R/meanSdPlot.R

In Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline

#' MeanSd plot for objects of class ChemoProtSet
#'
#' Shows the ranked means with a running median calculated with a window size of 10%
#'
#' @param x object of class 'ChemoProtSet'
#' @param ... other plot options
#'
#' @return meanSd plot for objects of class ChemoProtSet
#'
#' @export
#' @docType methods
#' @rdname meanSdPlot-methods
#' @examples
#'ex <- processedExample
#'ex <- runNormalisation(ex)
#'ex <- fitModel(ex)
#'meanSdPlot(ex)

setGeneric(name = "meanSdPlot", def = function(x, ...) {
    standardGeneric("meanSdPlot")
})

#' @rdname meanSdPlot-methods
#' @importFrom vsn meanSdPlot
#' @import grDevices
#' @aliases meanSdPlot,ANY,ANY-method
#'
setMethod(f = "meanSdPlot", signature = "ChemoProtSet", definition = function(x, ...) {
    if (x@parameters$dataType == "linear") {
        vsn::meanSdPlot(as.matrix(x@normData[, 1:(x@parameters$chans * x@parameters$reps)]))
    } else {
        vsn::meanSdPlot(as.matrix(x@normData[, 1:((x@parameters$chans - 1) * x@parameters$reps)]))
    }
})