heatmap.microbe.R

### debug DEFAULTS
## image matrix
# x
## dedrogram params
# 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"
## image map params info
# 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
# key = TRUE
# keysize = 1.5
# dendrosize = 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
# colRot=FALSE
##########################################################

"heatmap.microbe" <- 
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,ColSideNote,ColSideLabels=NULL, RowSideColors, cexRow = 0.2 + 1/log10(nr), 
    cexCol = 0.2 + 1/log10(nc), labRow = NULL, labCol = NULL, 
    key = TRUE, keysize = 0.5, dendrosize=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, 
    colRot=FALSE, ...) 
{
    require(gplots)
    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 (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

##############################################################################################
## SET UP the layout
    if (missing(lhei) || is.null(lhei)) 
        lhei <- c(0.1, 4)
    if (missing(lwid) || is.null(lwid)) 
        lwid <- c(3,1)
    if (missing(lmat) || is.null(lmat)) {
        lmat <- rbind(c(NA,NA),c(1,1))
        if (key) {
            lhei <- c(keysize, 4)
            lwid <- c(2,3)
            lmat <- rbind(c(2,NA),c(1,1))
        }
        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(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( c(rep(NA, nrow(lmat) - 1), 1), lmat + 1)
            lwid <- c(0.2, lwid)
        }
        if (dendrogram %in% c("both", "row")){
            lmat <- cbind( c(rep(NA, nrow(lmat) - 1), max(lmat,na.rm=TRUE)+1), lmat)
            lwid <- c(dendrosize, lwid)        
        }
        if (dendrogram %in% c("both", "col")){
            lmat <- rbind( lmat[1,], c(rep(NA, ncol(lmat) - 2), rep.int(max(lmat,na.rm=TRUE)+1,2)), lmat[-1,])
            lhei <- c(lhei[1],dendrosize,lhei[-1])        
        }
        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)
###############################################################################################

#### PLOT out ColSideColors and RowSideColors   Figures 1 and 2
    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)
        #if (!missing(colsep))
        #    for (csep in colsep) rect(xleft = csep + 0.5, ybottom = -1, xright = csep + 0.5 + sepwidth[1], 
        #        ytop = 1, lty = 1, lwd = 1, 
        #        col = sepcolor, border = sepcolor)
        #if (!missing(ColSideNote)) 
        #    text(y = c(row(ColSideNote))-0.5, x = c(col(ColSideNote)), labels = c(ColSideNote), 
        #        col = notecol, cex = notecex)
        axis(4, 0.0, labels = ColSideLabels, las = 2, line = -0.5, tick = 0, 
            cex.axis = cexRow+0.2, font=1)

    }

#### PLOT out main image plot

    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))) {
    if ( 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)
    }
### Modified to rotate axis if requested
    axis(1, 1:nc, labels = labCol, las = ifelse(colRot,1,2), line = -0.5, tick = 0, 
        cex.axis = cexCol,font=2)
    if (!is.null(xlab)) 
        mtext(xlab, side = 1, line = margins[1] - 1.25)
### Modified font type to be italics and bold
    axis(4, iy, labels = labRow, las = 2, line = -0.5, tick = 0, 
        cex.axis = cexRow, font=4)
########
    if (!is.null(ylab)) 
        mtext(ylab, side = 4, line = margins[2] - 1.25)
    if (!missing(add.expr)) 
        eval(substitute(add.expr))

### Column and Row seperator
    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)

### image trace 
    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")
        }
    }

### strings to be place in image
    if (!missing(cellnote)) 
        text(x = c(row(cellnote)), y = c(col(cellnote)), labels = c(cellnote), 
            col = notecol, cex = notecex)
### Produce Title
    if (!is.null(main)) 
        title(main, cex.main = 1.5 * op[["cex.main"]])

### Plot KEY
    if (key) {
        par(mar = c(4, 0, 0, margins[2]),cex=0.7)
        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,n=11)
        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, "Percent Abundance", line = 2.2,cex=0.7)
        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, "Frequency", line = 2, font=2)
        }
#        else title("Color Key")
    }

##### Dendrograms plots 4 and 5
    par(mar = c(margins[1], 0, 0, 0))
    if (dendrogram %in% c("both", "row")) {
        plot(ddr, horiz = TRUE, axes = FALSE, yaxs = "i", leaflab = "none")
    }
    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")
    }


    retval$colorTable <- data.frame(low = retval$breaks[-length(retval$breaks)], 
        high = retval$breaks[-1], color = retval$col)
    invisible(retval)
}