R/corrPlot.R

In Doscheda: A DownStream Chemo-Proteomics Analysis Pipeline

#'Plot showing correlation between all channels across replicates
#'
#' Plot of the correlation between all the channels in the data.
#'
#' @param x object of class 'ChemoProtSet'
#' @param ... corrplot options
#' @return correlation plot for objects of class ChemoProtSet
#'
#' @export
#' @docType methods
#' @rdname corrPlot-methods
#' @examples
#'
#'ex <- processedExample
#'ex <- runNormalisation(ex)
#'ex <- fitModel(ex)
#'corrPlot(ex)
#'
#'

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

#' @rdname corrPlot-methods
#' @importFrom corrgram corrgram
#' @importFrom stats cor
#' @aliases corrPlot,ANY,ANY-method
#'
setMethod(f = "corrPlot", signature = "ChemoProtSet", definition = function(x, ...) {
    
    if (x@parameters$modelType == "sigmoid") {
        su <- x@normData
        
    } else {
        
        if (x@parameters$reps == 1) {
            
            
            su <- x@normData
            
        } else {
            su <- x@finalData
        }
    }
    
    if (x@parameters$dataType == "intensity") {
        
        index <- 1:((x@parameters$chans - 1) * x@parameters$reps)
    } else {
        index <- 1:(x@parameters$chans * x@parameters$reps)
    }
    # panel.shadeNtext <- NULL; panel.pie <- NULL; panel.txt <- NULL ;
    
    index <- length(index)
    # panel.shadeNtext
    cmat <- cor(su[, 1:index], use = "pairwise", method = "pearson")
    corrgram(cmat, order = TRUE, lower.panel = function(x, y, corr = NULL, col.regions, ...) {
        if (is.null(corr)) 
            corr <- stats::cor(x, y, use = "
                                   pair")
        ncol <- 14
        pal <- col.regions(ncol)
        col.ind <- as.numeric(cut(corr, breaks = seq(from = -1, to = 1, length = ncol + 1), include.lowest = TRUE))
        usr <- graphics::par("usr")
        graphics::rect(usr[1], usr[3], usr[2], usr[4], col = pal[col.ind], border = NA)
        graphics::box(col = "lightgray")
        on.exit(graphics::par(usr))
        graphics::par(usr = c(0, 1, 0, 1))
        r <- formatC(corr, digits = 2, format = "f")
        cex.cor <- 0.8/graphics::strwidth("-X.xx")
        graphics::text(0.5, 0.5, r, cex = cex.cor)
    }, upper.panel = corrgram::panel.pie, text.panel = corrgram::panel.txt, main = "Corrgram Plots")
    
    
    
    
    
})