##  PLOTMDS.R

#	Class to hold multidimensional scaling output
setClass("MDS",representation("list"))

setMethod("show","MDS",function(object) {
	cat("An object of class MDS\n")
	print(unclass(object))
})

plotMDS <- function(x,...) UseMethod("plotMDS")

plotMDS.MDS <- function(x,labels=NULL,pch=NULL,cex=1,dim.plot=NULL,xlab=NULL,ylab=NULL,var.explained=TRUE,...)
#	Method for MDS objects
#	Create a new plot using MDS coordinates previously computed.
#	Gordon Smyth and Yifang Hu
#	21 May 2011.  Last modified 23 Aug 2025
{
#	Check labels
	if(is.null(labels) & is.null(pch)) {
		labels <- colnames(x$distance.matrix.squared)
		if(is.null(labels)) labels <- 1:length(x$x)
	}

#	Are new dimensions requested?
	if(is.null(dim.plot)) {
		dim.plot <- x$dim.plot
	} else {
		if(!identical(dim.plot,x$dim.plot)) {
			x$dim.plot <- dim.plot
			lambda <- pmax(x$eigen.values,0)
			i <- dim.plot[1]
			x$x <- x$eigen.vectors[,i] * sqrt(lambda[i])
			if(lambda[i] < 1e-13) warning("dimension ", i, " is degenerate or all zero")
			i <- dim.plot[2]
			x$y <- x$eigen.vectors[,i] * sqrt(lambda[i])
			if(lambda[i] < 1e-13) warning("dimension ", i, " is degenerate or all zero")
		}
	}

#	Axis labels
	if(is.null(x$axislabel)) x$axislabel <- "Principal Coordinate"
	if(is.null(xlab)) xlab <- paste(x$axislabel,dim.plot[1])
	if(is.null(ylab)) ylab <- paste(x$axislabel,dim.plot[2])
	if(var.explained) {
		Perc <- round(x$var.explained[dim.plot]*100)
		xlab <- paste0(xlab," (",Perc[1],"%)")
		ylab <- paste0(ylab," (",Perc[2],"%)")
	}

#	Make the plot
	if(is.null(labels)){
#		Plot symbols instead of text
		plot(x$x, x$y, pch = pch, xlab = xlab, ylab = ylab, cex = cex, ...)
	} else {
#		Plot text.
		labels <- as.character(labels)
#		Need to estimate width of labels in plot coordinates.
#		Estimate will be ok for default plot width, but maybe too small for smaller plots.
		StringRadius <- 0.01*cex*nchar(labels)
		left.x <- x$x-StringRadius
		right.x <- x$x+StringRadius
		plot(c(left.x, right.x), c(x$y, x$y), type = "n", xlab = xlab, ylab = ylab, ...)
		text(x$x, x$y, labels = labels, cex = cex, ...)
	}

	invisible(x)
}

plotMDS.default <- function(x,top=500,labels=NULL,pch=NULL,cex=1,dim.plot=c(1,2),gene.selection="pairwise",xlab=NULL,ylab=NULL,plot=TRUE,var.explained=TRUE,...)
#	Multi-dimensional scaling with top-distance
#	Di Wu and Gordon Smyth
#	19 March 2009.  Last modified 13 May 2021.
{
#	Check x
	x <- as.matrix(x)
	nsamples <- ncol(x)
	if(nsamples < 3) stop(paste("Only",nsamples,"columns of data: need at least 3"))
	cn <- colnames(x)
#	Remove rows with missing or Inf values
	bad <- rowSums(is.finite(x)) < nsamples
	if(any(bad)) x <- x[!bad,,drop=FALSE]
	nprobes <- nrow(x)

#	Check top
	top <- min(top,nprobes)

#	Check labels and pch
	if(is.null(pch) & is.null(labels)) {
		labels <- colnames(x)
		if(is.null(labels)) labels <- 1:nsamples
	}
	if(!is.null(labels)) labels <- as.character(labels)

#	Check dim.plot
	dim.plot <- unique(as.integer(dim.plot))
	if(length(dim.plot) != 2L) stop("dim.plot must specify two dimensions to plot")

#	Check dim
	ndim <- max(dim.plot)
	if(ndim < 2L) stop("Need at least two dim.plot")
	if(nsamples < ndim) stop("ndim is greater than number of samples")
	if(nprobes < ndim) stop("ndim is greater than number of rows of data")

#	Check gene.selection
	gene.selection <- match.arg(gene.selection,c("pairwise","common"))

#	Distance matrix from pairwise leading fold changes
	dd <- matrix(0,nrow=nsamples,ncol=nsamples,dimnames=list(cn,cn))
	if(identical(gene.selection,"pairwise")) {
#		Distance measure is mean of top squared deviations for each pair of arrays
		topindex <- nprobes-top+1L
		for (i in 2L:(nsamples))
		for (j in 1L:(i-1L))
			dd[i,j] <- mean(sort.int((x[,i]-x[,j])^2,partial=topindex)[topindex:nprobes])
		axislabel <- "Leading logFC dim"
	} else {
#		Same genes used for all comparisons
		if(nprobes > top) {
			s <- rowMeans((x-rowMeans(x))^2)
			o <- order(s,decreasing=TRUE)
			x <- x[o[1L:top],,drop=FALSE]
		}
		for (i in 2L:(nsamples))
			dd[i,1L:(i-1L)] <- colMeans((x[,i]-x[,1:(i-1),drop=FALSE])^2)
		axislabel <- "Principal Component"
	}

#	Multi-dimensional scaling
	dd <- dd + t(dd)
	rm <- rowMeans(dd)
	dd <- dd - rm
	dd <- t(dd) - (rm - mean(rm))
	mds <- eigen(-dd/2, symmetric=TRUE)
	names(mds) <- c("eigen.values","eigen.vectors")

#	Make MDS object
	lambda <- pmax(mds$eigen.values,0)
	mds$var.explained <- lambda / sum(lambda)
	mds$dim.plot <- dim.plot
	mds$distance.matrix.squared <- dd
	mds$top <- top
	mds$gene.selection <- gene.selection
	mds$axislabel <- axislabel
	mds <- new("MDS",unclass(mds))

#	Add coordinates for plot
	i <- dim.plot[1]
	mds$x <- mds$eigen.vectors[,i] * sqrt(lambda[i])
	if(lambda[i] < 1e-13) warning("dimension ", i, " is degenerate or all zero")
	i <- dim.plot[2]
	mds$y <- mds$eigen.vectors[,i] * sqrt(lambda[i])
	if(lambda[i] < 1e-13) warning("dimension ", i, " is degenerate or all zero")

	if(plot)
		plotMDS(mds,labels=labels,pch=pch,cex=cex,xlab=xlab,ylab=ylab,var.explained=var.explained,...)
	else
		mds
}