@@ -992,13 +992,13 @@ setMethod(f = "draw_hclust",

     pushViewport(viewport(name = paste(object@name, which, "cluster", sep = "_"), ...))

     if(side == "left") {

-        grid.dendrogram(dend, name = paste(object@name, "hclust_row", k, sep = "_"), max_height = max_height, facing = "right", order = "reverse", x = unit(1, "mm"), width = unit(1, "npc") - unit(1, "mm"), just = "left")

+        grid.dendrogram(dend, name = paste(object@name, "hclust_row", k, sep = "_"), max_height = max_height, facing = "right", order = "reverse", x = unit(1, "mm"), width = unit(1, "npc") - unit(3, "mm"), just = "left")

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

-        grid.dendrogram(dend, name = paste(object@name, "hclust_row", k, sep = "_"), max_height = max_height, facing = "left", order = "reverse", x = unit(0, "null"), width = unit(1, "npc") - unit(1, "mm"), just = "left")

+        grid.dendrogram(dend, name = paste(object@name, "hclust_row", k, sep = "_"), max_height = max_height, facing = "left", order = "reverse", x = unit(0, "null"), width = unit(1, "npc") - unit(3, "mm"), just = "left")

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

-        grid.dendrogram(dend, name = paste(object@name, "hclust_column", sep = "_"), max_height = max_height, facing = "bottom", y = unit(0, "null"), height = unit(1, "npc") - unit(1, "mm"), just = "bottom")

+        grid.dendrogram(dend, name = paste(object@name, "hclust_column", sep = "_"), max_height = max_height, facing = "bottom", y = unit(2, "mm"), height = unit(1, "npc") - unit(3, "mm"), just = "bottom")

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

-        grid.dendrogram(dend, name = paste(object@name, "hclust_column", sep = "_"), max_height = max_height, facing = "top", y = unit(1, "mm"), height = unit(1, "npc") - unit(1, "mm"), just = "bottom")

+        grid.dendrogram(dend, name = paste(object@name, "hclust_column", sep = "_"), max_height = max_height, facing = "top", y = unit(1, "mm"), height = unit(1, "npc") - unit(3, "mm"), just = "bottom")

     } 

     upViewport()

@@ -1171,7 +1171,11 @@ setMethod(f = "draw_annotation",

         return(invisible(NULL))

     }

-    draw(annotation, index = object@column_order)

+    if(which == "top") {

+        draw(annotation, index = object@column_order, y = unit(2, "mm"), height = unit(1, "npc") - unit(2, "mm"), just = "bottom")

+    } else {

+        draw(annotation, index = object@column_order, y = unit(0, "null"), height = unit(1, "npc") - unit(2, "mm"), just = "bottom")

+    }

 })

 # == title

@@ -40,7 +40,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 #

 # == param

 # -df a data frame. Each column will be treated as a simple annotation. The data frame must have column names.

-# -name name of the heatmap annotation

+# -name name of the heatmap annotation, optional.

 # -col a list of colors which contains color mapping to columns in ``df``. See `SingleAnnotation` for how to set colors.

 # -show_legend whether show legend for each column in ``df``.

 # -... functions which define complex annotations. Values should be named arguments.

@@ -54,7 +54,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 #

 # == details

 # The simple annotations are defined by ``df`` and ``col`` arguments. Complex annotations are

-# defined by the function list. 

+# defined by the function list. So you need to at least to define ``df` or a annotation function.

 #

 # == value

 # A `HeatmapAnnotation-class` object.

@@ -65,7 +65,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # == author

 # Zuguang Gu <z.gu@dkfz.de>

 #

-HeatmapAnnotation = function(df, name, col, show_legend, ..., 

+HeatmapAnnotation = function(df, name, col, show_legend = rep(TRUE, n_anno), ..., 

 	which = c("column", "row"), annotation_height = 1, annotation_width = 1, 

 	height = unit(1, "cm"), width = unit(1, "cm"), gp = gpar(col = NA),

 	gap = unit(0, "null")) {

@@ -90,9 +90,6 @@ HeatmapAnnotation = function(df, name, col, show_legend, ...,

 	    anno_name = colnames(df)

 	    n_anno = ncol(df)

-	    if(missing(show_legend)) {

-	    	show_legend = rep(TRUE, n_anno)

-	    }

 	    if(length(show_legend) == 1) {

 	    	show_legend = rep(show_legend, n_anno)

 	    }

@@ -111,6 +108,9 @@ HeatmapAnnotation = function(df, name, col, show_legend, ...,

 	        }

 	    }

 	}

+	if(which == "column") {

+		anno_list = rev(anno_list)

+	}

 	# self-defined anntatoin graph are passed by a list of named functions

 	fun_list = list(...)

@@ -518,6 +518,7 @@ setMethod(f = "make_layout",

 #

 # == param

 # -object a `HeatmapList-class` object

+# -padding padding of the plot. Elements correspond to bottom, left, top, right paddings.

 # -... pass to `make_layout,HeatmapList-method`

 # -newpage whether to create a new page

 #

@@ -535,7 +536,7 @@ setMethod(f = "make_layout",

 #

 setMethod(f = "draw",

     signature = "HeatmapList",

-    definition = function(object, ..., newpage= TRUE) {

+    definition = function(object, padding = unit(c(2, 2, 2, 2), "mm"), ..., newpage= TRUE) {

     if(! any(sapply(object@ht_list, inherits, "Heatmap"))) {

         stop("There should be at least one Heatmap in the heatmap list.")

@@ -547,8 +548,17 @@ setMethod(f = "draw",

     object = make_layout(object, ...)

+    if(length(padding) == 1) {

+        padding = rep(padding, 4)

+    } else if(length(padding) == 2) {

+        padding = rep(padding, 2)

+    } else if(length(padding) != 4) {

+        stop("`padding` can only have length of 1, 2, 4")

+    }

+

     layout = grid.layout(nrow = 7, ncol = 7, widths = component_width(object, 1:7), heights = component_height(object, 1:7))

-    pushViewport(viewport(layout = layout, name = "global"))

+    pushViewport(viewport(layout = layout, name = "global", width = unit(1, "npc") - padding[2] - padding[4],

+        height = unit(1, "npc") - padding[1] - padding[3]))

     ht_layout_index = object@layout$layout_index

     ht_graphic_fun_list = object@layout$graphic_fun_list

@@ -1097,6 +1107,8 @@ draw_legend = function(ColorMappingList, side = c("right", "left", "top", "botto

     if(side %in% c("left", "right")) {

+        ColorMappingList = rev(ColorMappingList)

+

         width = max(cm_width)

         height = sum(cm_height) + gap*(n + length(annotation_legend_list) -1)

@@ -49,7 +49,7 @@ default_col = function(x, main_matrix = FALSE) {

     if(is.character(x)) {  # discrete

         levels = unique(x)

-        colors = rainbow_hcl(length(levels), c = 60, l = 75)

+        colors = hsv(runif(length(levels)), runif(length(levels)), 1)

         names(colors) = levels

         return(colors)

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

@@ -60,7 +60,7 @@ default_col = function(x, main_matrix = FALSE) {

                 col_fun = colorRamp2(seq(min(x), max(x), length.out = 100), diverge_hcl(100, c = 100, l = c(50, 90), power = 1))

             }

         } else {

-            col_fun = colorRamp2(range(min(x), max(x)), c("white", rainbow_hcl(1, c = 60, l = 75)))

+            col_fun = colorRamp2(range(min(x), max(x)), c("white", hsv(runif(1), runif(1), 1)))

         }

         return(col_fun)

     }