R/densityPlot.R

In Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline

#' Density plot for objects of class ChemoProtSet
#'
#' Description
#'
#' @param x object of class 'ChemoProtSet'
#' @param rankProteins plot a the set of ranked proteins or plot the density of the channels
#' @param ... other plot options
#'
#' @return density plot for objects of class ChemoProtSet
#'
#' @export
#' @docType methods
#' @rdname densityPlot-methods
#' @examples
#'ex <- processedExample
#'ex <- runNormalisation(ex)
#'ex <- fitModel(ex)
#'densityPlot(ex)

setGeneric(name = "densityPlot", def = function(x, rankProteins = FALSE, ...) {
    standardGeneric("densityPlot")
})

#' @rdname densityPlot-methods
#' @importFrom graphics par legend lines plot points
#' @import grDevices
#' @aliases densityPlot,ANY,ANY-method
#'
setMethod(f = "densityPlot", signature = "ChemoProtSet", definition = function(x, rankProteins = FALSE, 
    ...) {
    if (x@parameters$dataType == "intensity") {
        vec <- 1:((x@parameters$chans - 1) * x@parameters$reps)
        
    } else {
        vec <- 1:(x@parameters$chans * x@parameters$reps)
    }
    pal <- grDevices::rainbow(length(vec))
    leg.nam <- standard_names(x@parameters$chans, x@parameters$reps, x@parameters$dataType)
    if (nrow(x@normData) == 0) {
        data.merged <- x@input
    } else {
        data.merged <- x@normData
    }
    
    missing_val <- 0
    
    if (rankProteins == TRUE) {
        plot(x = rank(data.merged[, 1]), y = data.merged[, 1], cex.axis = 1, main = c(paste("N. of Missing val. ", 
            missing_val, " \n Change Distribution after LOESS", sep = "")), col = pal[1], ylab = c("Log2(ratios)"), 
            xlab = c("Proteins"))
        if (length(vec) > 1) {
            for (i in 2:length(vec)) {
                points(x = rank(data.merged[, i]), y = data.merged[, i], cex.axis = 1, main = c(""), 
                  col = pal[i])
            }
        }
        legend("topleft", legend = leg.nam, fill = pal)
        
    } else {
        
        plot(stats::density(x = data.merged[, 1]), col = pal[1], main = c(" Density after LOESS"), 
            ylim = c(0, 5), cex.axis = 1)
        legend("topleft", legend = leg.nam, fill = pal, ...)
        
        if (length(vec) > 1) {
            for (i in 2:length(vec)) {
                lines(stats::density(x = data.merged[, i]), col = pal[i], main = c(""))
            }
        }
    }
    
})