R/correlationPlot.R

In PeteHaitch/RUVcorr: Removal of unwanted variation for gene-gene correlations and related analysis.

#' Correlation plot to compare estimated correlations with true correlations.
#'
#' \code{correlationPlot} produces a correlation plot to compare true and estimated
#'	correlations.
#'
#' @param true A matrix of true gene-gene correlation values.
#' @param est A matrix of estimated gene expression values.
#' @param plot.genes A vector of indices of genes used in plotting; the suggested length of this vector is 18.
#' @param boxes A logical scalar to indicate whether boxes 
#' are drawn around sets of 6 genes; only available if \code{plot.genes} has length 18.
#' @param title A character string describing the title of the plot.
#' @return \code{correlationPlot} returns a plot.
#'
#' @details
#' The upper triangle of the correlation plot shows the true gene-gene correlation values,
#' while the lower triangle of the correlation plot shows the gene-gene correlation values
#' calculated from the estimated gene expression values. This is possible because correlation
#' matrices are symmetric.
#' @inheritParams graphics::mtext
#' @examples
#' Y<-simulateGEdata(500, 500, 10, 2, 5, g=NULL, Sigma.eps=0.1, 250, 100, check.input=FALSE)
#' correlationPlot(Y$Sigma, Y$Y, title="Raw", 
#' plot.genes=c(sample(1:100,6), sample(101:250,6),sample(251:500, 6)))
#' @seealso \code{\link[corrplot]{corrplot}}
#' @author Saskia Freytag
#' @export
correlationPlot<-function(	
							true, #matrix 
							est,
							plot.genes=sample(1:dim(true)[1],18), # index of which genes to plot
							boxes=TRUE, # draw boxes FALSE/TRUE
							title, 
							line=-1){
							
	if(is.matrix(true)==FALSE) stop("true needs to be a matrix object.")
	if(is.matrix(est)==FALSE) stop("est needs to be a matrix object.")
	
	if(length(plot.genes)!=18 & boxes==TRUE){
	 	warning("No boxes can be drawn when not exactly 18 genes are specified.")
		boxes=FALSE
	}
							
	#require(corrplot) 
	#require library for plotting
	
	est.true<-mashUp(true,est,plot.genes)
	# lower triangle estimated values, upper triangle true values
	
	corrplot(est.true, method = c("color"), order = "original", tl.col = "black")
	# draw object
	mtext(paste(title), side=3,line=line, cex = 1)
	if(boxes){
		rect(0.5, 12.5, 6.5, 18.5, border = "black", lwd = 2)
		rect(6.5, 6.5, 12.5, 12.5, border="black", lwd=2)
    	rect(12.5, 0.5, 18.5, 6.5, border="black", lwd=2)
    }
}