#' Title
#'
#' @param x
#' @param Rowv
#' @param Colv
#' @param distfun
#' @param hclustfun
#' @param dendrogram
#' @param symm
#' @param scale
#' @param na.rm
#' @param revC
#' @param add.expr
#' @param breaks
#' @param symbreaks
#' @param col
#' @param colsep
#' @param rowsep
#' @param sepcolor
#' @param sepwidth
#' @param cellnote
#' @param notecex
#' @param notecol
#' @param na.color
#' @param trace
#' @param tracecol
#' @param hline
#' @param vline
#' @param linecol
#' @param margins
#' @param ColSideColors
#' @param RowSideColors
#' @param cexRow
#' @param cexCol
#' @param labRow
#' @param labCol
#' @param key
#' @param keysize
#' @param density.info
#' @param denscol
#' @param symkey
#' @param densadj
#' @param main
#' @param xlab
#' @param ylab
#' @param lmat
#' @param lhei
#' @param lwid
#' @param ...
#'
#' @return
#' @export
#'
#' @examples
heatmap.4 <- 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,
key = TRUE, keysize = 1, 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 = 0.01, lwid = NULL,
...)
{
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
}
if (exists("hcc")) {retval$hcc <- hcc}
if (exists("hcr")) {retval$hcr <- hcr}
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)) #|| ncol(ColSideColors) != nc)
stop("'ColSideColors' must be a character ") #vector of length ncol(x)")
lmat <- rbind(lmat[1, ] + 1, c(NA, 1), lmat[2, ] + 1)
if (is.vector(ColSideColors)) nnn=1
else nnn=nrow(ColSideColors)
lhei <- c(lhei[1], nnn*0.1, lhei[2])
}
if (!missing(RowSideColors)) {
if (!is.character(RowSideColors)) #|| length(RowSideColors) != nr)
stop("'RowSideColors' must be a character ")
if (is.vector(RowSideColors)) nnn=1
else nnn=ncol(RowSideColors)
lmat <- cbind(lmat[, 1] + 1, c(rep(NA, nrow(lmat) - 1), 1), lmat[, 2] + 1)
lwid <- c(lwid[1], nnn*0.1, 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)) {
par(mar = c(margins[1], 0, 0, 0.5))
if (is.vector(RowSideColors)) {
image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
}
if (is.matrix(RowSideColors)) {
jk.row = RowSideColors
jk.xy = matrix(which(jk.row != "0"), dim(jk.row))
colnames(jk.xy) <- colnames(jk.row)
#image(t(jk.xy), col = jk.row[rowInd, ], xaxt="n", yaxt="n")
#grid(nx=ncol(jk.row), ny=nrow(jk.row), lty=1, col="black")
image(t(jk.xy), col = jk.row[rowInd, ], xaxt="n", yaxt="n")
# axis(3, at=seq(0,1,1/(ncol(jk.xy)-1)),labels=colnames(jk.xy), las=2, cex.axis = cexCol, tick=0)
axis(1, at=seq(0,1,1/(ncol(jk.xy)-1)),labels=colnames(jk.xy), las=2, cex.axis = cexCol, tick=0)
# grid(nx=ncol(jk.row), ny=nrow(jk.row), lty=1, col="black")
}
}
if (!missing(ColSideColors)) {
par(mar = c(0.5, 0, 0, margins[2]))
if (is.vector(ColSideColors)) {
image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
}
if (is.matrix(ColSideColors)) {
jk.col = ColSideColors
jk.xy = matrix(which(jk.col != "0"), dim(jk.col))
rownames(jk.xy) <- rownames(jk.col)
jk.xy=t(jk.xy)
image(jk.xy, col = jk.col[, colInd], axes = FALSE)
axis(2, at=seq(0,1,1/(ncol(jk.xy)-1)),labels=colnames(jk.xy), las=2, tick=FALSE)
}
}
par(mar = c(margins[1], 0, 0, margins[2]))
if (!symm || scale != "none") {
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)
# }
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(3, 1:nc, labels = labCol, las = 2, line = -0.5, tick = 0,
# cex.axis = cexCol)
if (!is.null(xlab))
mtext(xlab, side = 3, 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, 3, 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))
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))
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)
mtext(side = 1, "", 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 and Density Plot", cex=0.25)
#title("Color Key and Density Plot", cex=0.25)
par(cex = 0.25)
mtext(side = 2, "", line = 2)
#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$counts)])
lines(hx, hy/max(hy) * 0.95, lwd = 1, type = "s",
col = denscol)
axis(2, at = pretty(hy)/max(hy) * 0.95, pretty(hy))
#title("Color Key and Histogram", cex=0.25)
title("", cex=0.25)
par(cex = 0.25)
mtext(side = 2, "", line = 2)
#mtext(side = 2, "Count", line = 2)
}
else { title("", cex=0.25)
#title("Color Key", cex=0.25)
}
}
else plot.new()
retval$colorTable <- data.frame(low = retval$breaks[-length(retval$breaks)],
high = retval$breaks[-1], color = retval$col)
invisible(retval)
}
#' Title
#'
#' @param norm.dat
#' @param cl
#' @param markers
#' @param prefix
#' @param hc
#' @param gene.hc
#' @param centered
#' @param labels
#' @param sorted
#' @param by.cl
#' @param ColSideColors
#' @param maxValue
#' @param min.sep
#' @param main
#' @param height
#' @param width
#' @param legend.dat
#'
#' @return
#' @export
#'
#' @examples
plot_cl_heatmap4 <- function(norm.dat, cl, markers, prefix=NULL,hc=NULL, gene.hc=NULL,centered=FALSE,labels=names(cl),sorted=FALSE,by.cl=TRUE,ColSideColors=NULL,maxValue=5,min.sep=4,main="", height=13, width=9, legend.dat=NULL)
{
select.cells=names(cl)
tmp.dat = as.matrix(norm.dat[markers,select.cells,drop=F])
if(!is.null(ColSideColors)){
ColSideColors=ColSideColors[, select.cells,drop=F]
}
if(centered){
tmp.dat = tmp.dat - rowMeans(tmp.dat)
breaks=c(min(min(tmp.dat)-0.1,-maxValue), seq(-maxValue,maxValue, length.out=99), max(max(tmp.dat)+1))
}
else{
tmp.dat = tmp.dat/pmax(rowMaxs(tmp.dat), 1)
breaks=c(0, seq(0.05, 1, length.out=100))
}
colnames(tmp.dat)=labels
cexCol = min(70/ncol(tmp.dat),1)
cexRow = min(60/nrow(tmp.dat),1)
if(is.null(gene.hc)){
gene.hc = hclust(dist(tmp.dat), method="ward.D")
}
if(is.null(hc) & !sorted & length(select.cells)< 2000){
hc = hclust(dist(t(tmp.dat)), method="ward.D")
}
col = blue.red(150)[51:150]
if(!is.null(prefix)){
pdf(paste(prefix,"pdf",sep="."), height=height, width=width)
}
if(by.cl){
if(sorted){
ord = 1:length(cl)
}
else{
if(!is.null(hc)){
ord = order(cl, order(hc$order))
}
else{
ord = order(cl)
}
}
sep = cl[ord]
sep=which(sep[-1]!=sep[-length(sep)])
sep = c(sep[1], sep[which(sep[-1] - sep[-length(sep)] >=min.sep)+1])
heatmap.4(tmp.dat[,ord],Rowv=as.dendrogram(gene.hc), Colv=NULL, col=col, trace="none", dendrogram="none", cexCol=cexCol,cexRow=cexRow,ColSideColors=ColSideColors[,ord],breaks=breaks,colsep=sep, sepcolor="black",main=main)
cells.order=colnames(tmp.dat)[ord]
}
else{
heatmap.4(tmp.dat,Rowv=as.dendrogram(gene.hc), Colv=as.dendrogram(hc), col=col, trace="none", dendrogram="none", cexCol=cexCol,cexRow=cexRow,ColSideColors=ColSideColors,breaks=breaks,main=main)
cells.order=colnames(tmp.dat)[hc$order]
}
jet.colors <-colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan","#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
cl.col = jet.colors(length(unique(cl)))[as.factor(cl)]
leg.clms = ceiling(length(unique(cl))/8)
legend(x=0,y=0.67,
legend=c("Female", "Male"),
fill=c("hotpink1", "dodgerblue3"),
cex=.7,
title="Gender",bty="n")
leg.region=as.matrix(legend.dat[[2]])
region.col=ColSideColors["Region",]
leg.region.u =leg.region[leg.region %in% region.col,]
leg.region.u=as.data.frame(leg.region.u)
leg.cols=factor(leg.region.u$leg.region.u, levels=unique(leg.region.u$leg.region.u))
#leg.region.u= leg.region.u %>% rownames_to_column("Region")
leg.cols= as.character(leg.cols)
reg.clms=ceiling(length(leg.cols)/8)
legend(x=0.4,y=1.0,
legend=rownames(leg.region.u),
fill=leg.cols,
cex=.7,
title="Region",
ncol=reg.clms)
#jet.colors <-colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan","#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
cl.col = rainbow(length(unique(cl)))[as.factor(cl)]
leg.clms = ceiling(length(unique(cl))/15)
legend(x=0,y=0.6,
legend = unique(cl),
fill=unique(cl.col),
cex=.7,
title="Cluster",
ncol= leg.clms,
bty="n"
)
if(!is.null(prefix)){
dev.off()
}
return(cells.order)
}
#' Title
#'
#' @param cl
#' @param norm.dat
#' @param prefix
#' @param plot
#' @param col
#' @param max.cl.size
#' @param markers
#' @param de.genes
#' @param main
#' @param height
#' @param width
#' @param min.sep
#' @param legend.dat
#' @param ...
#'
#' @return
#' @export
#'
#' @examples
display_cl4 <- function(cl, norm.dat,prefix=NULL, plot=!is.null(prefix), col=NULL, max.cl.size=NULL,markers=NULL,de.genes=NULL, main="",height=13, width=9, min.sep=10, legend.dat=NULL, ...)
{
select.cells=names(cl)
jet.colors <-colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan","#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
if(!is.null(max.cl.size)){
tmp.cells = sample_cells(cl, max.cl.size)
cl = cl[tmp.cells]
}
select.cells=names(cl)
cl.col = rainbow(length(unique(cl)))[as.factor(cl)]
tmp.col =t(as.matrix(cl.col, ncol=1))
colnames(tmp.col)= select.cells
rownames(tmp.col)= c("cluster")
if(!is.null(col)){
tmp.col = rbind(tmp.col, col[,select.cells])
}
tmp.dat = as.matrix(norm.dat[,names(cl)])
if(is.null(markers)){
tmp = select_markers(tmp.dat,cl, de.genes=de.genes, ...)
markers = tmp$markers
de.genes=tmp$de.genes
}
cells_order=NULL
if(plot & !is.null(markers)){
cells_order=plot_cl_heatmap4(tmp.dat, cl, markers, ColSideColors=tmp.col,legend.dat=legend.dat, prefix=prefix, labels=NULL, by.cl=TRUE,min.sep=min.sep,main=main, height=height, width=width)
}
return(list(markers=markers,de.genes=de.genes, cells_order= cells_order))
}
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