@@ -2656,7 +2656,9 @@ 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"), border = TRUE, bar_width = 0.8, 

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

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

+	ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6,

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

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

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

@@ -2668,7 +2670,11 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

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

 	axis_param = validate_axis_param(axis_param, which)

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

+	if(is.null(ylim)) {

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

+	} else {

+		axis_grob = if(axis) construct_axis_grob(axis_param, which, ylim) else NULL

+	}

 	row_fun = function(index) {

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

@@ -2691,7 +2697,7 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

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

 			popViewport()

 		} else {

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

+			

 		}

 	}

 	column_fun = function(index) {

@@ -2702,6 +2708,9 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

 		ng = length(order_list)

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

+			if(!is.null(ylim)) {

+				stop_wrap("For discrete matrix, `ylim` is not allowed to set. It is always c(0, 1).")

+			}

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

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

@@ -2715,7 +2724,39 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

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

 			popViewport()

 		} else {

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

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

+			nv = length(vl)

+			if(is.null(ylim)) {

+				if(!outline) {

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

+					data_scale = range(boxplot_stats)

+				} else {

+					data_scale = range(vl, na.rm = TRUE)

+				}

+			} else {

+				data_scale = ylim

+			}

+			data_scale = data_scale + c(-extend, extend)*(data_scale[2] - data_scale[1])

+

+			if(is.null(ylim)) {

+				axis_param = validate_axis_param(axis_param, which)

+				axis_grob = if(axis) construct_axis_grob(axis_param, which, data_scale) else NULL

+			}

+

+			gp = recycle_gp(gp, nv)

+			if(length(pch) == 1) pch = rep(pch, nv)

+			if(length(size) == 1) size = rep(size, nv)

+

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

+			for(i in 1:ng) {

+				x = i

+				v = vl[[i]]

+				grid.boxplot(v, pos = x, box_width = box_width, gp = subset_gp(gp, i),

+					pch = pch, size = size)

+			}

+			if(axis) grid.draw(axis_grob)

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

+			popViewport()

 		}

 	}

@@ -2731,7 +2772,8 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

 		which = which,

 		width = width,

 		height = height,

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

+		var_import = list(bar_width, border, axis, axis_grob, axis_param, which, ylim, extend, 

+			outline, box_width, pch, size, gp),

 		n = 1,

 		show_name = FALSE

 	)

@@ -330,7 +330,8 @@ setMethod(f = "draw",

     split = NULL,

     row_km = km,

     row_split = split,

-    heatmap_body_height = NULL,

+    height = NULL,

+    heatmap_height = NULL,

     column_gap = NULL,

     cluster_columns = NULL,

@@ -343,7 +344,8 @@ setMethod(f = "draw",

     column_order = NULL,

     column_km = NULL,

     column_split = NULL,

-    heatmap_body_width = NULL,

+    width = NULL,

+    heatmap_width = NULL,

     ### global setting

     heatmap_row_names_gp = NULL,

@@ -402,10 +404,37 @@ setMethod(f = "draw",

         }

         if(direction == "horizontal") {

             nr = ob[1]

-            object = object + Heatmap(matrix(ncol = 0, nrow = nr))

+            max_height = max(do.call("unit.c", lapply(object@ht_list, function(ha) {

+                h = height(ha)

+                if(is_abs_unit(h)) {

+                    convertHeight(h, "mm")

+                } else {

+                    unit(0, "mm")

+                }

+            })))

+            max_height = convertHeight(max_height, "mm")

+            if(max_height[[1]] == 0) {

+                object = object + Heatmap(matrix(ncol = 0, nrow = nr))

+            } else {

+                object = object + Heatmap(matrix(ncol = 0, nrow = nr), height = max_height)

+            }

+            

         } else {

             nc = ob[1]

-            object = object %v% Heatmap(matrix(nrow = 0, ncol = nc))

+            max_width = max(do.call("unit.c", lapply(object@ht_list, function(ha) {

+                w = width(ha)

+                if(is_abs_unit(w)) {

+                    convertWidth(w, "mm")

+                } else {

+                    unit(0, "mm")

+                }

+            })))

+            max_width = convertWidth(max_width, "mm")

+            if(max_width[[1]] == 0) {

+                object = object %v% Heatmap(matrix(nrow = 0, ncol = nc))

+            } else {

+                object = object %v% Heatmap(matrix(nrow = 0, ncol = nc), width = max_width)

+            }

         }

     }

@@ -463,7 +492,8 @@ setMethod(f = "draw",

         row_order = row_order,

         row_km = row_km,

         row_split = row_split,

-        heatmap_body_height = heatmap_body_height,

+        height = height,

+        heatmap_height = heatmap_height,

         column_gap = column_gap,

         cluster_columns = cluster_columns,

@@ -476,7 +506,8 @@ setMethod(f = "draw",

         column_order = column_order,

         column_km = column_km,

         column_split = column_split,

-        heatmap_body_width = heatmap_body_width

+        width = width,

+        heatmap_width = heatmap_width

     )

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

@@ -188,7 +188,7 @@ setMethod(f = "adjust_heatmap_list",

             max_left_component_width = unit(0, "mm")

             if(inherits(object@ht_list[[1]], "Heatmap")) {

                 ht_first = object@ht_list[[1]]

-                max_left_component_width = sum(component_width(ht_first, c("row_names_left", "row_dend_left", "row_anno_left")))

+                max_left_component_width = sum(component_width(ht_first, c("row_names_left", "row_dend_left", "row_anno_left", "row_title_left")))

                 u = unit(0, "mm")

                 if(!is.null(ht_first@top_annotation)) {

                     u = unit.c(u, ht_first@top_annotation@extended[2])

@@ -205,7 +205,7 @@ setMethod(f = "adjust_heatmap_list",

             max_right_component_width = unit(0, "mm")

             if(inherits(object@ht_list[[ length(object@ht_list) ]], "Heatmap")) {

                 ht_last = object@ht_list[[ length(object@ht_list) ]]

-                max_right_component_width = sum(component_width(ht_last, c("row_names_right", "row_dend_right", "row_anno_right")))

+                max_right_component_width = sum(component_width(ht_last, c("row_names_right", "row_dend_right", "row_anno_right", "row_title_right")))

                 u = unit(0, "mm")

                 if(!is.null(ht_last@top_annotation)) {

                     u = unit.c(u, ht_last@top_annotation@extended[4])

@@ -250,7 +250,7 @@ setMethod(f = "adjust_heatmap_list",

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

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

-                sum(component_width(ht, c("row_dend_left", "row_names_left", "row_anno_left")))   

+                sum(component_width(ht, c("row_dend_left", "row_names_left", "row_anno_left", "row_title_left")))   

             } else {

                 unit(0, "mm")

             }

@@ -258,7 +258,7 @@ setMethod(f = "adjust_heatmap_list",

         max_left_component_width = convertWidth(max_left_component_width, "mm")

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

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

-                sum(component_width(ht, c("row_dend_right", "row_names_right", "row_anno_right")))

+                sum(component_width(ht, c("row_dend_right", "row_names_right", "row_anno_right", "row_title_right")))

             } else {

                 unit(0, "mm")

             }

@@ -389,7 +389,7 @@ setMethod(f = "adjust_heatmap_list",

             max_top_component_height = unit(0, "mm")

             if(inherits(object@ht_list[[1]], "Heatmap")) {

                 ht_first = object@ht_list[[1]]

-                max_top_component_height = sum(component_height(ht_first, c("column_names_top", "column_dend_top", "column_anno_top")))

+                max_top_component_height = sum(component_height(ht_first, c("column_names_top", "column_dend_top", "column_anno_top", "column_title_top")))

                 u = unit(0, "mm")

                 if(!is.null(ht_first@left_annotation)) {

                     u = unit.c(u, ht_first@left_annotation@extended[3])

@@ -406,7 +406,7 @@ setMethod(f = "adjust_heatmap_list",

             max_bottom_component_height = unit(0, "mm")

             if(inherits(object@ht_list[[ length(object@ht_list) ]], "Heatmap")) {

                 ht_last = object@ht_list[[ length(object@ht_list) ]]

-                max_bottom_component_height = sum(component_height(ht_last, c("column_names_bottom", "column_dend_bottom", "column_anno_bottom")))

+                max_bottom_component_height = sum(component_height(ht_last, c("column_names_bottom", "column_dend_bottom", "column_anno_bottom", "column_title_bottom")))

                 u = unit(0, "mm")

                 if(!is.null(ht_last@left_annotation)) {

                     u = unit.c(u, ht_last@left_annotation@extended[1])

@@ -103,7 +103,8 @@ setMethod(f = "make_layout",

     row_order = NULL,

     row_km = NULL,

     row_split = NULL,

-    heatmap_body_height = NULL,

+    height = NULL,

+    heatmap_height = NULL,

     column_gap = NULL,

     cluster_columns = NULL,

@@ -116,7 +117,8 @@ setMethod(f = "make_layout",

     column_order = NULL,

     column_km = NULL,

     column_split = NULL,

-    heatmap_body_width = NULL) {

+    width = NULL,

+    heatmap_width = NULL) {

     verbose = ht_opt("verbose")

@@ -298,6 +300,37 @@ setMethod(f = "make_layout",

             object@ht_list[[i_main]]@row_order = row_order

             if(verbose) qqcat("set row_order to main heatmap\n")

         }

+

+        

+        if(!is.null(height) && !is.null(heatmap_height)) {

+            stop_wrap("You can only specify one of `height` and `heatmap_height` in draw().")

+        }

+        if(!is.null(height)) {

+            if(!inherits(height, "unit")) {

+                stop_wrap("`height` specified in `draw()` should be a unit.")

+            }

+            if(!is_abs_unit(height)) {

+                stop_wrap("`height` specified in `draw()` should be an absolute unit.")

+            }

+

+        }

+        if(!is.null(heatmap_height)) {

+            if(!inherits(heatmap_height, "unit")) {

+                stop_wrap("`heatmap_height` specified in `draw()` should be a unit.")

+            }

+            if(!is_abs_unit(heatmap_height)) {

+                stop_wrap("`heatmap_height` specified in `draw()` should be an absolute unit.")

+            }

+        }

+        

+        if(!is.null(height) && is.null(heatmap_height)) {

+            object@ht_list[[i_main]]@matrix_param$height = height

+            object@ht_list[[i_main]]@heatmap_param$height = unit(1, "npc")

+        } else if(is.null(height) && !is.null(heatmap_height)) {

+            object@ht_list[[i_main]]@matrix_param$height = unit(1, "npc")

+            object@ht_list[[i_main]]@heatmap_param$height = heatmap_height

+        } 

+        

     } else {

         if(!is.null(column_split)) {

             object@ht_list[[i_main]]@matrix_param$column_split = column_split

@@ -386,6 +419,35 @@ setMethod(f = "make_layout",

             object@ht_list[[i_main]]@column_order = column_order

             if(verbose) qqcat("set column_order to main heatmap\n")

         }

+

+        if(!is.null(width) && !is.null(heatmap_width)) {

+            stop_wrap("You can only specify one of `width` and `heatmap_width` in draw().")

+        }

+        if(!is.null(width)) {

+            if(!inherits(width, "unit")) {

+                stop_wrap("`width` specified in `draw()` should be a unit.")

+            }

+            if(!is_abs_unit(width)) {

+                stop_wrap("`width` specified in `draw()` should be an absolute unit.")

+            }

+

+        }

+        if(!is.null(heatmap_width)) {

+            if(!inherits(heatmap_width, "unit")) {

+                stop_wrap("`heatmap_width` specified in `draw()` should be a unit.")

+            }

+            if(!is_abs_unit(heatmap_width)) {

+                stop_wrap("`heatmap_width` specified in `draw()` should be an absolute unit.")

+            }

+        }

+        

+        if(!is.null(width) && is.null(heatmap_width)) {

+            object@ht_list[[i_main]]@matrix_param$width = width

+            object@ht_list[[i_main]]@heatmap_param$width = unit(1, "npc")

+        } else if(is.null(width) && !is.null(heatmap_width)) {

+            object@ht_list[[i_main]]@matrix_param$width = unit(1, "npc")

+            object@ht_list[[i_main]]@heatmap_param$width = heatmap_width

+        }  

     }

     if(verbose) qqcat("auto adjust all heatmap/annotations by the main heatmap\n")

@@ -486,6 +548,25 @@ setMethod(f = "make_layout",

         if(verbose) qqcat("adjust column order for all other heatmaps\n")

     }

+    # width and height

+    if(direction == "horizontal") {

+        for(i in seq_len(n_ht)) {

+            if(inherits(object@ht_list[[i]], "Heatmap") & i != i_main) {

+                object@ht_list[[i]]@matrix_param$height = object@ht_list[[i_main]]@matrix_param$height

+                object@ht_list[[i]]@heatmap_param$height = object@ht_list[[i_main]]@heatmap_param$height

+            }

+        }

+        if(verbose) qqcat("adjust heights for all other heatmaps\n")

+    } else {

+        for(i in seq_len(n_ht)) {

+            if(inherits(object@ht_list[[i]], "Heatmap") & i != i_main) {

+                object@ht_list[[i]]@matrix_param$width = object@ht_list[[i_main]]@matrix_param$width

+                object@ht_list[[i]]@heatmap_param$width = object@ht_list[[i_main]]@heatmap_param$width

+            }

+        }

+        if(verbose) qqcat("adjust width for all other heatmaps\n")

+    }

+

     if(auto_adjust) {

         if(direction == "horizontal") {

             for(i in seq_len(n_ht)) {

@@ -969,18 +1050,48 @@ setMethod(f = "component_width",

     } else {

         component_name = k

     }

+

+    direction = object@direction

     # this function is used for grid.layout, so null unit is allowed

-    .single_unit = function(nm) {

+    .single_unit_horizontal = function(nm) {

         if(nm == "heatmap_list") {

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

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

                         ht@heatmap_param$width

                     } else {

-                        size(ht)

+                        width(ht) # width of the row annotation, always a fixed unit

                     }

                 })))

             if(is_abs_unit(width)) {

-                width + sum(object@ht_list_param$ht_gap)

+                width + sum(object@ht_list_param$ht_gap) - object@ht_list_param$ht_gap[length(object@ht_list_param$ht_gap)]

+            } else {

+                unit(1, "null") 

+            }

+        } else {

+            object@layout[[paste0("layout_", nm, "_width")]]

+        }

+    }

+

+    .single_unit_vertical = function(nm) {

+        if(nm == "heatmap_list") {

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

+                    if(inherits(ht, "Heatmap")) {

+                        ht@heatmap_param$width

+                    } else {

+                        # the width of column annotation is always unit(1, "npc")

+                        w = width(ht)

+                        # if a relative unit, reset to unit(0, "mm")

+                        if(!is_abs_unit(w)) w = unit(0, "mm")

+                        w

+                    }

+                })))

+            if(is_abs_unit(width)) {

+                # if height is zeor, this means, there is no heatmap and no width is set for all heatmapannotations

+                if(convertWidth(width, "mm", valueOnly = TRUE) == 0) {

+                    unit(1, "null")

+                } else {

+                    width

+                }

             } else {

                 unit(1, "null") 

             }

@@ -989,7 +1100,11 @@ setMethod(f = "component_width",

         }

     }

-    do.call("unit.c", lapply(component_name, .single_unit))

+    if(direction == "horizontal") {

+        do.call("unit.c", lapply(component_name, .single_unit_horizontal))

+    } else {

+        do.call("unit.c", lapply(component_name, .single_unit_vertical))

+    }

 })

 # == title

@@ -1014,18 +1129,19 @@ setMethod(f = "component_height",

     } else {

         component_name = k

     }

+    direction = object@direction

     # this function is used for grid.layout, so null unit is allowed

-    .single_unit = function(nm) {

+    .single_unit_vertical = function(nm) {

         if(nm == "heatmap_list") {

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

+             height = sum(do.call("unit.c", lapply(object@ht_list, function(ht) {

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

                         ht@heatmap_param$height

                     } else {

-                        size(ht)

+                        height(ht) # width of the row annotation, always a fixed unit

                     }

                 })))

             if(is_abs_unit(height)) {

-                height

+                height + sum(object@ht_list_param$ht_gap) - object@ht_list_param$ht_gap[length(object@ht_list_param$ht_gap)]

             } else {

                 unit(1, "null") 

             }

@@ -1034,5 +1150,35 @@ setMethod(f = "component_height",

         }

     }

-    do.call("unit.c", lapply(component_name, .single_unit))

+    .single_unit_horizontal = function(nm) {

+        if(nm == "heatmap_list") {

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

+                    if(inherits(ht, "Heatmap")) {

+                        ht@heatmap_param$height

+                    } else {

+                        h = height(ht)

+                        if(!is_abs_unit(h)) h = unit(0, "mm")

+                        h

+                    }

+                })))

+            if(is_abs_unit(height)) {

+                # if height is zeor, this means, there is no heatmap and no width is set for all heatmapannotations

+                if(convertWidth(height, "mm", valueOnly = TRUE) == 0) {

+                    unit(1, "null")

+                } else {

+                    height

+                }

+            } else {

+                unit(1, "null") 

+            }

+        } else {

+            object@layout[[paste0("layout_", nm, "_height")]]

+        }

+    }

+    

+    if(direction == "horizontal") {

+        do.call("unit.c", lapply(component_name, .single_unit_horizontal))

+    } else {

+        do.call("unit.c", lapply(component_name, .single_unit_vertical))

+    }

 })

@@ -111,7 +111,7 @@ ht_opt = setGlobalOptions(

 			}

 		},

 		.length = 1),

-	show_vp_border = FALSE,

+	show_vp = FALSE,

 	anno_simple_size = list(

 		.value = unit(5, "mm"),

 		.class = "unit"

new file mode 100644

@@ -0,0 +1,21 @@

+

+

+# stacked_simple = function(..., name, which = c("row", "column")) {

+# 	which = match.arg(which)

+# 	arg_list = list()

+# 	arg_list$which = which

+# 	arg_list[[name]] = anno_simple(..., which = which)

+# 	do.call("HeatmapAnnotation", arg_list)

+# }

+# stacked_points

+# stacked_lines

+# stacked_image

+# stacked_text

+# stacked_barplot

+# stacked_boxplot

+# stacked_histogram

+# stacked_joyplot

+# stacked_horizon

+

+

+# draw

\ No newline at end of file

@@ -73,7 +73,13 @@ default_col = function(x, main_matrix = FALSE) {

     } else if(is.numeric(x)) {

         if(main_matrix) {

             if(length(unique(x)) > 100) {

-                col_fun = colorRamp2(seq(quantile(x, 0.01), quantile(x, 0.99), length = 3), c("blue", "#EEEEEE", "red"))

+                q1 = quantile(x, 0.01)

+                q2 = quantile(x, 0.99)

+                if(length(unique(x[x > q1 & x < q2])) == 1) {

+                     col_fun = colorRamp2(seq(min(x), max(x), length = 3), c("blue", "#EEEEEE", "red"))

+                } else {

+                    col_fun = colorRamp2(seq(q1, q2, length = 3), c("blue", "#EEEEEE", "red"))

+                }

             } else {

                 col_fun = colorRamp2(seq(min(x), max(x), length = 3), c("blue", "#EEEEEE", "red"))

             }

@@ -404,7 +410,7 @@ add_vp_name = function(vpname) {

 }

 upViewport = function(...) {

-    if(ht_global_opt$show_vp_border) {

+    if(ht_global_opt$show_vp) {

         grid.rect(gp = gpar(fill = "transparent", col = "black", lty = 3))

         vpname = current.viewport()$name

         if(!grepl("^GRID.VP", vpname)) {

@@ -415,7 +421,7 @@ upViewport = function(...) {

 }

 popViewport = function(...) {

-    if(ht_global_opt$show_vp_border) {

+    if(ht_global_opt$show_vp) {

         grid.rect(gp = gpar(fill = "transparent", col = "black", lty = 3))

         vpname = current.viewport()$name

         if(!grepl("^GRID.VP", vpname)) {

@@ -5,7 +5,7 @@

 ", pkgname, " version ", version, "

 Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/

 Github page: https://github.com/jokergoo/ComplexHeatmap

-Documentation: http://bioconductor.org/packages/ComplexHeatmap/

+Documentation: http://jokergoo.github.io/ComplexHeatmap_book

 If you use it in published research, please cite:

 Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 

@@ -71,3 +71,16 @@ rowAnnotation(foo = 1:10, bar = anno_points(10:1))

 HeatmapAnnotation(1:10)

 HeatmapAnnotation(data.frame(1:10))

+

+

+

+ha = HeatmapAnnotation(summary = anno_summary(height = unit(4, "cm")))

+v = sample(letters[1:2], 50, replace = TRUE)

+split = sample(letters[1:2], 50, replace = TRUE)

+

+Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split)

+

+ha = HeatmapAnnotation(summary = anno_summary(gp = gpar(fill = 2:3), height = unit(4, "cm")))

+v = rnorm(50)

+Heatmap(v, top_annotation = ha, width = unit(1, "cm"), split = split)

+