R/plotCountsPerFeature-methods.R

In hbc/bcbioRnaseq: Bcbio RNA-Seq

#' @name plotCountsPerFeature
#' @author Michael Steinbaugh, Rory Kirchner, Victor Barrera
#' @inherit AcidPlots::plotCountsPerFeature
#' @note Updated 2022-03-07.
#'
#' @inheritParams plotCounts
#' @inheritParams AcidRoxygen::params
#' @param ... Passthrough to `SummarizedExperiment` method defined in AcidPlots.
#' See `AcidPlots::plotCountsPerFeature()` for details.
#'
#' @examples
#' data(bcb)
#'
#' ## bcbioRNASeq ====
#' plotCountsPerFeature(bcb)
NULL



## Updated 2019-09-16.
`plotCountsPerFeature,bcbioRNASeq` <- # nolint
    function(object, normalized, ...) {
        do.call(
            what = plotCountsPerFeature,
            args = .normalizedPlotArgs(
                object = object,
                normalized = match.arg(normalized),
                ...
            )
        )
    }

formals(`plotCountsPerFeature,bcbioRNASeq`)[["normalized"]] <- # nolint
    unique(c("tmm", .normalized))



#' @rdname plotCountsPerFeature
#' @export
setMethod(
    f = "plotCountsPerFeature",
    signature = signature(object = "bcbioRNASeq"),
    definition = `plotCountsPerFeature,bcbioRNASeq`
)



## Note that this function is defined in F1000 v2 workflow paper.

#' @rdname plotCountsPerFeature
#' @export
plotCountDensity <- function(object, ...) {
    plotCountsPerFeature(object = object, geom = "density", ...)
}