R/arrange.R

In llrs/BaseSet: Working with Sets the Tidy Way

#' @include AllClasses.R AllGenerics.R
#' @importFrom dplyr arrange
#' @importFrom rlang !!
#' @export
dplyr::arrange

#' Arrange the order of a TidySet
#'
#' Use arrange to extract the columns of a TidySet object. You can use activate
#' with filter or use the specific function. The S3 method filters using all
#' the information on the TidySet.
#' @param .data The TidySet object
#' @param ... Comma separated list of variables names or expressions
#' integer column position to be used to reorder the TidySet.
#' @return A TidySet object
#' @export
#' @seealso [dplyr::arrange()] and [activate()]
#' @family methods
#' @examples
#' relations <- data.frame(
#'     sets = c(rep("A", 5), "B", rep("A2", 5), "B2"),
#'     elements = rep(letters[seq_len(6)], 2),
#'     fuzzy = runif(12)
#' )
#' a <- tidySet(relations)
#' a <- mutate_element(a,
#'     type = c(rep("Gene", 4), rep("lncRNA", 2))
#' )
#'
#' b <- arrange(a, desc(type))
#' elements(b)
#' b <- arrange_element(a, elements)
#' elements(b)
#' # Arrange sets
#' arrange_set(a, sets)
#' @rdname arrange_
#' @export
#' @method arrange TidySet
arrange.TidySet <- function(.data, ...) {
    if (is.null(active(.data))) {
        out <- dplyr::arrange(as.data.frame(.data), ...)
        df2TS(.data = .data, df = out)
    } else {
        switch(
            active(.data),
            elements = arrange_element(.data, ...),
            sets = arrange_set(.data, ...),
            relations = arrange_relation(.data, ...)
        )
    }
}

#' @rdname arrange_
#' @export
arrange_set <- function(.data, ...) {
    UseMethod("arrange_set")
}

#' @rdname arrange_
#' @export
arrange_element <- function(.data, ...) {
    UseMethod("arrange_element")
}

#' @rdname arrange_
#' @export
arrange_relation <- function(.data, ...) {
    UseMethod("arrange_relation")
}

#' @export
#' @method arrange_set TidySet
arrange_set.TidySet <- function(.data, ...) {
    sets <- sets(.data)
    out <- dplyr::arrange(sets, ...)
    .data@sets <- out
    validObject(.data)
    .data
}

#' @export
#' @method arrange_element TidySet
arrange_element.TidySet <- function(.data, ...) {
    elements <- elements(.data)
    out <- dplyr::arrange(elements, ...)
    .data@elements <- out
    validObject(.data)
    .data
}

#' @export
#' @method arrange_relation TidySet
arrange_relation.TidySet <- function(.data, ...) {
    relations <- relations(.data)
    out <- dplyr::arrange(relations, ...)
    .data@relations <- out
    validObject(.data)
    .data
}