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heatmap.3.R
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heatmap.3.R
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# EXAMPLE USAGE
library("gplots")
library("devtools")
source_url("https://raw.githubusercontent.com/Shicheng-Guo/GscRbasement/master/heatmap3.R")
# example of colsidecolors rowsidecolors (single column, single row)
mat <- matrix(1:100, byrow=T, nrow=10) # x is a matrix of observations by variables.
column_annotation <- sample(c("red", "blue", "green"), 10, replace=T)
column_annotation <- as.matrix(column_annotation)
colnames(column_annotation) <- c("Variable X")
row_annotation <- sample(c("red", "blue", "green"), 10, replace=T)
row_annotation <- as.matrix(t(row_annotation))
rownames(row_annotation) <- c("Variable Y")
heatmap3(mat, RowSideColors=row_annotation, ColSideColors=column_annotation)
# multiple column and row -- Example A (Remember clab and rlab should be color matrix, not character, not numeric)
mat <- matrix(1:100, byrow=T, nrow=10) # x is a matrix of observations by variables.
column_annotation <- matrix(sample(c("red", "blue", "green"), 20, replace=T), ncol=2)
colnames(column_annotation) <- c("Variable X1", "Variable X2")
row_annotation <- matrix(sample(c("red", "blue", "green"), 20, replace=T), nrow=2)
rownames(row_annotation) <- c("Variable Y1", "Variable Y2")
heatmap3(mat, RowSideColors=row_annotation, ColSideColors=column_annotation)
# multiple column and row -- Example B (Remember clab and rlab should be color matrix, not character, not numeric)
# you can use the following way to creat color based rlab and clab
# clab<-data.matrix(apply(clab,2,function(x) as.numeric(as.factor(x)))) # change to numeric
# clab<-data.matrix(apply(rlab,1,function(x) as.numeric(as.factor(x)))) # change to numeric
# clab<-apply(clab,2,function(x) rainbow(length(unique(x)))[x]) # assign color by the numeric
# rlab<-apply(rlab,1,function(x) rainbow(length(unique(x)))[x]) # assign color by the numeric
# colnames(clab)=c("S1","S2","S3","S4")
# rownames(clab)=c("V1","V2","V3","V4","V5")
# multiple column and row -- Example C with multiple legends
# pdf(file="serum-2i-heatmap3.pdf")
# main_title="Serum vs 2i ScRNAseq"
# par(cex.main=1,cex.axis=0.5)
# heatmap.3(data, hclustfun=myclust, distfun=mydist, na.rm = TRUE, scale="column", dendrogram="both", margins=c(6,12),
# Rowv=TRUE, Colv=F, ColSideColors=clab, symbreaks=FALSE, key=TRUE, symkey=FALSE,cex.key.xlab=0.7,
# density.info="none", trace="none", main=main_title, labCol=FALSE, labRow=rownames(data), cexRow=0.5, col=rev(rainbow(20)),
# ColSideColorsSize=6, KeyValueName="Gene Expression")
# legend("topright",legend=c("A","B"),fill=c("red","blue"), border=FALSE, bty="n", y.intersp = 0.7, cex=0.7)
# legend("right",legend=c("A","B"),fill=c("red","blue"), border=FALSE, bty="n", y.intersp = 0.7, cex=0.7)
# legend("bottomright",legend=c("A","B"),fill=c("red","blue"), border=FALSE, bty="n", y.intersp = 0.7, cex=0.7)
# dev.off()
# adjust cex.key.axis by par(cex.axis), for example: par(cex.axis=0.5)
pdf(file="serum-2i-heatmap3.pdf")
par(cex.axis=0.5)
heatmap.3(mat, RowSideColors=row_annotation, ColSideColors=column_annotation)
dev.off()
# CODE
heatmap.3 <- 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 = max(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("none", "column","row", "both"),
tracecol = "cyan",
hline = median(breaks),
vline = median(breaks),
linecol = tracecol,
margins = c(5,5),
ColSideColors,
RowSideColors,
side.height.fraction=0.3,
cexRow = 0.2 + 1/log10(nr),
cexCol = 0.2 + 1/log10(nc),
labRow = NULL,
labCol = NULL,
key = TRUE,
keysize = 1.5,
density.info = c("none", "histogram", "density"),
denscol = tracecol,
symkey = max(x < 0, na.rm = TRUE) || symbreaks,
densadj = 0.25,
main = NULL,
xlab = NULL,
ylab = NULL,
lmat = NULL,
lhei = NULL,
lwid = NULL,
NumColSideColors = 1,
NumRowSideColors = 1,
KeyValueName="Value",...){
invalid <- function (x) {
if (missing(x) || is.null(x) || length(x) == 0)
return(TRUE)
if (is.list(x))
return(all(sapply(x, invalid)))
else if (is.vector(x))
return(all(is.na(x)))
else return(FALSE)
}
x <- as.matrix(x)
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
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.matrix(ColSideColors))
#stop("'ColSideColors' must be a matrix")
if (!is.character(ColSideColors) || nrow(ColSideColors) != nc)
stop("'ColSideColors' must be a matrix of nrow(x) rows")
lmat <- rbind(lmat[1, ] + 1, c(NA, 1), lmat[2, ] + 1)
#lhei <- c(lhei[1], 0.2, lhei[2])
lhei=c(lhei[1], side.height.fraction*NumColSideColors, lhei[2])
}
if (!missing(RowSideColors)) {
#if (!is.matrix(RowSideColors))
#stop("'RowSideColors' must be a matrix")
if (!is.character(RowSideColors) || ncol(RowSideColors) != nr)
stop("'RowSideColors' must be a matrix of ncol(x) columns")
lmat <- cbind(lmat[, 1] + 1, c(rep(NA, nrow(lmat) - 1), 1), lmat[,2] + 1)
#lwid <- c(lwid[1], 0.2, lwid[2])
lwid <- c(lwid[1], side.height.fraction*NumRowSideColors, 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)
if (!missing(RowSideColors)) {
if (!is.matrix(RowSideColors)){
par(mar = c(margins[1], 0, 0, 0.5))
image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
} else {
par(mar = c(margins[1], 0, 0, 0.5))
rsc = t(RowSideColors[,rowInd, drop=F])
rsc.colors = matrix()
rsc.names = names(table(rsc))
rsc.i = 1
for (rsc.name in rsc.names) {
rsc.colors[rsc.i] = rsc.name
rsc[rsc == rsc.name] = rsc.i
rsc.i = rsc.i + 1
}
rsc = matrix(as.numeric(rsc), nrow = dim(rsc)[1])
image(t(rsc), col = as.vector(rsc.colors), axes = FALSE)
if (length(colnames(RowSideColors)) > 0) {
axis(1, 0:(dim(rsc)[2] - 1)/(dim(rsc)[2] - 1), colnames(RowSideColors), las = 2, tick = FALSE)
}
}
}
if (!missing(ColSideColors)) {
if (!is.matrix(ColSideColors)){
par(mar = c(0.5, 0, 0, margins[2]))
image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
} else {
par(mar = c(0.5, 0, 0, margins[2]))
csc = ColSideColors[colInd, , drop=F]
csc.colors = matrix()
csc.names = names(table(csc))
csc.i = 1
for (csc.name in csc.names) {
csc.colors[csc.i] = csc.name
csc[csc == csc.name] = csc.i
csc.i = csc.i + 1
}
csc = matrix(as.numeric(csc), nrow = dim(csc)[1])
image(csc, col = as.vector(csc.colors), axes = FALSE)
if (length(colnames(ColSideColors)) > 0) {
axis(2, 0:(dim(csc)[2] - 1)/max(1,(dim(csc)[2] - 1)), colnames(ColSideColors), las = 2, tick = 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))) { # load library(gplots)
mmat <- ifelse(is.na(x), 1, NA)
image(1:nc, 1:nr, mmat, axes = FALSE, xlab = "", ylab = "",
col = na.color, add = TRUE)
}
axis(1, 1:nc, labels = labCol, las = 2, line = -0.5, tick = 0,
cex.axis = cexCol)
if (!is.null(xlab))
mtext(xlab, side = 1, line = margins[1] - 1.25)
axis(4, iy, labels = labRow, las = 2, line = -0.5, tick = 0,
cex.axis = cexRow)
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
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 (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, KeyValueName, 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)
}