#  Plot regularized linear discriminant functions

plotRLDF <- function(y,design=NULL,z=NULL,nprobes=100,plot=TRUE,labels.y=NULL,labels.z=NULL,pch.y=NULL,pch.z=NULL,col.y="black",col.z="black",show.dimensions=c(1,2),ndim=max(show.dimensions),var.prior=NULL,df.prior=NULL,trend=FALSE,robust=FALSE,...)
#	Regularized linear discriminant function
#	Di Wu and Gordon Smyth
#	29 June 2009.  Last revised 4 Sep 2016.
{
#	Check y
	y <- as.matrix(y)
	g <- nrow(y)
	n <- ncol(y)

#	Check labels.y
	if(is.null(labels.y)) {
		labels.y <- colnames(y)
	} else {
		if(length(labels.y) != n) stop("length(labels.y) doesn't agree with ncol(y)")
		labels.y <- as.character(labels.y)
	}
	if(is.null(labels.y)) labels.y <- as.character(1:n)

#	Check z and labels.z
	if(is.null(z)) {
		labels.z <- character(0)
	} else {
		z <- as.matrix(z)
		if(nrow(z) != g) stop("nrow(z) disagrees with nrow(y)")
		if(is.null(labels.z)) labels.z <- colnames(z)
		if(is.null(labels.z)) labels.z <- letters[1:ncol(z)]
		if(length(labels.z) != ncol(z)) stop("length(labels.z) doesn't agree with ncol(z)")
		labels.z <- as.character(labels.z)
		if(!all(rownames(z)==rownames(y))) warning("y and z have different rownames - they are assumed to correspond to same probes")
	}

#	Check design
	if(is.null(design)) {
		if(is.null(labels.y)) stop("groups not specified")
		if(!anyDuplicated(labels.y)) stop("design not specified and all labels.y are different")
		f <- as.factor(labels.y)
		design <- model.matrix(~f)
	} else {
		design <- as.matrix(design)
		if(nrow(design) != n) stop("nrow(design) doesn't match ncol(y)")
	}

#	Check show.dimensions
	show.dimensions <- as.integer(show.dimensions)[1:2]
	if(show.dimensions[1]==show.dimensions[2]) stop("show.dimensions must specify two different columns")
	if(any(show.dimensions<1) || any(show.dimensions)>n) stop("show.dimensions must be a column number of y")

#	Check ndim
	if(any(show.dimensions)>ndim) ndim <- max(show.dimensions)

#	Check nprobes
	if(nprobes<1) stop("'nprobes' must be at least 1")

#	Project onto between and within spaces
#	Discard first column as intercept
	qrd <- qr(design)
	p <- qrd$rank
	df.residual <- n-p
	if(df.residual==0) stop("No residual degrees of freedom")
	U <- qr.qty(qrd, t(y))
	UB <- U[2:p,,drop=FALSE]
	UW <- U[(p+1):n,,drop=FALSE]
	s2 <- colMeans(UW*UW)

#	Prior variance and prior df
	if(is.null(var.prior) || is.null(df.prior)) {
		if(trend) covariate <- rowMeans(y) else covariate <- NULL
		sv <- squeezeVar(s2, df=df.residual, covariate=covariate, robust=robust)
		var.prior <- sv$var.prior
		df.prior <- sv$df.prior
	} else {
		if(!any(length(var.prior)==c(1,g))) stop("var.prior wrong length")
		if(!any(length(df.prior)==c(1,g))) stop("df.prior wrong length")
	}
	df.prior <- pmin(df.prior, (g-1)*df.residual)
	df.prior <- pmax(df.prior, 1)

#	Select probes by moderated F
	if(g>nprobes) {
		modF <- colMeans(UB*UB)/(s2+df.prior*var.prior)
		o <- order(modF,decreasing=TRUE)
		top <- o[1:nprobes]
		y <- y[top,,drop=FALSE]
		if(!is.null(z)) z <- z[top,,drop=FALSE]
		UB <- UB[,top,drop=FALSE]
		UW <- UW[,top,drop=FALSE]
		if(length(df.prior)>1) df.prior <- df.prior[top]
		if(length(var.prior)>1) var.prior <- var.prior[top]
		g <- nprobes
	} else {
		top <- 1:nprobes
	}

#	Within group SS
	W <- crossprod(UW)

#	Regularize the within-group covariance matrix
	Wreg <- W
	diag(Wreg) <- diag(Wreg) + df.prior*var.prior
	df.total <- df.prior + df.residual
	if(length(df.total)>1) {
		df.total <- sqrt(df.total)
		Wreg <- Wreg / df.total
		Wreg <- (t(Wreg) / df.total)
	} else {
		Wreg <- Wreg / df.total
	}

#	Ratio of between to within SS
	WintoB <- backsolve(chol(Wreg),t(UB),transpose=TRUE)

#	Linear discriminant gene weights
	d1 <- show.dimensions[1]
	d2 <- show.dimensions[2]
	SVD <- svd(WintoB,nu=ndim,nv=0)
	metagenes <- SVD$u

	rank <- min(dim(WintoB))
#	if(ndim > rank) message("Note: only ",rank," of the discriminant functions have any predictive power")

#	LDF for training set
	d.y <- t(y) %*% metagenes
	d1.y <- d.y[,d1]
	d2.y <- d.y[,d2]

#	LDF for classified set
	if(is.null(z)) {
		d1.z <- d2.z <- numeric(0)
	} else {
		d.z <- t(z) %*% metagenes
		d1.z <- d.z[,d1]
		d2.z <- d.z[,d2]
	}

#	Make plot
	if(plot) {
		plot(c(d1.y,d1.z),c(d2.y,d2.z),type="n", xlab=paste("Discriminant Function",d1), ylab=paste("Discriminant Function",d2))
		if(is.null(pch.y)) {
			text(d1.y,d2.y,labels=labels.y,col=col.y,...)
		} else {
			points(d1.y,d2.y,pch=pch.y,col=col.y,...)
		}
		if(!is.null(z)) {
			if(is.null(pch.z)) {
				text(d1.z,d2.z,labels=labels.z,col=col.z,...)
			} else {
				points(d1.z,d2.z,pch=pch.z,col=col.z,...)
			}
		}
	}

#	Output
	out <- list(training=d.y,top=top,metagenes=metagenes,singular.values=SVD$d,rank=rank)
	if(!is.null(z)) out$predicting <- d.z
	out$var.prior <- var.prior
	out$df.prior <- df.prior
	invisible(out)
}