@@ -2655,8 +2655,9 @@ row_anno_link = function(...) {

 # 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, ...) {

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

+	axis = TRUE, axis_param = default_axis_param(which), 

+	width = NULL, height = NULL, ...) {

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

 		which = match.arg(which)[1]

@@ -2666,11 +2667,32 @@ anno_summary = function(which = c("column", "row"), bar_width = 0.8,

 	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.

+	axis_param = validate_axis_param(axis_param, which)

+	axis_grob = if(axis) construct_axis_grob(axis_param, which, c(0, 1)) else NULL

+

 	row_fun = function(index) {

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

+		mat = ht@matrix

+		cm = ht@matrix_color_mapping

+		order_list = ht@column_order_list

+		ng = length(order_list)

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

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

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

+

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

+			for(i in 1:ng) {

+				x = i

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

+				grid.rect(y, x, height = bar_width, width = tl[[i]], just = "right", gp = gpar(fill = map_to_colors(cm, names(y))), default.units = "native")

+			}

+			if(axis) grid.draw(axis_grob)

+			if(border) grid.rect(gp = gpar(fill = "transparent"))

+			popViewport()

+		} else {

+			stop_wrap("`anno_summary()` currently only supports discrete matrix.")

+		}

 	}

 	column_fun = function(index) {

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

@@ -2682,16 +2704,19 @@ anno_summary = function(which = c("column", "row"), bar_width = 0.8,

 		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))))

+				grid.rect(x, y, width = bar_width, height = tl[[i]], just = "top", gp = gpar(fill = map_to_colors(cm, names(y))), default.units = "native")

 			}

-			# axis

+			if(axis) grid.draw(axis_grob)

+			if(border) grid.rect(gp = gpar(fill = "transparent"))

 			popViewport()

+		} else {

+			stop_wrap("`anno_summary()` currently only supports discrete matrix.")

 		}

-

 	}

 	if(which == "row") {

@@ -2706,11 +2731,14 @@ anno_summary = function(which = c("column", "row"), bar_width = 0.8,

 		which = which,

 		width = width,

 		height = height,

+		var_import = list(bar_width, border, axis, axis_grob),

 		n = 1,

 		show_name = FALSE

 	)

 	anno@subsetable = FALSE

+	anno@extended = update_anno_extend(anno, axis_grob, axis_param)

+

 	return(anno)

 }

@@ -339,7 +339,7 @@ setMethod(f = "adjust_heatmap_list",

         object@layout$max_right_component_width = max_right_component_width

         # and calcualte proper paddings

-        if(is.null(object@ht_list_param$padding)) {

+        if(TRUE) {

             object@ht_list_param$padding = GLOBAL_PADDING

             column_anno_max_left_extended = max(do.call("unit.c", lapply(object@ht_list, function(ht) {

                 if(inherits(ht, "HeatmapAnnotation")) {

@@ -146,12 +146,15 @@ setMethod(f = "make_layout",

     # i_main is aleays numeric index

     if(is.character(i_main)) {

         i_main = which(names(object@ht_list) == i_main)[1]

+        if(length(i_main) == 0) {

+            stop_wrap(qq("cannot find heatmap '@{main_heatmap}'"))

+        }

     }

     if(verbose) qqcat("@{n_ht} heatmaps/annotations, main heatmap: @{i_main}th\n")

     if(inherits(object@ht_list[[i_main]], "HeatmapAnnotation")) {

-        stop("the main heatmap can only be the heatmap.")

+        stop_wrap("the main heatmap can only be the heatmap.")

     }

     nr = nrow(object@ht_list[[i_main]]@matrix)

@@ -404,11 +404,11 @@ SingleAnnotation = function(name, value, col, fun,

                 extended[[3]] = text_width

             }

         }

-        for(i in 1:4) {

-            extended[[i]] = max(anno_fun_extend[[i]], extended[[i]])

-        }

-        .Object@extended = extended

     }

+    for(i in 1:4) {

+        extended[[i]] = max(anno_fun_extend[[i]], extended[[i]])

+    }

+    .Object@extended = extended

     .Object@name_param = name_param

@@ -364,19 +364,19 @@ dev.null = function(...) {

 }

 stop_wrap = function (...) {

-    x = qq(paste0(...))

+    x = paste0(...)

     x = paste(strwrap(x), collapse = "\n")

     stop(x, call. = FALSE)

 }

 warning_wrap = function (...) {

-    x = qq(paste0(...))

+    x = paste0(...)

     x = paste(strwrap(x), collapse = "\n")

     warning(x, call. = FALSE)

 }

 message_wrap = function (...) {

-    x = qq(paste0(...))

+    x = paste0(...)

     x = paste(strwrap(x), collapse = "\n")

     message(x)

 }

@@ -597,3 +597,41 @@ unit_with_vp = function(..., vp = current.viewport()$name) {

 }

+grid.boxplot = function(value, pos, outline = TRUE, box_width = 0.6,

+    pch = 1, size = unit(2, "mm"), gp = gpar(fill = "#CCCCCC"), 

+    direction = c("vertical", "horizontal"), ...) {

+

+    direction = match.args(direction)[1]

+    boxplot_stats = boxplot(value, plot = FALSE)$stats

+

+    if(direction == "vertical") {

+    grid.rect(x = pos, y = boxplot_stats[2, ], 

+            height = boxplot_stats[4, ] - boxplot_stats[2, ], width = 1*box_width, just = "bottom", 

+            default.units = "native", gp = gp)

+        

+        grid.segments(seq_along(index) - 0.5*box_width, boxplot_stats[5, ],

+                      seq_along(index) + 0.5*box_width, boxplot_stats[5, ], 

+                      default.units = "native", gp = gp)

+        grid.segments(seq_along(index), boxplot_stats[5, ],

+                      seq_along(index), boxplot_stats[4, ], 

+                      default.units = "native", gp = gp)

+        grid.segments(seq_along(index), boxplot_stats[1, ],

+                      seq_along(index), boxplot_stats[2, ], 

+                      default.units = "native", gp = gp)

+        grid.segments(seq_along(index) - 0.5*box_width, boxplot_stats[1, ],

+                      seq_along(index) + 0.5*box_width, boxplot_stats[1, ], 

+                      default.units = "native", gp = gp)

+        grid.segments(seq_along(index) - 0.5*box_width, boxplot_stats[3, ],

+                      seq_along(index) + 0.5*box_width, boxplot_stats[3, ], 

+                      default.units = "native", gp = gp)

+        if(outline) {   

+            for(i in seq_along(value)) {

+                l1 = value[[i]] > boxplot_stats[5,i]

+                if(sum(l1)) grid.points(x = rep(i, sum(l1)), y = value[[i]][l1], 

+                    default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i])

+                l2 = value[[i]] < boxplot_stats[1,i]

+                if(sum(l2)) grid.points(x = rep(i, sum(l2)), y = value[[i]][l2], 

+                    default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i])

+            }

+        }

+}

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