R/plotCountsCorrelationHeatmap-methods.R

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

#' @name plotCountsCorrelationHeatmap
#' @inherit AcidGenerics::plotCountsCorrelationHeatmap
#' @note Updated 2022-03-07.
#'
#' @inheritParams AcidRoxygen::params
#'
#' @param method `character(1)`.
#' Correlation method.
#' Refer to `stats::cor()` for details.
#'
#' @param ... Passthrough arguments to `plotHeatmap()`.
#'
#' @examples
#' data(RangedSummarizedExperiment, package = "AcidTest")
#'
#' ## matrix ====
#' x <- SummarizedExperiment::assay(RangedSummarizedExperiment)
#' y <- x + 1L
#' plotCountsCorrelationHeatmap(x, y)
NULL



## Updated 2019-07-23.
`plotCountsCorrelationHeatmap,matrix` <- # nolint
    function(x,
             y,
             i = NULL,
             j = NULL,
             method = "pearson",
             ...) {
        validObject(x)
        validObject(y)
        assert(
            identical(dimnames(x), dimnames(y)),
            !anyNA(x), !anyNA(y),
            isString(method)
        )
        if (!is.null(i)) {
            x <- x[i, , drop = FALSE]
            y <- y[i, , drop = FALSE]
        }
        if (!is.null(j)) {
            x <- x[, j, drop = FALSE]
            y <- y[, j, drop = FALSE]
        }
        cor <- cor(x = x, y = y, method = method)
        se <- SummarizedExperiment(assays = list("cor" = cor))
        plotHeatmap(
            object = se,
            scale = "none",
            clusterRows = FALSE,
            clusterCols = FALSE,
            showRownames = TRUE,
            showColnames = TRUE,
            ...
        )
    }



#' @rdname plotCountsCorrelationHeatmap
#' @export
setMethod(
    f = "plotCountsCorrelationHeatmap",
    signature = signature(
        x = "matrix",
        y = "matrix"
    ),
    definition = `plotCountsCorrelationHeatmap,matrix`
)