R/methods-plotDispEsts.R

In roryk/bcbioRnaseq: RNA-Seq Utilities

#' Plot Dispersion Estimates
#'
#' Method support for plotting the dispersion of counts stored in a
#' `bcbioRNASeq` object. Here we're generating a `DESeqDataSet` object on the
#' fly, which already has method support for plotting dispersion, provided by
#' the DESeq2 package.
#'
#' @name plotDispEsts
#' @family Quality Control Functions
#' @author Michael Steinbaugh
#'
#' @importFrom BiocGenerics plotDispEsts
#'
#' @inheritParams general
#' @param ... Passthrough arguments to [DESeq2::plotDispEsts()].
#'
#' @seealso
#' - [DESeq2::plotDispEsts()].
#' - `getMethod("plotDispEsts", "DESeqDataSet")`.
#'
#' @return `ggplot`.
#'
#' @examples
#' # bcbioRNASeq ====
#' plotDispEsts(bcb_small)
#'
#' # Custom colors, using DESeq2 parameters
#' plotDispEsts(
#'     bcb_small,
#'     genecol = "gray",
#'     fitcol = "purple",
#'     finalcol = "orange"
#' )
NULL



# Methods ======================================================================
#' @rdname plotDispEsts
#' @export
setMethod(
    "plotDispEsts",
    signature("bcbioRNASeq"),
    function(object, ...) {
        validObject(object)
        dds <- as(object, "DESeqDataSet")
        plotDispEsts(dds, ...)
    }
)