@@ -2653,7 +2653,9 @@ row_anno_link = function(...) {

 	anno_link(..., which = "row")

 }

-anno_summarize = function(which = c("column", "row"),

+# only allow for one-column/one-row heamtap

+# discrete: barplot; continuous: boxplot (maybe also barplot, e.g. pct overlap)

+anno_summary = function(which = c("column", "row"), bar_width = 0.8,

 	width = NULL, height = NULL, border = FALSE, ...) {

 	if(is.null(.ENV$current_annotation_which)) {

@@ -2662,15 +2664,53 @@ anno_summarize = function(which = c("column", "row"),

 		which = .ENV$current_annotation_which

 	}

-	if(which == "column") {

-		stop_wrap("`anno_summarize()` is only allowed as a column annotation.")

-	}

-

 	anno_size = anno_width_and_height(which, width, height, unit(2, "cm"))

 	# get variables fron oncoPrint() function

 	pf = parent.frame()

 	# find where the heatmap object is.

+	row_fun = function(index) {

+

+	}

+	column_fun = function(index) {

+		ht = get("object", envir = parent.frame(7))

+		mat = ht@matrix

+		cm = ht@matrix_color_mapping

+		order_list = ht@row_order_list

+		ng = length(order_list)

+

+		if(cm@type == "discrete") {

+			tl = lapply(order_list, function(od) table(mat[od, 1]))

+			tl = lapply(tl, function(x) x/sum(x))

+			pushViewport(viewport(xscale = c(0.5, ng+0.5), yscale = c(0, 1)))

+			for(i in 1:ng) {

+				x = i

+				y = cumsum(tl[[i]])

+				grid.rect(x, y, w = bar_width, just = "top", gp = gpar(fill = map_to_colors(cm, names(y))))

+			}

+			# axis

+			popViewport()

+		}

+

+	}

+

+	if(which == "row") {

+		fun = row_fun

+	} else if(which == "column") {

+		fun = column_fun

+	}

+	anno = AnnotationFunction(

+		fun = fun,

+		fun_name = "anno_summary",

+		which = which,

+		width = width,

+		height = height,

+		n = 1,

+		show_name = FALSE

+	)

+

+	anno@subsetable = FALSE

+	return(anno)

 }

@@ -1244,6 +1244,9 @@ make_cluster = function(object, which = c("row", "column")) {

             } else {

                 slice_mean = sapply(order_list, function(ind) rowMeans(mat[, ind, drop = FALSE]))

             }

+            if(!is.matrix(slice_mean)) {

+                slice_mean = matrix(slice_mean, nrow = 1)

+            }

             dend_slice = as.dendrogram(hclust(dist(t(slice_mean))))

             if(verbose) qqcat("perform clustering on mean of @{which} slices\n")

         }

@@ -370,9 +370,9 @@ setMethod(f = "draw_title",

             grid.rect(gp = gpar(fill = gp$fill))

         }

         if(side == "left") {

-            grid.text(title, x = unit(1, "npc") - TITLE_PADDING, rot = rot, just = just, gp = gp)

+            grid.text(title, x = unit(1, "npc") - ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

         } else {

-            grid.text(title, x = TITLE_PADDING, rot = rot, just = just, gp = gp)

+            grid.text(title, x = ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

         }

         upViewport()

     } else {

@@ -381,9 +381,9 @@ setMethod(f = "draw_title",

             grid.rect(gp = gpar(fill = gp$fill))

         }

         if(side == "top") {

-            grid.text(title, y = TITLE_PADDING, rot = rot, just = just, gp = gp)

+            grid.text(title, y = ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

         } else {

-            grid.text(title, y = unit(1, "npc") - TITLE_PADDING, rot = rot, just = just, gp = gp)

+            grid.text(title, y = unit(1, "npc") - ht_opt$TITLE_PADDING, rot = rot, just = just, gp = gp)

         }

         upViewport()

     }

@@ -308,7 +308,7 @@ setMethod(f = "draw",

     ht_gap = gap, 

     main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],

-    padding = NULL,

+    padding = GLOBAL_PADDING,

     adjust_annotation_extension = TRUE,

     auto_adjust = TRUE,

@@ -479,12 +479,6 @@ setMethod(f = "draw",

         heatmap_body_width = heatmap_body_width

     )

-    # calculate proper padding

-    if(is.null(padding)) {

-        padding = GLOBAL_PADDING

-        object@ht_list_param$padding = padding

-    }

-

     layout = grid.layout(nrow = length(HEATMAP_LIST_LAYOUT_COLUMN_COMPONENT), 

         ncol = length(HEATMAP_LAYOUT_ROW_COMPONENT), 

         widths = component_width(object), 

@@ -84,7 +84,7 @@ setMethod(f = "make_layout",

     ht_gap = unit(2, "mm"), 

     main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],

-    padding = NULL,

+    padding = GLOBAL_PADDING,

     auto_adjust = TRUE,

     row_dend_side = c("original", "left", "right"),

@@ -125,6 +125,20 @@ setMethod(f = "make_layout",

         return(object)

     }

+    # the size of the plotting page

+    # if current viewport is top viewport

+    current_vp = current.viewport()$name

+    if(current_vp == "ROOT") {

+        object@layout$page_size = unit(dev.size("cm"), "cm")

+    } else {

+        grid::upViewport()

+        object@layout$page_size = unit.c(convertWidth(unit(1, "npc"), "mm"),

+                                         convertHeight(unit(1, "npc"), "mm"))

+        grid::downViewport()

+

+    }

+    object@ht_list_param$padding = padding

+

     n_ht = length(object@ht_list)

     i_main = main_heatmap[1]

     direction = object@direction

@@ -634,10 +648,10 @@ setMethod(f = "make_layout",

     object@column_title_param$side = column_title_side

     if(length(column_title) > 0) {

         if(column_title_side == "top") {

-            object@layout$layout_column_title_top_height = grobHeight(textGrob(column_title, gp = column_title_gp)) + TITLE_PADDING*2

+            object@layout$layout_column_title_top_height = grobHeight(textGrob(column_title, gp = column_title_gp)) + ht_opt$TITLE_PADDING*2

             object@layout$layout_index = rbind(object@layout$layout_index, column_title_top = heatmap_list_layout_index("column_title_top"))

         } else {

-            object@layout$layout_column_title_bottom_height = grobHeight(textGrob(column_title, gp = column_title_gp)) + TITLE_PADDING*2

+            object@layout$layout_column_title_bottom_height = grobHeight(textGrob(column_title, gp = column_title_gp)) + ht_opt$TITLE_PADDING*2

             object@layout$layout_index = rbind(object@layout$layout_index, column_title_bottom = heatmap_list_layout_index("column_title_bottom"))

         }

         object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) draw_title(object, which = "column"))

@@ -660,10 +674,10 @@ setMethod(f = "make_layout",

     object@row_title_param$side = row_title_side

     if(length(row_title) > 0) {

         if(row_title_side == "left") {

-            object@layout$layout_row_title_left_width = grobHeight(textGrob(row_title, gp = row_title_gp)) + TITLE_PADDING*2

+            object@layout$layout_row_title_left_width = grobHeight(textGrob(row_title, gp = row_title_gp)) + ht_opt$TITLE_PADDING*2

             object@layout$layout_index = rbind(object@layout$layout_index, row_title_left = heatmap_list_layout_index("row_title_left"))

         } else {

-            object@layout$layout_row_title_right_width = grobHeight(textGrob(row_title, gp = row_title_gp)) + TITLE_PADDING*2

+            object@layout$layout_row_title_right_width = grobHeight(textGrob(row_title, gp = row_title_gp)) + ht_opt$TITLE_PADDING*2

             object@layout$layout_index = rbind(object@layout$layout_index, row_title_right = heatmap_list_layout_index("row_title_right"))

         }

         object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) draw_title(object, which = "row"))

@@ -717,7 +731,10 @@ setMethod(f = "make_layout",

             }

         }

     }

-    if(length(ColorMappingList) == 0 && length(heatmap_legend_list) == 0) {

+    if(merge_legends) {

+        heatmap_legend_list = c(heatmap_legend_list, annotation_legend_list)

+    }

+     if(length(ColorMappingList) == 0 && length(heatmap_legend_list) == 0) {

         show_heatmap_legend = FALSE

     }

@@ -738,30 +755,34 @@ setMethod(f = "make_layout",

     if(show_heatmap_legend) {

         if(heatmap_legend_side == "top") {

             object@heatmap_legend_param$padding = unit(c(2, 0, 0, 0), "mm")

-            size = heatmap_legend_size(object, legend_list = heatmap_legend_list)

+            size = heatmap_legend_size(object, legend_list = heatmap_legend_list, max_width = calc_legends_max_width(object))

             object@heatmap_legend_param$size = size

             object@layout$layout_heatmap_legend_top_height = size[2]

             object@layout$layout_index = rbind(object@layout$layout_index, heatmap_legend_top = heatmap_list_layout_index("heatmap_legend_top"))

         } else if(heatmap_legend_side == "bottom") {

             object@heatmap_legend_param$padding = unit(c(0, 0, 2, 0), "mm")

-            size = heatmap_legend_size(object, legend_list = heatmap_legend_list)

+            size = heatmap_legend_size(object, legend_list = heatmap_legend_list, max_width = calc_legends_max_width(object))

             object@heatmap_legend_param$size = size

             object@layout$layout_heatmap_legend_bottom_height = size[2]

             object@layout$layout_index = rbind(object@layout$layout_index, heatmap_legend_bottom = heatmap_list_layout_index("heatmap_legend_bottom"))

         } else if(heatmap_legend_side == "left") {

             object@heatmap_legend_param$padding = unit(c(0, 0, 0, 2), "mm")

-            size = heatmap_legend_size(object, legend_list = heatmap_legend_list)

+            size = heatmap_legend_size(object, legend_list = heatmap_legend_list, max_height = calc_legends_max_height(object))

             object@heatmap_legend_param$size = size

             object@layout$layout_heatmap_legend_left_width = size[1]

             object@layout$layout_index = rbind(object@layout$layout_index, heatmap_legend_left = heatmap_list_layout_index("heatmap_legend_left"))

         } else if(heatmap_legend_side == "right") {

             object@heatmap_legend_param$padding = unit(c(0, 2, 0, 0), "mm")

-            size = heatmap_legend_size(object, legend_list = heatmap_legend_list)

+            size = heatmap_legend_size(object, legend_list = heatmap_legend_list, max_height = calc_legends_max_height(object))

             object@heatmap_legend_param$size = size

             object@layout$layout_heatmap_legend_right_width = size[1]

             object@layout$layout_index = rbind(object@layout$layout_index, heamap_legend_right = heatmap_list_layout_index("heatmap_legend_right"))

         }

-        object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) draw_heatmap_legend(object, legend_list = heatmap_legend_list))

+        if(heatmap_legend_side %in% c("top", "bottom")) {

+            object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) draw_heatmap_legend(object, legend_list = heatmap_legend_list, max_width = calc_legends_max_width(object)))

+        } else {

+            object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) draw_heatmap_legend(object, legend_list = heatmap_legend_list, max_height = calc_legends_max_height(object)))

+        }

     } else {

         object@heatmap_legend_param$size = unit(c(0, 0), "mm")

     }

@@ -805,30 +826,34 @@ setMethod(f = "make_layout",

     if(show_annotation_legend) {

         if(annotation_legend_side == "top") {

             object@annotation_legend_param$padding = unit(c(2, 0, 0, 0), "mm")

-            size = annotation_legend_size(object, legend_list = annotation_legend_list)

+            size = annotation_legend_size(object, legend_list = annotation_legend_list, max_width = calc_legends_max_width(object))

             object@annotation_legend_param$size = size

             object@layout$layout_annotation_legend_top_height = size[2]

             object@layout$layout_index = rbind(object@layout$layout_index, annotation_legend_top = heatmap_list_layout_index("annotation_legend_top"))

         } else if(annotation_legend_side == "bottom") {

             object@annotation_legend_param$padding = unit(c(0, 0, 2, 0), "mm")

-            size = annotation_legend_size(object, legend_list = annotation_legend_list)

+            size = annotation_legend_size(object, legend_list = annotation_legend_list, max_width = calc_legends_max_width(object))

             object@annotation_legend_param$size = size

             object@layout$layout_annotation_legend_bottom_height = size[2]

             object@layout$layout_index = rbind(object@layout$layout_index, annotation_legend_bottom = heatmap_list_layout_index("annotation_legend_bottom"))

         } else if(annotation_legend_side == "left") {

             object@annotation_legend_param$padding = unit(c(0, 0, 0, 2), "mm")

-            size = annotation_legend_size(object, legend_list = annotation_legend_list)

+            size = annotation_legend_size(object, legend_list = annotation_legend_list, max_height = calc_legends_max_height(object))

             object@annotation_legend_param$size = size

             object@layout$layout_annotation_legend_left_width = size[1]

             object@layout$layout_index = rbind(object@layout$layout_index, annotation_legend_left = heatmap_list_layout_index("annotation_legend_left"))

         } else if(annotation_legend_side == "right") {

             object@annotation_legend_param$padding = unit(c(0, 2, 0, 0), "mm")

-            size = annotation_legend_size(object, legend_list = annotation_legend_list)

+            size = annotation_legend_size(object, legend_list = annotation_legend_list, max_height = calc_legends_max_height(object))

             object@annotation_legend_param$size = size

             object@layout$layout_annotation_legend_right_width = size[1]

             object@layout$layout_index = rbind(object@layout$layout_index, annotation_legend_right = heatmap_list_layout_index("annotation_legend_right"))

         }

-        object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) draw_annotation_legend(object, legend_list = annotation_legend_list))

+        if(annotation_legend_side %in% c("top", "bottom")) {

+            object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) draw_annotation_legend(object, legend_list = annotation_legend_list, max_width = calc_legends_max_width(object)))

+        } else {

+            object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) draw_annotation_legend(object, legend_list = annotation_legend_list, max_height = calc_legends_max_height(object)))

+        }

     } else {

         object@annotation_legend_param$size = unit(c(0, 0), "null")

     }

@@ -876,8 +901,19 @@ setMethod(f = "make_layout",

     return(object)

 })

+calc_legends_max_height = function(object) {

+    gh = object@layout$page_size[2]

+    h = gh - object@layout$layout_column_title_top_height - object@layout$layout_column_title_bottom_height -

+             object@ht_list_param$padding[1] - object@ht_list_param$padding[3]

+    convertHeight(h, "mm")

+}

-

+calc_legends_max_width = function(object) {

+    gh = object@layout$page_size[1]

+    h = gh - object@layout$layout_row_title_right_width - object@layout$layout_row_title_left_width -

+             object@ht_list_param$padding[2] - object@ht_list_param$padding[4]

+    convertWidth(h, "mm")

+}

 HEATMAP_LIST_LAYOUT_COLUMN_COMPONENT = 1:7

 names(HEATMAP_LIST_LAYOUT_COLUMN_COMPONENT) = c("annotation_legend_top", "heatmap_legend_top", "column_title_top",

@@ -401,7 +401,7 @@ draw_legend = function(ColorMappingList, ColorMappingParamList, side = c("right"

         } else if(side == "top") {

             draw(pk, y = unit(1, "npc"), just = "top")

         } else if(side == "bottom") {

-            draw(pk, y = unit(1, "npc"), just = "top")

+            draw(pk, y = unit(0, "npc"), just = "bottom")

         }

     }

@@ -977,6 +977,8 @@ valid_just = function(just) {

 			"left" = c("left", "center"),

 			"right" = c("right", "center"),

 			"top" = c("center", "top"),

+			"bottom" = c("center", "bottom"),

+			"top" = c("center", "top"),

 			c("center", "center"))

 	}

 	if(length(just) != 2) {

@@ -589,3 +589,11 @@ pindex = function(m, i, j) {

     }

 }

+

+unit_with_vp = function(..., vp = current.viewport()$name) {

+    u = unit(...)

+    attr(u, "viewport") = vp

+    return(u)

+}

+

+