--- a
+++ b/R/pheatmapwh.R
@@ -0,0 +1,818 @@
+## The code in this file is based on that in the file pheatmap.r in the CRAN package pheatmap by  Raivo Kolde <rkolde@gmail.com>,
+##    with minor (but important to us) formatting modifications.
+
+## These global parameters were introduced by Wolfgang Huber. In Raivo's code, they were hardcoded numbers
+gaps_width <- c( col = 26, row = 10)
+horizonal_annot_mat <- 0 # 8
+
+lo = function(rown, coln, nrow, ncol, cellheight = NA, cellwidth = NA, treeheight_col, treeheight_row, legend, annotation_row, annotation_col, annotation_colors, annotation_legend, main, fontsize, fontsize_row, fontsize_col, gaps_row, gaps_col, ...){
+    # Get height of colnames and length of rownames
+    if(!is.null(coln[1])){
+        t = c(coln, colnames(annotation_row))
+        longest_coln = which.max(strwidth(t, units = 'in'))
+        gp = list(fontsize = fontsize_col, ...)
+        coln_height = unit(1, "grobheight", textGrob(t[longest_coln], rot = 90, gp = do.call(gpar, gp))) + unit(10, "bigpts")
+    }
+    else{
+        coln_height = unit(5, "bigpts")
+    }
+    
+    if(!is.null(rown[1])){
+        t = c(rown, colnames(annotation_col))
+        longest_rown = which.max(strwidth(t, units = 'in'))
+        gp = list(fontsize = fontsize_row, ...)
+        rown_width = unit(1, "grobwidth", textGrob(t[longest_rown], gp = do.call(gpar, gp))) ## + unit(10, "bigpts")
+    }
+    else{
+        rown_width = unit(5, "bigpts")
+    }
+    
+    gp = list(fontsize = fontsize, ...)
+    # Legend position
+    if(!is.na2(legend)){
+        longest_break = which.max(nchar(names(legend)))
+        longest_break = unit(1.1, "grobwidth", textGrob(as.character(names(legend))[longest_break], gp = do.call(gpar, gp)))
+        title_length = unit(1.1, "grobwidth", textGrob("Scale", gp = gpar(fontface = "bold", ...)))
+        legend_width = unit(12, "bigpts") + longest_break * 1.2
+        legend_width = max(title_length, legend_width)
+    }
+    else{
+        legend_width = unit(0, "bigpts")
+    }
+    
+    # Set main title height
+    if(is.na(main)){
+        main_height = unit(0, "npc")
+    }
+    else{
+        main_height = unit(1.5, "grobheight", textGrob(main, gp = gpar(fontsize = 1.3 * fontsize, ...)))
+    }
+    
+    # Column annotations
+    textheight = unit(fontsize, "bigpts")
+    
+    if(!is.na2(annotation_col)){
+        # Column annotation height 
+        annot_col_height = ncol(annotation_col) * (textheight + unit(2, "bigpts")) + unit(horizonal_annot_mat, "bigpts")
+        
+        # Width of the correponding legend
+        t = c(as.vector(as.matrix(annotation_col)), colnames(annotation_col)) 
+        annot_col_legend_width = unit(1.2, "grobwidth", textGrob(t[which.max(nchar(t))], gp = gpar(...))) + unit(12, "bigpts")
+        if(!annotation_legend){
+            annot_col_legend_width = unit(0, "npc")
+        }
+    }
+    else{
+        annot_col_height = unit(0, "bigpts")
+        annot_col_legend_width = unit(0, "bigpts")
+    }
+    
+    # Row annotations
+    if(!is.na2(annotation_row)){
+        # Row annotation width 
+        annot_row_width = ncol(annotation_row) * (textheight + unit(2, "bigpts")) + unit(2, "bigpts")
+        
+        # Width of the correponding legend
+        t = c(as.vector(as.matrix(annotation_row)), colnames(annotation_row)) 
+        annot_row_legend_width = unit(1.2, "grobwidth", textGrob(t[which.max(nchar(t))], gp = gpar(...))) + unit(12, "bigpts")
+        if(!annotation_legend){
+            annot_row_legend_width = unit(0, "npc")
+        }
+    }
+    else{
+        annot_row_width = unit(0, "bigpts")
+        annot_row_legend_width = unit(0, "bigpts")
+    }
+    
+    annot_legend_width = max(annot_row_legend_width, annot_col_legend_width)
+    
+    # Tree height
+    treeheight_col = unit(treeheight_col, "bigpts") + unit(5, "bigpts")
+    treeheight_row = unit(treeheight_row, "bigpts") + unit(5, "bigpts") 
+    
+    # Set cell sizes
+    mat_width = if(is.na(cellwidth)){
+        unit(1, "npc") - rown_width - legend_width - treeheight_row - annot_row_width - annot_legend_width 
+    } else{
+        unit(cellwidth * ncol, "bigpts") + length(gaps_col) * unit(gaps_width["col"], "bigpts")
+    }
+    
+    mat_height = if(is.na(cellheight)){
+        unit(1, "npc") - main_height - coln_height - treeheight_col - annot_col_height
+    } else{
+        unit(cellheight * nrow, "bigpts") + length(gaps_row) * unit(gaps_width["row"], "bigpts")
+    }    
+    
+    # Produce gtable
+    gt = gtable(widths = unit.c(             treeheight_row, annot_row_width,   mat_width, rown_width, legend_width, annot_legend_width),
+               heights = unit.c(main_height, treeheight_col, annot_col_height, mat_height, coln_height), vp = viewport(gp = do.call(gpar, gp)))
+    
+    cw = convertWidth( mat_width  - (length(gaps_col) * unit(gaps_width["col"], "bigpts")), "bigpts", valueOnly = TRUE) / ncol
+    ch = convertHeight(mat_height - (length(gaps_row) * unit(gaps_width["row"], "bigpts")), "bigpts", valueOnly = TRUE) / nrow
+    
+    # Return minimal cell dimension in bigpts to decide if borders are drawn
+    mindim = min(cw, ch) 
+    
+    res = list(gt = gt, mindim = mindim)
+    
+    return(res)
+}
+
+find_coordinates = function(n, gaps, m = 1:n, what) {
+    if (length(gaps) == 0)
+        return(list(coord = unit(m / n, "npc"), size = unit(1 / n, "npc") ))
+
+    if(max(gaps) > n)
+        stop("Gaps do not match with matrix size")
+
+    size = (1 / n) * (unit(1, "npc") - length(gaps) * unit(gaps_width[what], "bigpts"))
+    
+    gaps2 = apply(sapply(gaps, function(gap, x){x > gap}, m), 1, sum) 
+    coord = m * size + (gaps2 * unit(gaps_width[what], "bigpts"))
+    
+    return(list(coord = coord, size = size))
+}
+
+draw_dendrogram = function(hc, gaps, horizontal = TRUE){
+    h = hc$height / max(hc$height) / 1.05
+    m = hc$merge
+    o = hc$order
+    n = length(o)
+
+    m[m > 0] = n + m[m > 0] 
+    m[m < 0] = abs(m[m < 0])
+
+    dist = matrix(0, nrow = 2 * n - 1, ncol = 2, dimnames = list(NULL, c("x", "y"))) 
+    dist[1:n, 1] = 1 / n / 2 + (1 / n) * (match(1:n, o) - 1)
+
+    for(i in 1:nrow(m)){
+        dist[n + i, 1] = (dist[m[i, 1], 1] + dist[m[i, 2], 1]) / 2
+        dist[n + i, 2] = h[i]
+    }
+    
+    draw_connection = function(x1, x2, y1, y2, y){
+        res = list(
+            x = c(x1, x1, x2, x2),
+            y = c(y1, y, y, y2)
+        )
+        
+        return(res)
+    }
+    
+    x = rep(NA, nrow(m) * 4)
+    y = rep(NA, nrow(m) * 4)
+    id = rep(1:nrow(m), rep(4, nrow(m)))
+    
+    for(i in 1:nrow(m)){
+        c = draw_connection(dist[m[i, 1], 1], dist[m[i, 2], 1], dist[m[i, 1], 2], dist[m[i, 2], 2], h[i])
+        k = (i - 1) * 4 + 1
+        x[k : (k + 3)] = c$x
+        y[k : (k + 3)] = c$y
+    }
+    
+    x = find_coordinates(n, gaps, x * n, what = ifelse(horizontal, "col", "row"))$coord
+    y = unit(y, "npc")
+    
+    if(!horizontal){
+        a = x
+        x = unit(1, "npc") - y
+        y = unit(1, "npc") - a
+    }
+    res = polylineGrob(x = x, y = y, id = id)
+    
+    return(res)
+}
+
+draw_matrix = function(matrix, border_color, gaps_rows, gaps_cols, fmat, fontsize_number, number_color){
+    n = nrow(matrix)
+    m = ncol(matrix)
+    
+    coord_x = find_coordinates(m, gaps_cols, what = "col")
+    coord_y = find_coordinates(n, gaps_rows, what = "row")
+    
+    x = coord_x$coord - 0.5 * coord_x$size
+    y = unit(1, "npc") - (coord_y$coord - 0.5 * coord_y$size)
+    
+    coord = expand.grid(y = y, x = x)
+    
+    res = gList()
+    
+    res[["rect"]] = rectGrob(x = coord$x, y = coord$y, width = coord_x$size, height = coord_y$size, gp = gpar(fill = matrix, col = border_color))
+    
+    if(attr(fmat, "draw")){
+        res[["text"]] = textGrob(x = coord$x, y = coord$y, label = fmat, gp = gpar(col = number_color, fontsize = fontsize_number))
+    }
+    
+    res = gTree(children = res)
+    
+    return(res)
+}
+
+draw_colnames = function(coln, gaps, ...){
+    coord = find_coordinates(length(coln), gaps, what = "col")
+    x = coord$coord - 0.5 * coord$size
+    
+    res = textGrob(coln, x = x, y = unit(1, "npc") - unit(3, "bigpts"), vjust = 0.5, hjust = 0, rot = 270, gp = gpar(...))
+    
+    return(res)
+}
+
+draw_rownames = function(rown, gaps, ...){
+    coord = find_coordinates(length(rown), gaps, what = "row")
+    y = unit(1, "npc") - (coord$coord - 0.5 * coord$size)
+    
+    res = textGrob(rown, x = unit(3, "bigpts"), y = y, vjust = 0.5, hjust = 0, gp = gpar(...))
+    
+    return(res)
+}
+
+draw_legend = function(color, breaks, legend, ...){
+    height = min(unit(1, "npc"), unit(150, "bigpts"))
+    
+    legend_pos = (legend - min(breaks)) / (max(breaks) - min(breaks))
+    legend_pos = height * legend_pos + (unit(1, "npc") - height)
+    
+    breaks = (breaks - min(breaks)) / (max(breaks) - min(breaks))
+    breaks = height * breaks + (unit(1, "npc") - height)
+    
+    h = breaks[-1] - breaks[-length(breaks)]
+    
+    rect = rectGrob(x = 0, y = breaks[-length(breaks)], width = unit(10, "bigpts"), height = h, hjust = 0, vjust = 0, gp = gpar(fill = color, col = "#FFFFFF00"))
+    text = textGrob(names(legend), x = unit(14, "bigpts"), y = legend_pos, hjust = 0, gp = gpar(...))
+    
+    res = grobTree(rect, text)
+    
+    return(res)
+}
+
+convert_annotations = function(annotation, annotation_colors){
+    new = annotation
+    for(i in seq_len(ncol(annotation))) {
+        a = annotation[, i]
+        b = annotation_colors[[colnames(annotation)[i]]]
+        if (is.character(a) || is.factor(a)){
+            a = as.character(a)
+            
+            if(length(setdiff(setdiff(a, NA), names(b))) > 0){
+                stop(sprintf("Factor levels on variable %s do not match with annotation_colors", colnames(annotation)[i]))
+            }
+            new[, i] = b[a]
+        }
+        else{
+            a = cut(a, breaks = 100)
+            new[, i] = colorRampPalette(b)(100)[a]
+        }
+    }
+    return(as.matrix(new))
+}
+
+draw_annotations = function(converted_annotations, border_color, gaps, fontsize, horizontal){
+    n = ncol(converted_annotations)
+    m = nrow(converted_annotations)
+    
+    coord_x = find_coordinates(m, gaps, what = "col")
+    
+    x = coord_x$coord - 0.5 * coord_x$size
+    
+    # y = cumsum(rep(fontsize, n)) - 4 + cumsum(rep(2, n))
+    y = cumsum(rep(fontsize, n)) + cumsum(rep(2, n)) - fontsize / 2 + 1 
+    y = unit(y, "bigpts")
+    
+    if (horizontal) {
+        coord = expand.grid(x = x, y = y)
+        res = rectGrob(x = coord$x, y = coord$y, width = coord_x$size, height = unit(fontsize, "bigpts"), gp = gpar(fill = converted_annotations, col = border_color))
+    } else{
+        a = x
+        x = unit(1, "npc") - y
+        y = unit(1, "npc") - a
+        
+        coord = expand.grid(y = y, x = x)
+        res = rectGrob(x = coord$x, y = coord$y, width = unit(fontsize, "bigpts"), height = coord_x$size, gp = gpar(fill = converted_annotations, col = border_color))
+    }
+    
+    return(res)
+}
+
+draw_annotation_names = function(annotations, fontsize, horizontal){
+    n = ncol(annotations)
+    
+    x = unit(3, "bigpts")
+    
+    y = cumsum(rep(fontsize, n)) + cumsum(rep(2, n)) - fontsize / 2 + 1 
+    y = unit(y, "bigpts")
+    
+    if(horizontal){
+        res = textGrob(colnames(annotations), x = x, y = y, hjust = 0, gp = gpar(fontsize = fontsize, fontface = 2))
+    }
+    else{
+        a = x
+        x = unit(1, "npc") - y
+        y = unit(1, "npc") - a
+        
+        res = textGrob(colnames(annotations), x = x, y = y, vjust = 0.5, hjust = 0, rot = 270, gp = gpar(fontsize = fontsize, fontface = 2))
+    }
+    
+    return(res)
+}
+
+draw_annotation_legend = function(annotation, annotation_colors, border_color, ...){
+    y = unit(1, "npc")
+    text_height = unit(1, "grobheight", textGrob("FGH", gp = gpar(...)))
+    
+    res = gList()
+
+    ## by WH: remove those with leading blank, or "n.d."
+    columnsToDraw <- names(annotation)
+    columnsToDraw <- columnsToDraw[ !grepl("^ ", columnsToDraw) ]
+    
+    for(i in columnsToDraw) {
+        res[[i]] = textGrob(i, x = 0, y = y, vjust = 1, hjust = 0, gp = gpar(fontface = "bold", ...))
+        
+        y = y - 1.5 * text_height
+        if(is.character(annotation[[i]]) | is.factor(annotation[[i]])){
+            aci <- annotation_colors[[i]]
+            aci <- aci[ names(aci) != "n.d." ]
+            n <- length(aci)
+            yy <- y - (seq_len(n) - 1) * 2 * text_height
+            
+            res[[paste(i, "r")]] = rectGrob(x = unit(0, "npc"), y = yy, hjust = 0, vjust = 1, height = 2 * text_height, width = 2 * text_height, gp = gpar(col = border_color, fill = aci))
+            res[[paste(i, "t")]] = textGrob(names(aci), x = text_height * 2.4, y = yy - text_height, hjust = 0, vjust = 0.5, gp = gpar(...))
+            
+            y = y - n * 2 * text_height
+            
+        }
+        else{
+            yy = y - 8 * text_height + seq(0, 1, 0.25)[-1] * 8 * text_height
+            h = 8 * text_height * 0.25
+            
+            res[[paste(i, "r")]] = rectGrob(x = unit(0, "npc"), y = yy, hjust = 0, vjust = 1, height = h, width = 2 * text_height, gp = gpar(col = NA, fill = colorRampPalette(annotation_colors[[i]])(4)))
+            res[[paste(i, "r2")]] = rectGrob(x = unit(0, "npc"), y = y, hjust = 0, vjust = 1, height = 8 * text_height, width = 2 * text_height, gp = gpar(col = border_color, fill = NA))
+            
+            txt = rev(range(grid.pretty(range(annotation[[i]], na.rm = TRUE))))
+            yy = y - c(1, 7) * text_height
+            res[[paste(i, "t")]]  = textGrob(txt, x = text_height * 2.4, y = yy, hjust = 0, vjust = 0.5, gp = gpar(...))
+            y = y - 8 * text_height
+        }
+        y = y - 1.5 * text_height
+    }
+    
+    res = gTree(children = res)
+    
+    return(res)
+}
+
+draw_main = function(text, ...){
+    res = textGrob(text, gp = gpar(fontface = "bold", ...))
+    
+    return(res)
+}
+
+vplayout = function(x, y){
+    return(viewport(layout.pos.row = x, layout.pos.col = y))
+}
+
+heatmap_motor = function(matrix, border_color, cellwidth, cellheight, tree_col, tree_row, treeheight_col, treeheight_row, filename, width, height, breaks, color, legend, annotation_row, annotation_col, annotation_colors, annotation_legend, main, fontsize, fontsize_row, fontsize_col, fmat, fontsize_number, number_color, gaps_col, gaps_row, labels_row, labels_col, ...){
+    # Set layout
+    lo = lo(coln = labels_col, rown = labels_row, nrow = nrow(matrix), ncol = ncol(matrix), cellwidth = cellwidth, cellheight = cellheight, treeheight_col = treeheight_col, treeheight_row = treeheight_row, legend = legend, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = annotation_colors, annotation_legend = annotation_legend, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, gaps_row = gaps_row, gaps_col = gaps_col,  ...)
+    
+    res = lo$gt
+    mindim = lo$mindim
+    
+    if(!is.na(filename)){
+        if(is.na(height)){
+            height = convertHeight(gtable_height(res), "inches", valueOnly = T)
+        }
+        if(is.na(width)){
+            width = convertWidth(gtable_width(res), "inches", valueOnly = T)
+        }
+        
+        # Get file type
+        r = regexpr("\\.[a-zA-Z]*$", filename)
+        if(r == -1) stop("Improper filename")
+        ending = substr(filename, r + 1, r + attr(r, "match.length"))
+
+        f = switch(ending,
+            pdf = function(x, ...) pdf(x, ...),
+            png = function(x, ...) png(x, units = "in", res = 300, ...),
+            jpeg = function(x, ...) jpeg(x, units = "in", res = 300, ...),
+            jpg = function(x, ...) jpeg(x, units = "in", res = 300, ...),
+            tiff = function(x, ...) tiff(x, units = "in", res = 300, compression = "lzw", ...),
+            bmp = function(x, ...) bmp(x, units = "in", res = 300, ...),
+            stop("File type should be: pdf, png, bmp, jpg, tiff")
+        )
+        
+        # print(sprintf("height:%f width:%f", height, width))
+        
+        # gt = heatmap_motor(matrix, cellwidth = cellwidth, cellheight = cellheight, border_color = border_color, tree_col = tree_col, tree_row = tree_row, treeheight_col = treeheight_col, treeheight_row = treeheight_row, breaks = breaks, color = color, legend = legend, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = annotation_colors, annotation_legend = annotation_legend, filename = NA, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, fmat = fmat, fontsize_number =  fontsize_number, number_color = number_color, labels_row = labels_row, labels_col = labels_col, gaps_col = gaps_col, gaps_row = gaps_row, ...)
+
+        f(filename, height = height, width = width)
+        gt = heatmap_motor(matrix, cellwidth = cellwidth, cellheight = cellheight, border_color = border_color, tree_col = tree_col, tree_row = tree_row, treeheight_col = treeheight_col, treeheight_row = treeheight_row, breaks = breaks, color = color, legend = legend, annotation_col = annotation_col, annotation_row = annotation_row, annotation_colors = annotation_colors, annotation_legend = annotation_legend, filename = NA, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, fmat = fmat, fontsize_number =  fontsize_number, number_color = number_color, labels_row = labels_row, labels_col = labels_col, gaps_col = gaps_col, gaps_row = gaps_row, ...)
+        grid.draw(gt)
+        dev.off()
+        
+        return(gt)
+    }
+    
+    # Omit border color if cell size is too small 
+    if(mindim < 3) border_color = NA
+    
+    # Draw title
+    if(!is.na(main)){
+        elem = draw_main(main, fontsize = 1.3 * fontsize, ...)
+        res = gtable_add_grob(res, elem, t = 1, l = 3, name = "main")
+    }
+    
+    # Draw tree for the columns
+    if(!is.na2(tree_col) & treeheight_col != 0){
+        elem = draw_dendrogram(tree_col, gaps_col, horizontal = T)
+        res = gtable_add_grob(res, elem, t = 2, l = 3, name = "col_tree")
+    }
+    
+    # Draw tree for the rows
+    if(!is.na2(tree_row) & treeheight_row != 0){
+        elem = draw_dendrogram(tree_row, gaps_row, horizontal = F)
+        res = gtable_add_grob(res, elem, t = 4, l = 1, name = "row_tree")
+    }
+    
+    # Draw matrix
+    elem = draw_matrix(matrix, border_color, gaps_row, gaps_col, fmat, fontsize_number, number_color)
+    res = gtable_add_grob(res, elem, t = 4, l = 3, clip = "off", name = "matrix")
+    
+    # Draw colnames
+    if(length(labels_col) != 0){
+        pars = list(labels_col, gaps = gaps_col, fontsize = fontsize_col, ...)
+        elem = do.call(draw_colnames, pars)
+        res = gtable_add_grob(res, elem, t = 5, l = 3, clip = "off", name = "col_names")
+    }
+    
+    # Draw rownames
+    if(length(labels_row) != 0){
+        pars = list(labels_row, gaps = gaps_row, fontsize = fontsize_row, ...)
+        elem = do.call(draw_rownames, pars)
+        res = gtable_add_grob(res, elem, t = 4, l = 4, clip = "off", name = "row_names")
+    }
+    
+    # Draw annotation tracks on cols
+    if(!is.na2(annotation_col)){
+        # Draw tracks
+        converted_annotation = convert_annotations(annotation_col, annotation_colors)
+        elem = draw_annotations(converted_annotation, border_color, gaps_col, fontsize, horizontal = T)
+        res = gtable_add_grob(res, elem, t = 3, l = 3, clip = "off", name = "col_annotation")
+        
+        # Draw names
+        elem = draw_annotation_names(annotation_col, fontsize, horizontal = T)
+        res = gtable_add_grob(res, elem, t = 3, l = 4, clip = "off", name = "row_annotation_names")
+        
+    }
+    
+    # Draw annotation tracks on rows
+    if(!is.na2(annotation_row)){
+        # Draw tracks
+        converted_annotation = convert_annotations(annotation_row, annotation_colors)
+        elem = draw_annotations(converted_annotation, border_color, gaps_row, fontsize, horizontal = F)
+        res = gtable_add_grob(res, elem, t = 4, l = 2, clip = "off", name = "row_annotation")
+        
+        # Draw names
+        if(length(labels_col) != 0){
+            elem = draw_annotation_names(annotation_row, fontsize, horizontal = F)
+            res = gtable_add_grob(res, elem, t = 5, l = 2, clip = "off", name = "row_annotation_names")
+        }
+    }
+    
+    # Draw annotation legend
+    annotation = c(annotation_col[length(annotation_col):1], annotation_row[length(annotation_row):1])
+    annotation = annotation[unlist(lapply(annotation, function(x) !is.na2(x)))]
+    
+    if(length(annotation) > 0 & annotation_legend){
+        elem = draw_annotation_legend(annotation, annotation_colors, border_color, fontsize = fontsize, ...)
+        
+        t = ifelse(is.null(labels_row), 4, 3)
+        res = gtable_add_grob(res, elem, t = t, l = 6, b = 5, clip = "off", name = "annotation_legend")
+    }
+    
+    # Draw legend
+    if(!is.na2(legend)){
+        elem = draw_legend(color, breaks, legend, fontsize = fontsize, ...)
+        
+        t = ifelse(is.null(labels_row), 4, 3)
+        res = gtable_add_grob(res, elem, t = t, l = 5, b = 5, clip = "off", name = "legend")
+    }
+    
+    return(res)
+}
+
+generate_breaks = function(x, n, center = F){
+    if(center){
+        m = max(abs(c(min(x, na.rm = T), max(x, na.rm = T))))
+        res = seq(-m, m, length.out = n + 1)
+    }
+    else{
+        res = seq(min(x, na.rm = T), max(x, na.rm = T), length.out = n + 1)
+    }
+    
+    return(res)
+}
+
+scale_vec_colours = function(x, col = rainbow(10), breaks = NA){
+    return(col[as.numeric(cut(x, breaks = breaks, include.lowest = T))])
+}
+
+scale_colours = function(mat, col = rainbow(10), breaks = NA){
+    mat = as.matrix(mat)
+    return(matrix(scale_vec_colours(as.vector(mat), col = col, breaks = breaks), nrow(mat), ncol(mat), dimnames = list(rownames(mat), colnames(mat))))
+}
+
+cluster_mat = function(mat, distance, method){
+    if(!(method %in% c("ward.D", "ward.D2", "ward", "single", "complete", "average", "mcquitty", "median", "centroid"))){
+        stop("clustering method has to one form the list: 'ward', 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'.")
+    }
+    if(!(distance[1] %in% c("correlation", "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski")) & class(distance) != "dist"){
+        stop("distance has to be a dissimilarity structure as produced by dist or one measure  form the list: 'correlation', 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'minkowski'")
+    }
+    if(distance[1] == "correlation"){
+        d = as.dist(1 - cor(t(mat)))
+    }
+    else{
+        if(class(distance) == "dist"){
+            d = distance
+        }
+        else{
+            d = dist(mat, method = distance)
+        }
+    }
+    
+    return(hclust(d, method = method))
+}
+
+scale_rows = function(x){
+    m = apply(x, 1, mean, na.rm = T)
+    s = apply(x, 1, sd, na.rm = T)
+    return((x - m) / s)
+}
+
+scale_mat = function(mat, scale){
+    if(!(scale %in% c("none", "row", "column"))){
+        stop("scale argument shoud take values: 'none', 'row' or 'column'")
+    }
+    mat = switch(scale, none = mat, row = scale_rows(mat), column = t(scale_rows(t(mat))))
+    return(mat)
+}
+
+generate_annotation_colours = function(annotation, annotation_colors, drop){
+    if(is.na2(annotation_colors)){
+        annotation_colors = list()
+    }
+    count = 0
+    for(i in 1:length(annotation)){
+        annotation[[i]] = annotation[[i]][!is.na(annotation[[i]])]
+        if(is.character(annotation[[i]]) | is.factor(annotation[[i]])){
+            if (is.factor(annotation[[i]]) & !drop){
+                count = count + length(levels(annotation[[i]]))
+            }
+            else{
+                count = count + length(unique(annotation[[i]]))
+            }
+        }
+    }
+    
+    factor_colors = dscale(factor(1:count), hue_pal(l = 75))
+    
+    set.seed(3453)
+    
+    cont_counter = 2
+    for(i in 1:length(annotation)){
+        if(!(names(annotation)[i] %in% names(annotation_colors))){
+            if(is.character(annotation[[i]]) | is.factor(annotation[[i]])){
+                n = length(unique(annotation[[i]]))
+                if (is.factor(annotation[[i]]) & !drop){
+                    n = length(levels(annotation[[i]]))
+                }
+                ind = sample(1:length(factor_colors), n)
+                annotation_colors[[names(annotation)[i]]] = factor_colors[ind]
+                l = levels(as.factor(annotation[[i]]))
+                l = l[l %in% unique(annotation[[i]])]
+                if (is.factor(annotation[[i]]) & !drop){
+                    l = levels(annotation[[i]])
+                }
+                
+                names(annotation_colors[[names(annotation)[i]]]) = l
+                factor_colors = factor_colors[-ind]
+            }
+            else{
+                annotation_colors[[names(annotation)[i]]] = brewer_pal("seq", cont_counter)(5)[1:4]
+                cont_counter = cont_counter + 1
+            }
+        }
+    }
+    return(annotation_colors)
+}
+
+kmeans_pheatmap = function(mat, k = min(nrow(mat), 150), sd_limit = NA, ...){
+    # Filter data
+    if(!is.na(sd_limit)){
+        s = apply(mat, 1, sd)
+        mat = mat[s > sd_limit, ]    
+    }
+    
+    # Cluster data
+    set.seed(1245678)
+    km = kmeans(mat, k, iter.max = 100)
+    mat2 = km$centers
+    
+    # Compose rownames
+    t = table(km$cluster)
+    rownames(mat2) = sprintf("cl%s_size_%d", names(t), t)
+    
+    # Draw heatmap
+    pheatmapwh(mat2, ...)
+}
+
+find_gaps = function(tree, cutree_n){
+    v = cutree(tree, cutree_n)[tree$order]
+    gaps = which((v[-1] - v[-length(v)]) != 0)
+    
+}
+
+is.na2 = function(x){
+    if(is.list(x) | length(x) > 1){
+        return(FALSE)
+    }
+    if(length(x) == 0){
+        return(TRUE)
+    }
+    
+    return(is.na(x))
+}
+
+identity2 = function(x, ...){
+    return(x)
+}
+
+pheatmapwh = function(mat, color = colorRampPalette(rev(brewer.pal(n = 7, name = "RdYlBu")))(100), kmeans_k = NA, breaks = NA, border_color = "grey60", cellwidth = NA, cellheight = NA, scale = "none", cluster_rows = TRUE, cluster_cols = TRUE, clustering_distance_rows = "euclidean", clustering_distance_cols = "euclidean", clustering_method = "complete", clustering_callback = identity2, cutree_rows = NA, cutree_cols = NA,  treeheight_row = ifelse(cluster_rows, 50, 0), treeheight_col = ifelse(cluster_cols, 50, 0), legend = TRUE, legend_breaks = NA, legend_labels = NA, annotation_row = NA, annotation_col = NA, annotation = NA, annotation_colors = NA, annotation_legend = TRUE, drop_levels = TRUE, show_rownames = T, show_colnames = T, main = NA, fontsize = 10, fontsize_row = fontsize, fontsize_col = fontsize, display_numbers = F, number_format = "%.2f", number_color = "grey30", fontsize_number = 0.8 * fontsize, gaps_row = NULL, gaps_col = NULL, labels_row = NULL, labels_col = NULL, filename = NA, width = NA, height = NA, silent = FALSE, ...){
+    
+    # Set labels
+    if(is.null(labels_row)){
+        labels_row = rownames(mat)
+    }
+    if(is.null(labels_col)){
+        labels_col = colnames(mat)
+    }
+    
+    # Preprocess matrix
+    mat = as.matrix(mat)
+    if(scale != "none"){
+        mat = scale_mat(mat, scale)
+        if(is.na2(breaks)){
+            breaks = generate_breaks(mat, length(color), center = T)
+        }
+    }
+    
+    
+    # Kmeans
+    if(!is.na(kmeans_k)){
+        # Cluster data
+        km = kmeans(mat, kmeans_k, iter.max = 100)
+        mat = km$centers
+        
+        # Compose rownames
+        t = table(km$cluster)
+        labels_row = sprintf("Cluster: %s Size: %d", names(t), t)
+    }
+    else{
+        km = NA
+    }
+    
+    # Format numbers to be displayed in cells
+    if(is.matrix(display_numbers) | is.data.frame(display_numbers)){
+        if(nrow(display_numbers) != nrow(mat) | ncol(display_numbers) != ncol(mat)){
+            stop("If display_numbers provided as matrix, its dimensions have to match with mat")
+        }
+        
+        display_numbers = as.matrix(display_numbers)
+        fmat = matrix(as.character(display_numbers), nrow = nrow(display_numbers), ncol = ncol(display_numbers))
+        fmat_draw = TRUE
+        
+    }
+    else{
+        if(display_numbers){
+            fmat = matrix(sprintf(number_format, mat), nrow = nrow(mat), ncol = ncol(mat))
+            fmat_draw = TRUE
+        }
+        else{
+            fmat = matrix(NA, nrow = nrow(mat), ncol = ncol(mat))
+            fmat_draw = FALSE
+        }
+    }
+    
+    # Do clustering
+    if(cluster_rows){
+        tree_row = cluster_mat(mat, distance = clustering_distance_rows, method = clustering_method)
+        tree_row = clustering_callback(tree_row, mat)
+        mat = mat[tree_row$order, , drop = FALSE]
+        fmat = fmat[tree_row$order, , drop = FALSE]
+        labels_row = labels_row[tree_row$order]
+        if(!is.na(cutree_rows)){
+            gaps_row = find_gaps(tree_row, cutree_rows)
+        }
+        else{
+            gaps_row = NULL
+        }
+    }
+    else{
+        tree_row = NA
+        treeheight_row = 0
+    }
+    
+    if(cluster_cols){
+        tree_col = cluster_mat(t(mat), distance = clustering_distance_cols, method = clustering_method)
+        tree_col = clustering_callback(tree_col, t(mat))
+        mat = mat[, tree_col$order, drop = FALSE]
+        fmat = fmat[, tree_col$order, drop = FALSE]
+        labels_col = labels_col[tree_col$order]
+        if(!is.na(cutree_cols)){
+            gaps_col = find_gaps(tree_col, cutree_cols)
+        }
+        else{
+            gaps_col = NULL
+        }
+    }
+    else{
+        tree_col = NA
+        treeheight_col = 0
+    }
+    
+    attr(fmat, "draw") = fmat_draw
+    
+    # Colors and scales
+    if(!is.na2(legend_breaks) & !is.na2(legend_labels)){
+        if(length(legend_breaks) != length(legend_labels)){
+            stop("Lengths of legend_breaks and legend_labels must be the same")
+        }
+    }
+    
+    
+    if(is.na2(breaks)){
+        breaks = generate_breaks(as.vector(mat), length(color))
+    }
+    if (legend & is.na2(legend_breaks)) {
+        legend = grid.pretty(range(as.vector(breaks)))
+        names(legend) = legend
+    }
+    else if(legend & !is.na2(legend_breaks)){
+        legend = legend_breaks[legend_breaks >= min(breaks) & legend_breaks <= max(breaks)]
+        
+        if(!is.na2(legend_labels)){
+            legend_labels = legend_labels[legend_breaks >= min(breaks) & legend_breaks <= max(breaks)]
+            names(legend) = legend_labels
+        }
+        else{
+            names(legend) = legend
+        }
+    }
+    else {
+        legend = NA
+    }
+    mat = scale_colours(mat, col = color, breaks = breaks)
+    
+    # Preparing annotations
+    if(is.na2(annotation_col) & !is.na2(annotation)){
+        annotation_col = annotation
+    }
+    # Select only the ones present in the matrix
+    if(!is.na2(annotation_col)){
+        annotation_col = annotation_col[colnames(mat), , drop = F]
+    }
+    
+    if(!is.na2(annotation_row)){
+        annotation_row = annotation_row[rownames(mat), , drop = F]
+    }
+    
+    annotation = c(annotation_row, annotation_col)
+    annotation = annotation[unlist(lapply(annotation, function(x) !is.na2(x)))]
+    if(length(annotation) != 0){
+        annotation_colors = generate_annotation_colours(annotation, annotation_colors, drop = drop_levels)
+    }
+    else{
+        annotation_colors = NA
+    }
+    
+    if(!show_rownames){
+        labels_row = NULL
+    }
+    
+    if(!show_colnames){
+        labels_col = NULL
+    }
+    
+    # Draw heatmap
+    gt = heatmap_motor(mat, border_color = border_color, cellwidth = cellwidth, cellheight = cellheight, treeheight_col = treeheight_col, treeheight_row = treeheight_row, tree_col = tree_col, tree_row = tree_row, filename = filename, width = width, height = height, breaks = breaks, color = color, legend = legend, annotation_row = annotation_row, annotation_col = annotation_col, annotation_colors = annotation_colors, annotation_legend = annotation_legend, main = main, fontsize = fontsize, fontsize_row = fontsize_row, fontsize_col = fontsize_col, fmat = fmat, fontsize_number = fontsize_number, number_color = number_color, gaps_row = gaps_row, gaps_col = gaps_col, labels_row = labels_row, labels_col = labels_col, ...)
+    
+    if(is.na(filename) & !silent){
+        grid.newpage()
+        grid.draw(gt)
+    }
+    
+    invisible(list(tree_row = tree_row, tree_col = tree_col, kmeans = km, gtable = gt))
+}
+
+