R/DMHeatMap.R

In kyotil: Utility Functions for Statistical Analysis Report Generation and Monte Carlo Studies

#a change upon Daryl's change of heatmap
# 
DMHeatMap <- 
function (x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE, 
    distfun = dist, hclustfun = hclust, dendrogram = c("both", 
        "row", "column", "none"), symm = FALSE, scale = c("none", 
        "row", "column"), na.rm = TRUE, revC = identical(Colv, 
        "Rowv"), add.expr, breaks, symbreaks = min(x < 0, na.rm = TRUE) || 
        scale != "none", col = "heat.colors", colsep, rowsep, 
    sepcolor = "white", sepwidth = c(0.05, 0.05), cellnote, notecex = 1, 
    notecol = "cyan", na.color = par("bg"), trace = c("column", 
        "row", "both", "none"), tracecol = "cyan", hline = median(breaks), 
    vline = median(breaks), linecol = tracecol, margins = c(5, 
        5), ColSideColors, RowSideColors, cexRow = 0.2 + 1/log10(nr), 
    cexCol = 0.2 + 1/log10(nc), labRow = NULL, labCol = NULL, 
    labColor = NULL, axis=TRUE, heatmapOnly=FALSE,
    key = TRUE, keysize = 1.5, density.info = c("histogram", 
        "density", "none"), denscol = tracecol, symkey = min(x < 
        0, na.rm = TRUE) || symbreaks, densadj = 0.25, main = NULL, 
    xlab = NULL, ylab = NULL, lmat = NULL, lhei = NULL, lwid = NULL, lower.left.only=TRUE, legend=TRUE,
    legend.x="topright", verbose=FALSE,
    ...) 
{
    usr <- par("usr"); on.exit(par(usr))
    
    if (heatmapOnly) {
        lhei=c(1, 100); lwid=c(1, 100)
    }

      scale01 <- function(x, low = min(x), high = max(x)) {
        x <- (x - low)/(high - low)
        x
      }
      retval <- list()
      scale <- if (symm && missing(scale)) 
        "none"
      else match.arg(scale)
      dendrogram <- match.arg(dendrogram)
      trace <- match.arg(trace)
      density.info <- match.arg(density.info)
      if (length(col) == 1 && is.character(col)) 
        col <- get(col, mode = "function")
      if (!missing(breaks) && (scale != "none")) 
        warning("Using scale=\"row\" or scale=\"column\" when breaks are", 
          "specified can produce unpredictable results.", 
          "Please consider using only one or the other.")
      if (is.null(Rowv) || is.na(Rowv)) 
        Rowv <- FALSE
      if (is.null(Colv) || is.na(Colv)) 
        Colv <- FALSE
      else if (Colv == "Rowv" && !isTRUE(Rowv)) 
        Colv <- FALSE
      if (length(di <- dim(x)) != 2 || !is.numeric(x)) 
        stop("`x' must be a numeric matrix")
      nr <- di[1]
      nc <- di[2]
      if (nr <= 1 || nc <= 1) 
        stop("`x' must have at least 2 rows and 2 columns")
      if (!is.numeric(margins) || length(margins) != 2) 
        stop("`margins' must be a numeric vector of length 2")
      if (missing(cellnote)) 
        cellnote <- matrix("", ncol = ncol(x), nrow = nrow(x))
      if (!inherits(Rowv, "dendrogram")) {
        if (((!isTRUE(Rowv)) || (is.null(Rowv))) && (dendrogram %in% 
          c("both", "row"))) {
          if (is.logical(Colv) && (Colv)) 
            dendrogram <- "column"
          else dedrogram <- "none"
          warning("Discrepancy: Rowv is FALSE, while dendrogram is `", 
            dendrogram, "'. Omitting row dendogram.")
        }
      }
      if (!inherits(Colv, "dendrogram")) {
        if (((!isTRUE(Colv)) || (is.null(Colv))) && (dendrogram %in% 
          c("both", "column"))) {
          if (is.logical(Rowv) && (Rowv)) 
            dendrogram <- "row"
          else dendrogram <- "none"
#          warning("Discrepancy: Colv is FALSE, while dendrogram is `", 
#            dendrogram, "'. Omitting column dendogram.")
        }
      }
      if (inherits(Rowv, "dendrogram")) {
        ddr <- Rowv
        rowInd <- order.dendrogram(ddr)
      }
      else if (is.integer(Rowv)) {
        hcr <- hclustfun(distfun(x))
        ddr <- as.dendrogram(hcr)
        ddr <- reorder(ddr, Rowv)
        rowInd <- order.dendrogram(ddr)
        if (nr != length(rowInd)) 
          stop("row dendrogram ordering gave index of wrong length")
      }
      else if (isTRUE(Rowv)) {
        Rowv <- rowMeans(x, na.rm = na.rm)
        hcr <- hclustfun(distfun(x))
        ddr <- as.dendrogram(hcr)
        ddr <- reorder(ddr, Rowv)
        rowInd <- order.dendrogram(ddr)
        if (nr != length(rowInd)) 
          stop("row dendrogram ordering gave index of wrong length")
      }
      else {
        rowInd <- nr:1
      }
      if (inherits(Colv, "dendrogram")) {
        ddc <- Colv
        colInd <- order.dendrogram(ddc)
      }
      else if (identical(Colv, "Rowv")) {
        if (nr != nc) 
          stop("Colv = \"Rowv\" but nrow(x) != ncol(x)")
        if (exists("ddr")) {
          ddc <- ddr
          colInd <- order.dendrogram(ddc)
        }
        else colInd <- rowInd
      }
      else if (is.integer(Colv)) {
        hcc <- hclustfun(distfun(if (symm) 
          x
        else t(x)))
        ddc <- as.dendrogram(hcc)
        ddc <- reorder(ddc, Colv)
        colInd <- order.dendrogram(ddc)
        if (nc != length(colInd)) 
          stop("column dendrogram ordering gave index of wrong length")
      }
      else if (isTRUE(Colv)) {
        Colv <- colMeans(x, na.rm = na.rm)
        hcc <- hclustfun(distfun(if (symm) 
          x
        else t(x)))
        ddc <- as.dendrogram(hcc)
        ddc <- reorder(ddc, Colv)
        colInd <- order.dendrogram(ddc)
        if (nc != length(colInd)) 
          stop("column dendrogram ordering gave index of wrong length")
      }
      else {
        colInd <- 1:nc
      }
      retval$rowInd <- rowInd
      retval$colInd <- colInd
      retval$call <- match.call()
      x <- x[rowInd, colInd]
      x.unscaled <- x
      cellnote <- cellnote[rowInd, colInd]
      if (is.null(labRow)) 
        labRow <- if (is.null(rownames(x))) 
          (1:nr)[rowInd]
        else rownames(x)
      else labRow <- labRow[rowInd]
      if (is.null(labCol)) 
        labCol <- if (is.null(colnames(x))) 
          (1:nc)[colInd]
        else colnames(x)
      else labCol <- labCol[colInd]
      if (scale == "row") {
        retval$rowMeans <- rm <- rowMeans(x, na.rm = na.rm)
        x <- sweep(x, 1, rm)
        retval$rowSDs <- sx <- apply(x, 1, sd, na.rm = na.rm)
        x <- sweep(x, 1, sx, "/")
      }
      else if (scale == "column") {
        retval$colMeans <- rm <- colMeans(x, na.rm = na.rm)
        x <- sweep(x, 2, rm)
        retval$colSDs <- sx <- apply(x, 2, sd, na.rm = na.rm)
        x <- sweep(x, 2, sx, "/")
      }
      if (missing(breaks) || is.null(breaks) || length(breaks) < 1) {
        if (missing(col) || is.function(col)) 
          breaks <- 16
        else breaks <- length(col) + 1
      }
      if (length(breaks) == 1) {
        if (!symbreaks) 
          breaks <- seq(min(x, na.rm = na.rm), max(x, na.rm = na.rm), 
            length = breaks)
        else {
          extreme <- max(abs(x), na.rm = TRUE)
          breaks <- seq(-extreme, extreme, length = breaks)
        }
      }
      nbr <- length(breaks)
      ncol <- length(breaks) - 1
      if (inherits(col, "function"))
        col <- col(ncol)
      min.breaks <- min(breaks)
      max.breaks <- max(breaks)
      x[x < min.breaks] <- min.breaks
      x[x > max.breaks] <- max.breaks
      if (missing(lhei) || is.null(lhei)) 
        lhei <- c(keysize, 4)
      if (missing(lwid) || is.null(lwid)) 
        lwid <- c(keysize, 4)
      if (missing(lmat) || is.null(lmat)) {
        lmat <- rbind(4:3, 2:1)
        if (!missing(ColSideColors)) {
          if (!is.character(ColSideColors) || length(ColSideColors) != nc) 
              stop("'ColSideColors' must be a character vector of length ncol(x)")
          lmat <- rbind(lmat[1, ] + 1, c(NA, 1), lmat[2, ] + 1)
          lhei <- c(lhei[1], 0.2, lhei[2])
        }
        if (!missing(RowSideColors)) {
          if (!is.character(RowSideColors) || length(RowSideColors) != nr) 
            stop("'RowSideColors' must be a character vector of length nrow(x)")
          lmat <- cbind(lmat[, 1] + 1, c(rep(NA, nrow(lmat) - 
            1), 1), lmat[, 2] + 1)
          lwid <- c(lwid[1], 0.2, lwid[2])
        }
        lmat[is.na(lmat)] <- 0
      }
      if (length(lhei) != nrow(lmat)) 
        stop("lhei must have length = nrow(lmat) = ", nrow(lmat))
      if (length(lwid) != ncol(lmat)) 
        stop("lwid must have length = ncol(lmat) =", ncol(lmat))
      op <- par(no.readonly = TRUE)
      on.exit(par(op))
      
      layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
    
    # commented out by YF
    #margins[1] = 0
    
      if (!missing(RowSideColors)) {
        par(mar = c(margins[1], 0, 0, 0.5))
        image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
      }
      if (!missing(ColSideColors)) {
        par(mar = c(0.5, 0, 0, margins[2]))
        image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
      }
    #ALTERATION
    #moved 4th margin to 2nd margin and got rid of 1st margin
      par(mar = c(margins[1], margins[2], 0, 0))
      x <- t(x)
      cellnote <- t(cellnote)
      if (revC) {
        iy <- nr:1
        if (exists("ddr")) 
          ddr <- rev(ddr)
        x <- x[, iy]
        cellnote <- cellnote[, iy]
      }
      else iy <- 1:nr
    
      #### ALTERATION BEGINS HERE
      xImage = x
      if(lower.left.only) {
          for(iii in 1:nc) { for(jjj in 1:nr) {
            if(iii >= (nr+1-jjj)) xImage[jjj,iii] = -5
          }}
      }
      breaksImage = c(-5,breaks)
      colImage = c("white",col)
    
    if(verbose) myprint(breaks)
    if(verbose) myprint(colImage)
    
      image(1:nc, 1:nr, xImage, xlim = 0.5 + c(0, nc), ylim = 0.5 + 
        c(0, nr), axes = FALSE, xlab = "", ylab = "", col = colImage, 
        breaks = breaksImage, ...)
      #ENDS HERE
# a hack
#    abline(v=cumsum(c(7,2,15,10))+.5)
    
      retval$carpet <- x
      if (exists("ddr")) 
        retval$rowDendrogram <- ddr
      if (exists("ddc")) 
        retval$colDendrogram <- ddc
      retval$breaks <- breaks
      retval$col <- col
#      if (!invalid(na.color) & any(is.na(x))) {
#        mmat <- ifelse(is.na(x), 1, NA)
#        image(1:nc, 1:nr, mmat, axes = FALSE, xlab = "", ylab = "", 
#          col = na.color, add = TRUE)
#      }
    #ALTERATION nc - 1
    if(axis) {
          if(!is.null(labColor)) {
            for(cc in 1:(nc)) {
              axis(1, cc, labels = labCol[cc], las = 2, line = -0.5, tick = 0, 
                 cex.axis = cexCol,col.axis=labColor[cc])
            }
          } else {
            axis(1, 1:(nc), labels = labCol, las = 2, line = -0.5, tick = 0, 
                 cex.axis = cexCol)
          }
      axis(2, iy, labels = labRow, las = 2, line = -0.5, tick = 0, 
        cex.axis = cexRow)
    }
      if(legend) {
        ltext = rev(paste("[",breaks[-length(breaks)], ",", breaks[-1],")",sep=""))
        legend(legend.x,fill=rev(col),legend=ltext,bty="n")
      }
      if (!is.null(xlab)) 
        mtext(xlab, side = 1, line = margins[1] - 1.25)
    #ALTERATION changed 4 to 2 below
      if (!is.null(ylab)) 
        mtext(ylab, side = 4, line = margins[2] - 1.25)
      if (!missing(add.expr)) 
        eval(substitute(add.expr))
      if (!missing(colsep)) 
        for (csep in colsep) rect(xleft = csep + 0.5, ybottom = rep(0, 
          length(csep)), xright = csep + 0.5 + sepwidth[1], 
          ytop = rep(ncol(x) + 1, csep), lty = 1, lwd = 1, 
          col = sepcolor, border = sepcolor)
      if (!missing(rowsep)) 
        for (rsep in rowsep) rect(xleft = 0, ybottom = (ncol(x) + 
          1 - rsep) - 0.5, xright = nrow(x) + 1, ytop = (ncol(x) + 
          1 - rsep) - 0.5 - sepwidth[2], lty = 1, lwd = 1, 
          col = sepcolor, border = sepcolor)
      min.scale <- min(breaks)
      max.scale <- max(breaks)
      x.scaled <- scale01(t(x), min.scale, max.scale)
      if (trace %in% c("both", "column")) {
        retval$vline <- vline
        vline.vals <- scale01(vline, min.scale, max.scale)
        for (i in colInd) {
          if (!is.null(vline)) {
            abline(v = i - 0.5 + vline.vals, col = linecol, 
              lty = 2)
          }
          xv <- rep(i, nrow(x.scaled)) + x.scaled[, i] - 0.5
          xv <- c(xv[1], xv)
          yv <- 1:length(xv) - 0.5
          lines(x = xv, y = yv, lwd = 1, col = tracecol, type = "s")
        }
      }
      if (trace %in% c("both", "row")) {
        retval$hline <- hline
        hline.vals <- scale01(hline, min.scale, max.scale)
        for (i in rowInd) {
          if (!is.null(hline)) {
            abline(h = i + hline, col = linecol, lty = 2)
          }
          yv <- rep(i, ncol(x.scaled)) + x.scaled[i, ] - 0.5
          yv <- rev(c(yv[1], yv))
          xv <- length(yv):1 - 0.5
          lines(x = xv, y = yv, lwd = 1, col = tracecol, type = "s")
        }
      }
      if (!missing(cellnote)) 
        text(x = c(row(cellnote)), y = c(col(cellnote)), labels = c(cellnote), 
          col = notecol, cex = notecex)
      par(mar = c(margins[1], 0, 0, 0))
      if (dendrogram %in% c("both", "row")) {
        plot(ddr, horiz = TRUE, axes = FALSE, yaxs = "i", leaflab = "none")
      }
      else plot.new()
      par(mar = c(0, 0, if (!is.null(main)) 5 else 0, margins[2]))
      if (dendrogram %in% c("both", "column")) {
        plot(ddc, axes = FALSE, xaxs = "i", leaflab = "none")
      }
      else plot.new()
      if (!is.null(main)) 
        title(main, cex.main = 1.5 * op[["cex.main"]])
      if (key) {
        par(mar = c(5, 4, 2, 1), cex = 0.75)
        tmpbreaks <- breaks
       # ALTERATION HERE ... Don't like the variation in histograms...
    #      I'll set the range of the histogram with my breaks.
#   if (symkey) {
#     max.raw <- max(abs(c(x, breaks)), na.rm = TRUE)
#     min.raw <- -max.raw
#     tmpbreaks[1] <- -max(abs(x))
#     tmpbreaks[length(tmpbreaks)] <- max(abs(x))
#   }
#   else {
#     min.raw <- min(x, na.rm = TRUE)
#     max.raw <- max(x, na.rm = TRUE)
#   }
# z <- seq(min.raw, max.raw, length = length(col))
    
       # previously z assumed equal spacing,
       #     INSTEAD, we'll assume that the spacing breaks into
       #     multiples of the smallest range
          min.raw <- min(tmpbreaks)
          max.raw <- max(tmpbreaks)
    
        difftemp = min(diff(tmpbreaks))
        z = seq(min(tmpbreaks)+.5*difftemp,max(tmpbreaks)-.5*difftemp,difftemp)
        image(z = matrix(z, ncol = 1), col = col, breaks = tmpbreaks, 
          xaxt = "n", yaxt = "n")
        par(usr = c(0, 1, 0, 1))
        lv <- pretty(breaks)
        xv <- scale01(as.numeric(lv), min.raw, max.raw)
        axis(1, at = xv, labels = lv)
        if (scale == "row") 
          mtext(side = 1, "Row Z-Score", line = 2)
        else if (scale == "column") 
          mtext(side = 1, "Column Z-Score", line = 2)
        else mtext(side = 1, "Value", line = 2)
        if (density.info == "density") {
          dens <- density(x, adjust = densadj, na.rm = TRUE)
          omit <- dens$x < min(breaks) | dens$x > max(breaks)
          dens$x <- dens$x[-omit]
          dens$y <- dens$y[-omit]
          dens$x <- scale01(dens$x, min.raw, max.raw)
          lines(dens$x, dens$y/max(dens$y) * 0.95, col = denscol, 
            lwd = 1)
          axis(2, at = pretty(dens$y)/max(dens$y) * 0.95, pretty(dens$y))
          title("Color Key\nand Density Plot")
          par(cex = 0.5)
          mtext(side = 2, "Density", line = 2)
        }
        else if (density.info == "histogram") {
          h <- hist(x, plot = FALSE, breaks = breaks)
          hx <- scale01(breaks, min.raw, max.raw)
          hy <- c(h$counts, h$counts[length(h$counts)])
          lines(hx, hy/max(hy) * 0.95, lwd = 1, type = "s", 
            col = denscol)
          axis(2, at = pretty(hy)/max(hy) * 0.95, pretty(hy))
          title("Color Key\nand Histogram")
          par(cex = 0.5)
          mtext(side = 2, "Count", line = 2)
        }
        else title("Color Key")
      }
      else plot.new()
      retval$colorTable <- data.frame(low = retval$breaks[-length(retval$breaks)], 
        high = retval$breaks[-1], color = retval$col)
      invisible(retval)
}