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#' Plots an object of class \code{Threshold}.
#'
#' \code{plotThreshold} plots the objects of class \code{Threshold}.
#'
#' @param x An object of class \code{Threshold} or a list of objects of class \code{Threshold}.
#' @param main A character string describing the title of the plot.
#' @param legend A vector of character strings decribing the different \code{Threshold} objects in
#' \code{x}; only applicable when x is a list.
#' @param col A vector giving the colors, if \code{NULL} colors
#' are generated automatically.
#' @param ... Further arguments passed to or from other methods.
#' @return \code{plotThreshold} returns a plot.
#'
#' @examples
#' Y<-simulateGEdata(500, 500, 10, 2, 5, g=NULL, Sigma.eps=0.1,
#' 250, 100, intercept=FALSE, check.input=FALSE)
#' anno<-as.matrix(sample(1:4, dim(Y$Y)[1], replace=TRUE))
#' colnames(anno)<-"Factor"
#' weights<-findWeights(Y$Y, anno, "Factor")
#' Thresh<-calculateThreshold(Y$Y, exclude=1:100, index.ref=1:10,
#' Weights=weights, anno=anno, Factor="Factor")
#' plotThreshold(Thresh)
#' @author Saskia Freytag
#' @seealso \code{\link{calculateThreshold}}
#' @export
plotThreshold<-function(x,
main="",
legend,
col=NULL,
...)
{
if(class(x)!="Threshold" & class(x)!="list"){
stop("x must be of class Threshold or a list of Threshold objects.")
}
if(class(x)=="Threshold"){
plot(x$Thresholds, x$Prop.values, type="b", lwd=2, xlim=c(0, 1),
ylim=c(0, 1), col="red", ylab="Proportion Prioritised", xlab="Threshold", bty="l", ...)
}
if(class(x)=="list"){
if(any(sapply(x, function(i) class(i)=="Threshold"))==FALSE) {
stop("x must be of class Threshold or a list of Threshold objects.")
}
plot(x[[1]]$Thresholds, x[[1]]$Prop.values, type="n", lwd=2, xlim=c(0, 1),
ylim=c(0, 1), ylab="Proportion Priortised", xlab="Threshold", bty="l", main=main, ...)
if(is.null(col)){
col<-hcl(h = seq(0, 360, round(360/length(x), 2)), c=45, l=70)
}
lapply(1:length(x), function(i) points(x[[i]]$Thresholds, x[[i]]$Prop.values,
type="b", col=col[i], lwd=2))
legend("bottomleft", legend, col=col[1:length(x)], bty="n", lwd=2)
}
}
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