            " ", paste(changed_columns, collapse=", "),
            " (it is not present in the colData).",
            " If you want to rename a view-only column, make a copy",
            " (e.g., mutate(", cols_from[1], "=",  changed_columns[1], ")).")
    }

    .data@meta.data <- dplyr::rename( .data[[]],  ...)

    .data
}

#' @name rowwise
#' @rdname rowwise
#' @inherit dplyr::rowwise
#'
#' @examples
#' # TODO
#'
#' @importFrom dplyr rowwise
#' @export
rowwise.Seurat <- function(data, ...) {
    message(data_frame_returned_message)

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

}

#' @name left_join
#' @rdname left_join
#' @inherit dplyr::left_join
#'
#' @examples
#' data(pbmc_small)
#' tt <- pbmc_small
#' tt |> left_join(tt |>  
#'   distinct(groups) |> 
#'   mutate(new_column=1:2))
#'
#' @importFrom dplyr left_join
#' @importFrom dplyr count
#' @export
left_join.Seurat <- function (x, y, by=NULL, copy=FALSE,
    suffix=c(".x", ".y"), ...) {

    # Deprecation of special column names
    .cols <- if (!is.null(by)) by else colnames(y)
    if (is_sample_feature_deprecated_used(x, .cols)) {
        x <- ping_old_special_column_into_metadata(x)
    }

    x %>%
        as_tibble() %>%
        dplyr::left_join( y, by=by, copy=copy, suffix=suffix, ...) %>%

        when(

            # If duplicated cells returns tibble
            count(., !!c_(x)$symbol) %>% filter(n>1) %>% nrow %>% gt(0) ~ {
                message(duplicated_cell_names)
                (.)
            },

            # Otherwise return updated tidyseurat
            ~ {
                x@meta.data <- (.) %>% as_meta_data(x)
                x
            }
        )

}

#' @name inner_join
#' @rdname inner_join
#' @inherit dplyr::inner_join
#'
#' @examples
#' data(pbmc_small)
#' tt <- pbmc_small
#' tt |> inner_join(tt |> 
#'   distinct(groups) |>  
#'   mutate(new_column=1:2) |> 
#'   slice(1))
#'
#' @importFrom dplyr inner_join
#' @importFrom dplyr pull
#' @export
inner_join.Seurat <- function (x, y, by=NULL, copy=FALSE,
    suffix=c(".x", ".y"), ...) {

    # Deprecation of special column names
    .cols <- if (!is.null(by)) by else colnames(y)
    if (is_sample_feature_deprecated_used(x, .cols)) {
        x <- ping_old_special_column_into_metadata(x)
    }

    x %>%
        as_tibble() %>%
        dplyr::inner_join( y, by=by, copy=copy, suffix=suffix, ...)  %>%

        when(

            # If duplicated cells returns tibble
            count(., !!c_(x)$symbol) %>% filter(n>1) %>% nrow %>% gt(0) ~ {
                message(duplicated_cell_names)
                (.)
            },

            # Otherwise return updated tidyseurat
            ~ {
                new_obj <- subset(x, cells= pull(., c_(x)$name))
                new_obj@meta.data <- (.) %>% as_meta_data(new_obj)
                new_obj
            }
        )

}

#' @name right_join
#' @rdname right_join
#' @inherit dplyr::right_join
#'
#' @examples
#' data(pbmc_small)
#' tt <- pbmc_small
#' tt |> right_join(tt |> 
#'   distinct(groups) |> 
#'   mutate(new_column=1:2) |> 
#'   slice(1))
#'
#' @importFrom dplyr right_join
#' @importFrom dplyr pull
#' @export
right_join.Seurat <- function (x, y, by=NULL, copy=FALSE,
    suffix=c(".x", ".y"), ...) {

    # Deprecation of special column names
    .cols <- if (!is.null(by)) by else colnames(y)
    if (is_sample_feature_deprecated_used(x, .cols)) {
        x <- ping_old_special_column_into_metadata(x)
    }

    x %>%
        as_tibble() %>%
        dplyr::right_join( y, by=by, copy=copy, suffix=suffix, ...) %>%

        when(

            # If duplicated cells returns tibble
            count(., !!c_(x)$symbol) %>% filter(n>1) %>% nrow %>% gt(0) ~ {
                message(duplicated_cell_names)
                (.)
            },

            # Otherwise return updated tidyseurat
            ~ {
                new_obj <- subset(x, cells=(.) %>% pull(c_(x)$name))
                new_obj@meta.data <- (.) %>% as_meta_data(new_obj)
                new_obj
            }
        )

}

#' @name full_join
#' @rdname full_join
#' @inherit dplyr::full_join
#'
#' @examples
#' data(pbmc_small)
#' tt <- pbmc_small
#' tt |> full_join(tibble::tibble(groups="g1", other=1:4))
#'
#' @importFrom dplyr full_join
#' @export
full_join.Seurat <- function (x, y, by=NULL, copy=FALSE,
    suffix=c(".x", ".y"), ...) {

    # Deprecation of special column names
    .cols <- if (!is.null(by)) by else colnames(y)
    if (is_sample_feature_deprecated_used(x, .cols)) {
        x <- ping_old_special_column_into_metadata(x)
    }

    x %>%
        as_tibble() %>%
        dplyr::full_join( y, by=by, copy=copy, suffix=suffix, ...) %>%

        when(

            # If duplicated cells returns tibble
            count(., !!c_(x)$symbol) %>% filter(n>1) %>% nrow %>% gt(0) ~ {
                message(duplicated_cell_names)
                (.)
            },

            # Otherwise return updated tidyseurat
            ~ {
                x@meta.data <- (.) %>% as_meta_data(x)
                x
            }
        )

}

#' @name slice
#' @rdname slice
#' @aliases slice_head slice_tail 
#'   slice_sample slice_min slice_max
#' @inherit dplyr::slice
#' @family single table verbs
#' 
#' @examples
#' data(pbmc_small)
#' pbmc_small |> slice(1)
#' 
#' # Slice group-wise using .by
#' pbmc_small |> slice(1:2, .by=groups)
#'
#' @importFrom dplyr slice
#' @importFrom tibble rowid_to_column
#' @export
slice.Seurat <- function (.data, ..., .by=NULL, .preserve=FALSE)
{
    row_number___ <- NULL
    idx <- .data[[]] |>
        select(-everything(), {{ .by }}) |>
        rowid_to_column(var='row_number___')  |>
        slice(..., .by={{ .by }}, .preserve=.preserve) |>
        pull(row_number___)

    if (length(idx) == 0) {
        stop("tidyseurat says: the resulting data container is empty.",
            " Seurat does not allow for empty containers.")
    }

    new_obj <- subset(.data,   cells=colnames(.data)[idx])
    new_obj
}

#' @name slice_sample
#' @rdname slice
#' @inherit dplyr::slice_sample
#' @examples
#'
#' # slice_sample() allows you to random select with or without replacement
#' pbmc_small |> slice_sample(n=5)
#'
#' # if using replacement, and duplicate cells are returned, a tibble will be
#' # returned because duplicate cells cannot exist in Seurat objects
#' pbmc_small |> slice_sample(n=1, replace=TRUE) # returns Seurat
#' pbmc_small |> slice_sample(n=100, replace=TRUE) # returns tibble
#'
#' # weight by a variable
#' pbmc_small |> slice_sample(n=5, weight_by=nCount_RNA)
#'
#' # sample by group
#' pbmc_small |> slice_sample(n=5, by=groups)
#'
#' # sample using proportions
#' pbmc_small |> slice_sample(prop=0.10)
#'
#' @importFrom dplyr slice_sample
#' @export
slice_sample.Seurat <- function(.data, ..., n=NULL,
    prop=NULL, by=NULL, weight_by=NULL, replace=FALSE) {

    # Solve CRAN NOTES
    cell <- NULL
    . <- NULL

    lifecycle::signal_superseded("1.0.0", "sample_n()", "slice_sample()")

    if (!is.null(n))
        new_meta <-
            .data[[]] |>
            as_tibble(rownames=c_(.data)$name) |>
            select(-everything(), c_(.data)$name, {{ by }}, {{ weight_by }}) |>
            slice_sample(..., n=n, by={{ by }},
                weight_by={{ weight_by }}, replace=replace)
    else if (!is.null(prop))
        new_meta <-
            .data[[]] |>
            as_tibble(rownames=c_(.data)$name) |>
            select(-everything(), c_(.data)$name, {{ by }}, {{ weight_by }}) |>
            slice_sample(..., prop=prop, by={{ by }},
                weight_by={{ weight_by }}, replace=replace)
    else
        stop("tidyseurat says: you should provide `n` or `prop` arguments")

    count_cells <- new_meta %>%
        select(!!c_(.data)$symbol) %>%
        count(!!c_(.data)$symbol)
    .max_cell_count <- ifelse(nrow(count_cells)==0, 0, max(count_cells$n))

    # If repeated cells due to replacement
    if (.max_cell_count |> gt(1)){
        message("tidyseurat says: When sampling with replacement",
            " a data frame is returned for independent data analysis.")
        .data |>
            as_tibble()  |>
            right_join(new_meta %>% 
                select(!!c_(.data)$symbol), by=c_(.data)$name)
    } else {
        new_obj <- subset(.data, cells=new_meta %>% pull(!!c_(.data)$symbol))
        new_obj
    }
}

#' @name slice_head
#' @rdname slice
#' @inherit dplyr::slice_head
#' @examples
#'
#' # First rows based on existing order
#' pbmc_small |> slice_head(n=5)
#' 
#' @importFrom dplyr slice_head
#' @importFrom tibble rowid_to_column
#' @export
slice_head.Seurat <- function(.data, ..., n, prop, by=NULL) {
    row_number___ <- NULL
    idx <- .data[[]] |>
        select(-everything(), {{ by }}) |>
        rowid_to_column(var='row_number___')  |>
        slice_head(..., n=n, prop=prop, by={{ by }}) |>
        pull(row_number___)

    if (length(idx) == 0) {
        stop("tidyseurat says: the resulting data container is empty.",
            " Seurat does not allow for empty containers.")
    }
    new_obj <- subset(.data, cells=colnames(.data)[idx])
    new_obj
}

#' @name slice_tail
#' @rdname slice
#' @inherit dplyr::slice_tail
#' @examples
#'
#' # Last rows based on existing order
#' pbmc_small |> slice_tail(n=5)
#' 
#' @importFrom dplyr slice_tail
#' @importFrom tibble rowid_to_column
#' @export
slice_tail.Seurat <- function(.data, ..., n, prop, by=NULL) {
    row_number___ <- NULL
    idx <- .data[[]] |>
        select(-everything(), {{ by }}) |>
        rowid_to_column(var='row_number___')  |>
        slice_tail(..., n=n, prop=prop, by={{ by }}) |>
        pull(row_number___)

    if (length(idx) == 0) {
        stop("tidyseurat says: the resulting data container is empty.",
            " Seurat does not allow for empty containers.")
    }

    new_obj <- subset(.data, cells=colnames(.data)[idx])
    new_obj
}

#' @name slice_min
#' @rdname slice
#' @inherit dplyr::slice_min
#' @examples
#'
#' # Rows with minimum and maximum values of a metadata variable
#' pbmc_small |> slice_min(nFeature_RNA, n=5)
#'
#' # slice_min() and slice_max() may return more rows than requested
#' # in the presence of ties.
#' pbmc_small |>  slice_min(nFeature_RNA, n=2)
#'
#' # Use with_ties=FALSE to return exactly n matches
#' pbmc_small |> slice_min(nFeature_RNA, n=2, with_ties=FALSE)
#'
#' # Or use additional variables to break the tie:
#' pbmc_small |> slice_min(tibble::tibble(nFeature_RNA, nCount_RNA), n=2)
#'
#' # Use by for group-wise operations
#' pbmc_small |> slice_min(nFeature_RNA, n=5, by=groups)
#'
#' @importFrom dplyr slice_min
#' @importFrom tibble rowid_to_column
#' @export
slice_min.Seurat <- function(.data, order_by, ..., n, prop,
    by=NULL, with_ties=TRUE, na_rm=FALSE) {
    row_number___ <- NULL
    order_by_variables <- return_arguments_of(!!enexpr(order_by))

    idx <- .data[[]] |>
        select(-everything(), !!!order_by_variables, {{ by }}) |>
        rowid_to_column(var ='row_number___')  |>
        slice_min(
            order_by={{ order_by }}, ..., n=n, prop=prop, by={{ by }},
            with_ties=with_ties, na_rm=na_rm
        ) |>
        pull(row_number___)

    if (length(idx) == 0) {
        stop("tidyseurat says: the resulting data container is empty.",
            " Seurat does not allow for empty containers.")
    }

    new_obj <- subset(.data, cells=colnames(.data)[idx])
    new_obj
}

#' @name slice_max
#' @rdname slice
#' @inherit dplyr::slice_max
#' @examples
#'
#' # Rows with minimum and maximum values of a metadata variable
#' pbmc_small |> slice_max(nFeature_RNA, n=5)
#' 
#' @importFrom dplyr slice_max
#' @importFrom tibble rowid_to_column
#' @export
slice_max.Seurat <- function(.data, order_by, ..., n, prop,
    by=NULL, with_ties=TRUE, na_rm=FALSE) {
    row_number___ <- NULL

    order_by_variables <- return_arguments_of(!!enexpr(order_by))

    idx <- .data[[]] |>
        select(-everything(), !!!order_by_variables, {{ by }}) |>
        rowid_to_column(var ='row_number___')  |>
        slice_max(
            order_by={{ order_by }}, ..., n=n, prop=prop, by={{ by }},
            with_ties=with_ties, na_rm=na_rm
        ) |>
        pull(row_number___)

    if (length(idx) == 0) {
        stop("tidyseurat says: the resulting data container is empty.",
            " Seurat does not allow for empty containers.")
    }

    new_obj <- subset(.data, cells=colnames(.data)[idx])
    new_obj
}

#' @name select
#' @rdname select
#' @inherit dplyr::select
#'
#' @examples
#' data(pbmc_small)
#' pbmc_small |> select(cell, orig.ident)
#' 
#' @importFrom dplyr select
#' @export
select.Seurat <- function (.data, ...)
{
    # Deprecation of special column names
    .cols <- enquos(..., .ignore_empty="all") %>% 
        map(~ quo_name(.x)) %>% unlist()
    if (is_sample_feature_deprecated_used(.data, .cols)) {
        .data <- ping_old_special_column_into_metadata(.data)
    }

    .data %>%
        as_tibble() %>%
        select_helper(...) %>%
        when(

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

            # If valid seurat meta data
            ~ {
                .data@meta.data <- (.) %>% as_meta_data(.data)
                .data
            }
        )

}

#' @name sample_n
#' @rdname sample_n
#' @aliases sample_frac
#' @inherit dplyr::sample_n
#' 
#' @examples
#' data(pbmc_small)
#' pbmc_small |> sample_n(50)
#' pbmc_small |> sample_frac(0.1)
#' 
#' @importFrom dplyr sample_n
#' @export
sample_n.Seurat <- function(tbl, size, replace=FALSE,
                                weight=NULL, .env=NULL, ...) {
    # Solve CRAN NOTES
    cell <- NULL
    . <- NULL

    lifecycle::signal_superseded("1.0.0", "sample_n()", "slice_sample()")

    new_meta <- tbl[[]] %>%
        as_tibble(rownames=c_(tbl)$name) %>%
        dplyr::sample_n(size, replace=replace, weight=weight, .env=.env, ...)

    count_cells <- new_meta %>%
        select(!!c_(tbl)$symbol) %>%
        count(!!c_(tbl)$symbol)

    # If repeted cells
    if (count_cells$n %>% max() %>% gt(1)){
        message("tidyseurat says: When sampling with replacement",
            " a data frame is returned for independent data analysis.")
        tbl %>%
            as_tibble() %>%
            right_join(new_meta %>% select(!!c_(tbl)$symbol),  by=c_(tbl)$name)
    } else {
        new_obj <- subset(tbl, cells=new_meta %>% pull(!!c_(tbl)$symbol))
        new_obj@meta.data <-
            new_meta %>%
            data.frame(row.names=pull(.,!!c_(tbl)$symbol),
                check.names=FALSE) %>%
            select(- !!c_(tbl)$symbol)
        new_obj
    }
}

#' @rdname sample_n
#' @importFrom dplyr sample_frac
#' @export
sample_frac.Seurat <- function(tbl, size=1, replace=FALSE,
                                   weight=NULL, .env=NULL, ...) {

    # Solve CRAN NOTES
    cell <- NULL
    . <- NULL

    lifecycle::signal_superseded("1.0.0", "sample_frac()", "slice_sample()")

    new_meta <- tbl[[]] %>% 
        as_tibble(rownames=c_(tbl)$name) %>%
        dplyr::sample_frac(size, replace=replace,
            weight=weight, .env=.env, ...)

    count_cells <- new_meta %>%
        select(!!c_(tbl)$symbol) %>%
        count(!!c_(tbl)$symbol)

    # If repeted cells
    if (count_cells$n %>% max() %>% gt(1)){
        message("tidyseurat says: When sampling with replacement",
            " a data frame is returned for independent data analysis.")
        tbl %>%
            as_tibble() %>%
            right_join(new_meta %>% select(!!c_(tbl)$symbol),  by=c_(tbl)$name)
    } else {
        new_obj <- subset(tbl, cells=new_meta %>% pull(!!c_(tbl)$symbol))
        new_obj@meta.data <-
            new_meta %>%
            data.frame(row.names=pull(.,!!c_(tbl)$symbol),
                check.names=FALSE) %>%
            select(- !!c_(tbl)$symbol)
        new_obj
    }
}

#' @name count
#' @rdname count
#' @inherit dplyr::count
#' 
#' @examples
#' data(pbmc_small)
#' pbmc_small |> count(groups)
#'     
#' @importFrom dplyr count
#' @export
count.Seurat <- function(x, ..., wt=NULL, sort=FALSE,
    name=NULL, .drop=group_by_drop_default(x)) {

    message("tidyseurat says: A data frame is",
        " returned for independent data analysis.")

    # Deprecation of special column names
    .cols <- enquos(..., .ignore_empty="all") %>% 
        map(~ quo_name(.x)) %>% unlist()
    if (is_sample_feature_deprecated_used(x, .cols)) {
        x <- ping_old_special_column_into_metadata(x)
    }

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

#' @rdname count
#' @aliases add_count
#' @importFrom dplyr add_count
#' @export
add_count.Seurat <- function(x, ..., wt=NULL,
    sort=FALSE, name=NULL, .drop=group_by_drop_default(x)) {

    # Deprecation of special column names
    .cols <- enquos(..., .ignore_empty="all") %>% 
        map(~ quo_name(.x)) %>% unlist()
    if (is_sample_feature_deprecated_used(x, .cols)) {
        x <- ping_old_special_column_into_metadata(x)
    }

    x@meta.data <-
        x %>%
        as_tibble %>%
        dplyr::add_count(..., wt=!!enquo(wt), sort=sort,
            name=name, .drop=.drop) %>%
        as_meta_data(x)

    x
}

#' @name pull
#' @rdname pull
#' @inherit dplyr::pull
#' 
#' @examples
#' data(pbmc_small)
#' pbmc_small |> pull(groups)
#' 
#' @importFrom dplyr pull
#' @export
pull.Seurat <- function(.data, var=-1, name=NULL, ...) {
    var <- enquo(var)
    name <- enquo(name)

    message("tidyseurat says: A data frame is",
        " returned for independent data analysis.")

    # Deprecation of special column names
    if(is_sample_feature_deprecated_used(
        .data,
        quo_name(var)
    )){
        .data <- ping_old_special_column_into_metadata(.data)
    }

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