R/ggplot2_methods.R

In tidySummarizedExperiment: Brings SummarizedExperiment to the Tidyverse

#' Create a new ggplot from a tidySummarizedExperiment object
#'
#'
#' `ggplot()` initializes a ggplot object. It can be used to
#' declare the input data frame for a graphic and to specify the
#' set of plot aesthetics intended to be common throughout all
#' subsequent layers unless specifically overridden.
#'
#' `ggplot()` is used to construct the initial plot object,
#' and is almost always followed by `+` to add component to the
#' plot. There are three common ways to invoke `ggplot()`:
#'
#'
#' The first method is recommended if all layers use the same
#' data and the same set of aesthetics, although this method
#' can also be used to add a layer using data from another
#' data frame. See the first example below. The second
#' method specifies the default data frame to use for the plot,
#' but no aesthetics are defined up front. This is useful when
#' one data frame is used predominantly as layers are added,
#' but the aesthetics may vary from one layer to another. The
#' third method initializes a skeleton `ggplot` object which
#' is fleshed out as layers are added. This method is useful when
#' multiple data frames are used to produce different layers, as
#' is often the case in complex graphics.
#'
#' @importFrom ggplot2 aes
#' @importFrom ggplot2 ggplot
#'
#' @param .data Default dataset to use for plot. If not already a data.frame,
#'   will be converted to one by [fortify()]. If not specified,
#'   must be supplied in each layer added to the plot.
#' @param mapping Default list of aesthetic mappings to use for plot.
#'   If not specified, must be supplied in each layer added to the plot.
#' @param ... Other arguments passed on to methods. Not currently used.
#' @param environment DEPRECATED. Used prior to tidy evaluation.
#'
#' @return A ggplot
#'
#' @export
#'
#' @rdname ggplot2-methods
#' @name ggplot
#'
#' @examples
#'
#' library(ggplot2)
#'
#' tidySummarizedExperiment::pasilla %>%
#'     tidy() %>%
#'     tidySummarizedExperiment::ggplot(aes(sample, counts)) +
#'     geom_boxplot()
NULL

#' @export
ggplot.tidySummarizedExperiment <- function(data=NULL, mapping=aes(), ..., environment=parent.frame()) {
    data %>%
        as_tibble() %>%
        ggplot2::ggplot(mapping=mapping)
}