R/heatmap.mark.R

In rnaseqWrapper: Wrapper for several R packages and scripts to automate RNA-seq analysis

heatmap.mark <-
function (x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE, 
                          distfun = dist, hclustfun = hclust, 
                          dendrogram = c("both", "row", "column", "none"), 
                          symm = FALSE, scale = c("row","none", "column"),
                          na.rm = TRUE, revC = identical(Colv,"Rowv"),
                          add.expr, breaks, 
                          symbreaks = min(x < 0, na.rm = TRUE) || scale != "none",
                          col = "rnaSeqColors", colsep, rowsep, 
                          sepcolor = "white", sepwidth = c(0.05, 0.05), cellnote, notecex = 1, 
                          notecol = "cyan", na.color = par("bg"), 
                          trace = c("none","column", "row", "both"), 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, 
                          srtRow = NULL, srtCol = NULL, adjRow = c(0, NA), 
                          adjCol = c(NA, 0), offsetRow = 0.5, offsetCol = 0.5,
                          key = TRUE, keysize = 1.5, 
                          density.info = c("none","histogram", "density"), 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, 
                          scaleLabel=NULL, plotNew = TRUE ,
                          ...) 
{
  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 != "rnaSeqColors") 
    col <- get(col, mode = "function")
  if (length(col) == 1 && is.character(col) && col == "rnaSeqColors") 
    col <- colorRampPalette(c("white","darkblue"))(100)
  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 (class(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)
  
  
  ## To allow suppressing of layout to enable multiple plots
  if(plotNew){
    layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
    on.exit(par(op))
  }

  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)
  }
  par(mar = c(margins[1], 0, 0, margins[2]))
  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
  image(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 + 
          c(0, nr), axes = FALSE, xlab = "", ylab = "", col = col, 
        breaks = breaks, ...)
  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)
  }
  if (is.null(srtCol)) 
    axis(1, 1:nc, labels = labCol, las = 2, line = -0.5 + 
           offsetCol, tick = 0, cex.axis = cexCol, hadj = adjCol[1], 
         padj = adjCol[2])
  else {
    if (is.numeric(srtCol)) {
      if (missing(adjCol) || is.null(adjCol)) 
        adjCol = c(1, NA)
      xpd.orig <- par("xpd")
      par(xpd = NA)
      xpos <- axis(1, 1:nc, labels = rep("", nc), las = 2, 
                   tick = 0)
      text(x = xpos, y = par("usr")[3] - (1 + offsetCol) * 
             strheight("M"), labels = labCol, adj = adjCol, 
           cex = cexCol, srt = srtCol)
      par(xpd = xpd.orig)
    }
    else warning("Invalid value for srtCol ignored.")
  }
  if (is.null(srtRow)) {
    axis(4, iy, labels = labRow, las = 2, line = -0.5 + offsetRow, 
         tick = 0, cex.axis = cexRow, hadj = adjRow[1], padj = adjRow[2])
  }
  else {
    if (is.numeric(srtRow)) {
      xpd.orig <- par("xpd")
      par(xpd = NA)
      ypos <- axis(4, iy, labels = rep("", nr), las = 2, 
                   line = -0.5, tick = 0)
      text(x = par("usr")[2] + (1 + offsetRow) * strwidth("M"), 
           y = ypos, labels = labRow, adj = adjRow, cex = cexRow, 
           srt = srtRow)
      par(xpd = xpd.orig)
    }
    else warning("Invalid value for srtRow ignored.")
  }
  if (!is.null(xlab)) 
    mtext(xlab, side = 1, line = margins[1] - 1.25)
  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 = 0, 
                              xright = csep + 0.5 + sepwidth[1], ytop = ncol(x) + 
                                1, 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
    if (symkey) {
      max.raw <- max(abs(c(x, breaks)), na.rm = TRUE)
      min.raw <- -max.raw
      tmpbreaks[1] <- -max(abs(x), na.rm = TRUE)
      tmpbreaks[length(tmpbreaks)] <- max(abs(x), na.rm = TRUE)
    }
    else {
      min.raw <- min(x, na.rm = TRUE)
      max.raw <- max(x, na.rm = TRUE)
    }
    z <- seq(min.raw, max.raw, length = length(col))
    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(!is.null(scaleLabel))
      mtext(side = 1, scaleLabel, line = 2)
    else{
      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)
}