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heatmap-mik-tk.R
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heatmap.mik.tk<-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, 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,srtRow = NULL, srtCol = NULL, adjRow = c(0,NA), adjCol = c(NA, 0),
offsetRow = 0.5, offsetCol = 0.5, colRow = NULL, colCol = NULL, key = TRUE, keysize = 1.5,
density.info = c("histogram", "density", "none"), denscol = tracecol, symkey = min(x < 0, na.rm = TRUE), densadj = 0.25, main = NULL, xlab = NULL,
ylab = NULL, ...)
{
scale01 <- function(x, low = min(x), high = max(x)) {
x <- (x - low)/(high - low)
x
}
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 (!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 ((Colv == "Rowv") && (!isTRUE(Rowv) || is.null(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 dendrogram <- "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
}
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") {
x <- sweep(x, 1, rowMeans(x, na.rm = na.rm))
sx <- apply(x, 1, sd, na.rm = na.rm)
x <- sweep(x, 1, sx, "/")
}
else if (scale == "column") {
x <- sweep(x, 2, colMeans(x, na.rm = na.rm))
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))
breaks <- 16
else breaks <- length(col) + 1
if (length(breaks) == 1) {
breaks <- seq(min(x, na.rm = na.rm), max(x, na.rm = na.rm),
length = breaks)
}
nbr <- length(breaks)
ncol <- length(breaks) - 1
if (class(col) == "function")
col <- col(ncol)
else if (is.character(col) && length(col) == 1)
col <- do.call(col, list(ncol))
min.breaks <- min(breaks)
max.breaks <- max(breaks)
x[] <- ifelse(x < min.breaks, min.breaks, x)
x[] <- ifelse(x > max.breaks, max.breaks, x)
lmat <- rbind(4:3, 2:1)
lhei <- lwid <- c(keysize, 4)
if (!missing(ColSideColors)) {
# if (!is.character(ColSideColors) || length(ColSideColors) !=
# nc)
# stop("'ColSideColors' must be a character vector of length ncol(x)")
if(is.null(nrow(ColSideColors))){
lmat <- rbind(lmat[1, ] + 1, c(NA, 1), lmat[2, ] + 1)
lhei <- c(lhei[1], 0.2, lhei[2])
}
else{
lmat <- rbind(lmat[1, ] + nrow(ColSideColors),
t(matrix(as.numeric(unlist(strsplit(paste("NA",1:nrow(ColSideColors))," "))),2,nrow(ColSideColors))),
lmat[2, ] + nrow(ColSideColors))
# lhei <- c(lhei[1], 0.2*nrow(ColSideColors), lhei[2])
lhei <- c(lhei[1], rep(0.2,nrow(ColSideColors)), 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
op <- par(no.readonly = TRUE)
on.exit(par(op))
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
if (!missing(RowSideColors)) {
par(mar = c(margins[1], 0, 0, 0.5))
image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
}
if (!missing(ColSideColors)) {
if(is.null(nrow(ColSideColors))) {
par(mar = c(0.5, 0, 0, margins[2]))
image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
}
else{
for(kk in 1:nrow(ColSideColors)){
par(mar = c(0.5, 0, 0, margins[2]))
image(cbind(1:nc), col = ColSideColors[kk,colInd], axes = FALSE)
axis(4, 0, labels = rownames(ColSideColors)[kk], las = 2,
line = -0.5, tick = 0, cex.axis = cexCol)
}
}
}
par(mar = c(margins[1], 0, 0, margins[2]))
if (!symm || scale != "none") {
x <- t(x)
cellnote <- t(cellnote)
}
if (revC) {
iy <- nr:1
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, ...)
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) && is.null(colCol))
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.null(srtCol) || 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, col = colCol)
print(colCol)
par(xpd = xpd.orig)
}
else warning("Invalid value for srtCol ignored.")
}
if (is.null(srtRow) && is.null(colRow)) {
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.null(srtRow) || 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, col = colRow)
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 = 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 = ncol(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")) {
for (i in colInd) {
if (!is.null(vline)) {
vline.vals <- scale01(vline, min.scale, max.scale)
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")) {
for (i in rowInd) {
if (!is.null(hline)) {
hline.vals <- scale01(hline, min.scale, max.scale)
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)
if (symkey) {
max.raw <- max(abs(x), na.rm = TRUE)
min.raw <- -max.raw
}
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 = breaks,
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()
invisible(list(rowInd = rowInd, colInd = colInd))
}