@@ -3106,7 +3106,7 @@ anno_mark = function(at, labels, which = c("column", "row"),

 	link_gp = subset_gp(link_gp, od)

 	labels_gp = subset_gp(labels_gp, od)

-	labels2index = structure(seq_along(at), names = as.character(labels))

+	at2index = structure(seq_along(at), names = as.character(at))

 	at2labels = structure(labels, names = at)

 	if(length(extend) == 1) extend = rep(extend, 2)

@@ -3148,8 +3148,8 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		}

 		labels = rev(at2labels[as.character(at)])

-		labels_gp = subset_gp(labels_gp, labels2index[as.character(labels)])

-		link_gp = subset_gp(link_gp, labels2index[as.character(labels)])

+		labels_gp = subset_gp(labels_gp, rev(at2index[as.character(at)]))

+		link_gp = subset_gp(link_gp, rev(at2index[as.character(at)]))

 		if(is.null(.scale)) {

 			.scale = c(0.5, n+0.5)

@@ -3225,8 +3225,8 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		}

 		labels = at2labels[as.character(at)]

-		labels_gp = subset_gp(labels_gp, labels2index[as.character(labels)])

-		link_gp = subset_gp(link_gp, labels2index[as.character(labels)])

+		labels_gp = subset_gp(labels_gp, rev(at2index[as.character(at)]))

+		link_gp = subset_gp(link_gp, rev(at2index[as.character(at)]))

 		if(is.null(.scale)) {

 			.scale = c(0.5, n+0.5)

@@ -3300,7 +3300,7 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		width = width,

 		height = height,

 		n = -1,

-		var_import = list(at, labels2index, at2labels, link_gp, labels_gp, labels_rot, padding, .pos, .scale,

+		var_import = list(at, at2index, at2labels, link_gp, labels_gp, labels_rot, padding, .pos, .scale,

 			side, link_width, link_height, extend),

 		show_name = FALSE

 	)

@@ -4414,7 +4414,6 @@ anno_numeric = function(x, rg = range(x), labels_gp = gpar(), x_convert = NULL,

     }

     cell_fun_pct = function(i) {

-

     	min_x = rg[1]

     	max_x = rg[2]

         pushViewport(viewport(xscale = rg))

@@ -4445,24 +4444,24 @@ anno_numeric = function(x, rg = range(x), labels_gp = gpar(), x_convert = NULL,

         		if(round_corners) {

 		        	grid.roundrect(x = unit(0, "native"), 

 		                width = unit(-x[i], "native"), height = bar_width,  r = r,

-		                just = "right", gp = subset_gp(bg_gp, 1))

+		                just = "right", gp = subset_gp(bg_gp, i))

 		        } else {

 		        	grid.rect(x = unit(0, "native"), 

 		                width = unit(-x[i], "native"), height = bar_width, 

-		                just = "right", gp = subset_gp(bg_gp, 1))

+		                just = "right", gp = subset_gp(bg_gp, i))

 		        }

-	            grid.text(labels[i], x = unit(0, "native") - labels_offset, just = "right", gp = subset_gp(labels_gp, 1))

+	            grid.text(labels[i], x = unit(0, "native") - labels_offset, just = "right", gp = subset_gp(labels_gp, i))

 	        } else {

 	        	if(round_corners) {

 		        	grid.roundrect(x = unit(0, "native"), 

 		                width = unit(x[i], "native"), height = bar_width,  r = r,

-		                just = "left", gp = subset_gp(bg_gp, 2))

+		                just = "left", gp = subset_gp(bg_gp, i))

 		        } else {

 		        	grid.rect(x = unit(0, "native"), 

 		                width = unit(x[i], "native"), height = bar_width,

-		                just = "left", gp = subset_gp(bg_gp, 2))

+		                just = "left", gp = subset_gp(bg_gp, i))

 		        }

-	            grid.text(labels[i], x = unit(0, "native") + labels_offset, just = "left", gp = subset_gp(labels_gp, 2))

+	            grid.text(labels[i], x = unit(0, "native") + labels_offset, just = "left", gp = subset_gp(labels_gp, i))

 	        }

         }

         popViewport()

@@ -1561,8 +1561,10 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 # -extend The extension to both side of ``ylim``. The value is a percent value corresponding to ``ylim[2] - ylim[1]``.

 # -outline Whether draw outline of boxplots?

 # -box_width Relative width of boxes. The value should be smaller than one.

+# -add_points Whether add points on top of the boxes?

 # -pch Point style.

 # -size Point size.

+# -pt_gp Graphics parameters for points.

 # -axis Whether to add axis?

 # -axis_param parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters.

 # -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.

@@ -1584,8 +1586,8 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 # draw(anno, test = "anno_boxplot with gp")

 anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

 	gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6,

-	pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which),

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

+	add_points = FALSE, pch = 16, size = unit(4, "pt"), pt_gp = gpar(), axis = TRUE, 

+	axis_param = default_axis_param(which), width = NULL, height = NULL, ...) {

 	other_args = list(...)

 	if(length(other_args)) {

@@ -1639,6 +1641,7 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

 	n = length(value)

 	gp = recycle_gp(gp, n)

+	pt_gp = recycle_gp(pt_gp, n)

 	if(length(pch) == 1) pch = rep(pch, n)

 	if(length(size) == 1) size = rep(size, n)

@@ -1657,6 +1660,7 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

 		n = length(index)

 		gp = subset_gp(gp, index)

+		pt_gp = subset_gp(pt_gp, index)

 		pch = pch[index]

 		size = size[index]

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

@@ -1680,18 +1684,25 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

 		grid.segments(boxplot_stats[3, ], n - seq_along(index) + 1 - 0.5*box_width, 

 			          boxplot_stats[3, ], n - seq_along(index) + 1 + 0.5*box_width, 

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

-		if(outline) {

+		if(!add_points && outline) {

 			for(i in seq_along(value)) {

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

 				l1[is.na(l1)] = FALSE

 				if(sum(l1)) grid.points(y = rep(n - i + 1, sum(l1)), x = value[[i]][l1], 

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

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

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

 				l2[is.na(l2)] = FALSE

 				if(sum(l2)) grid.points(y = rep(n - i + 1, sum(l2)), x = value[[i]][l2], 

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

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

+			}

+		}

+		if(add_points && outline) {

+			for(i in seq_along(value)) {

+				grid.points(y = n - runif(length(value[[i]]), min = i - 0.5*0.5*box_width, max = i + 0.5*0.5*box_width) + 1,

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

 			}

 		}

+

 		if(axis_param$side == "top") {

 			if(k > 1) axis = FALSE

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

@@ -1712,6 +1723,7 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

 		n = length(index)

 		gp = subset_gp(gp, index)

+		pt_gp = subset_gp(pt_gp, index)

 		pch = pch[index]

 		size = size[index]

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

@@ -1734,16 +1746,24 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

 		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) {	

+		

+		if(!add_points && outline) {	

 			for(i in seq_along(value)) {

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

 				l1[is.na(l1)] = FALSE

 				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])

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

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

 				l2[is.na(l2)] = FALSE

 				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])

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

+			}

+		}

+

+		if(add_points && outline) {

+			for(i in seq_along(value)) {

+				grid.points(x = runif(length(value[[i]]), min = i - 0.5*0.5*box_width, max = i + 0.5*0.5*box_width),

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

 			}

 		}

 		if(axis_param$side == "left") {

@@ -1770,11 +1790,12 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

 		width = anno_size$width,

 		height = anno_size$height,

 		data_scale = data_scale,

-		var_import = list(value, gp, border, box_width, axis, axis_param, axis_grob, data_scale, pch, size, outline)

+		var_import = list(value, gp, border, box_width, axis, axis_param, axis_grob, data_scale, add_points, pch, pt_gp, size, outline)

 	)

 	anno@subset_rule$value = subset_vector

 	anno@subset_rule$gp = subset_gp

+	anno@subset_rule$pt_gp = subset_gp

 	anno@subset_rule$pch = subset_vector

 	anno@subset_rule$size = subset_vector

@@ -1396,7 +1396,7 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 		} else {

 			if(beside) {

 				nbar = ncol(value)

-				nr = nrow(value)

+				nr = length(index)

 				for(i in seq_along(index)) {

 			        for(j in 1:nbar) {

 			        	if(attach) {

@@ -1471,7 +1471,7 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 		} else {

 			if(beside) {

 				nbar = ncol(value)

-				nr = nrow(value)

+				nr = length(index)

 				for(i in seq_along(index)) {

 			        for(j in 1:nbar) {

 			        	if(attach) {

@@ -2112,17 +2112,17 @@ anno_density = function(x, which = c("column", "row"),

 					width = density_x[[i]][-1] - density_x[[i]][-n_breaks], height = 1, 

 					just = c("right", "bottom"), default.units = "native", 

 					gp = gpar(fill = col_fun((density_y[[i]][-1] + density_y[[i]][-n_breaks])/2), 

-						col = NA))

+						col = col_fun((density_y[[i]][-1] + density_y[[i]][-n_breaks])/2)))

 				if(density_x[[i]][1] - min_density_x > 0) {

 					grid.rect(x = density_x[[i]][1], y = 0, width = density_x[[i]][1] - min_density_x, 

 						height = 1, just = c("right", "bottom"), default.units = "native", 

-						gp = gpar(fill = col_fun(0), col = NA))

+						gp = gpar(fill = col_fun(0), col = col_fun(0)))

 				}

 				if(max_density_x - density_x[[i]][n_breaks] > 0) {

 					grid.rect(x = density_x[[i]][n_breaks], y = 0, 

 						width = max_density_x - density_x[[i]][n_breaks], height = 1, 

 						just = c("left", "bottom"), default.units = "native", 

-						gp = gpar(fill = col_fun(0), col = NA))

+						gp = gpar(fill = col_fun(0), col = col_fun(0)))

 				}

 			}

 			popViewport()

@@ -2149,8 +2149,6 @@ anno_density = function(x, which = c("column", "row"),

 		density_x = density_x[index]

 		density_y = density_y[index]

-		yscale = range(unlist(density_x), na.rm = TRUE)

-		yscale = yscale + c(0, 0.05)*(yscale[2] - yscale[1])

 		if(type == "lines") {

 			xscale = c(0, max(unlist(density_y)))

 			xscale[2] = xscale[2]*1.05

@@ -2158,7 +2156,6 @@ anno_density = function(x, which = c("column", "row"),

 			xscale = max(unlist(density_y))

 			xscale = c(-xscale*1.05, xscale*1.05)

 		} else if(type == "heatmap") {

-			yscale = range(unlist(density_x), na.rm = TRUE)

 			xscale = c(0, 1)

 			min_y = min(unlist(density_y))

 			max_y = max(unlist(density_y))

@@ -2192,17 +2189,17 @@ anno_density = function(x, which = c("column", "row"),

 					height = density_x[[i]][-1] - density_x[[i]][-n_breaks], width = 1, 

 					just = c("left", "top"), default.units = "native", 

 					gp = gpar(fill = col_fun((density_y[[i]][-1] + density_y[[i]][-n_breaks])/2), 

-						col = NA))

+						col = col_fun((density_y[[i]][-1] + density_y[[i]][-n_breaks])/2)))

 				if(density_x[[i]][1] - min_density_x > 0) {

 					grid.rect(y = density_x[[i]][1], x = 0, height = density_x[[i]][1] - min_density_x, 

 						width = 1, just = c("left", "top"), default.units = "native", 

-						gp = gpar(fill = col_fun(0), col = NA))

+						gp = gpar(fill = col_fun(0), col = col_fun(0)))

 				}

 				if(max_density_x - density_x[[i]][n_breaks] > 0) {

 					grid.rect(y = density_x[[i]][n_breaks], x = 0, 

 						height = max_density_x - density_x[[i]][n_breaks], width = 1, 

 						just = c("left", "bottom"), default.units = "native", 

-						gp = gpar(fill = col_fun(0), col = NA))

+						gp = gpar(fill = col_fun(0), col = col_fun(0)))

 				}

 			}

 			popViewport()

@@ -2042,6 +2042,8 @@ anno_density = function(x, which = c("column", "row"),

 			density_x[[i]] = c(density_x[[i]][ 1 ], density_x[[i]], density_x[[i]][ length(density_x[[i]]) ])

 			density_y[[i]] = c(0, density_y[[i]], 0)

 		}

+		min_density_x = xlim[1]

+		max_density_x = xlim[2]

 	}

 	if(type == "lines") {

@@ -2111,13 +2113,17 @@ anno_density = function(x, which = c("column", "row"),

 					just = c("right", "bottom"), default.units = "native", 

 					gp = gpar(fill = col_fun((density_y[[i]][-1] + density_y[[i]][-n_breaks])/2), 

 						col = NA))

-				grid.rect(x = density_x[[i]][1], y = 0, width = density_x[[i]][1] - min_density_x, 

-					height = 1, just = c("right", "bottom"), default.units = "native", 

-					gp = gpar(fill = col_fun(0), col = NA))

-				grid.rect(x = density_x[[i]][n_breaks], y = 0, 

-					width = max_density_x - density_x[[i]][n_breaks], height = 1, 

-					just = c("left", "bottom"), default.units = "native", 

-					gp = gpar(fill = col_fun(0), col = NA))

+				if(density_x[[i]][1] - min_density_x > 0) {

+					grid.rect(x = density_x[[i]][1], y = 0, width = density_x[[i]][1] - min_density_x, 

+						height = 1, just = c("right", "bottom"), default.units = "native", 

+						gp = gpar(fill = col_fun(0), col = NA))

+				}

+				if(max_density_x - density_x[[i]][n_breaks] > 0) {

+					grid.rect(x = density_x[[i]][n_breaks], y = 0, 

+						width = max_density_x - density_x[[i]][n_breaks], height = 1, 

+						just = c("left", "bottom"), default.units = "native", 

+						gp = gpar(fill = col_fun(0), col = NA))

+				}

 			}

 			popViewport()

 		}

@@ -2187,13 +2193,17 @@ anno_density = function(x, which = c("column", "row"),

 					just = c("left", "top"), default.units = "native", 

 					gp = gpar(fill = col_fun((density_y[[i]][-1] + density_y[[i]][-n_breaks])/2), 

 						col = NA))

-				grid.rect(y = density_x[[i]][1], x = 0, height = density_x[[i]][1] - min_density_x, 

-					width = 1, just = c("left", "top"), default.units = "native", 

-					gp = gpar(fill = col_fun(0), col = NA))

-				grid.rect(y = density_x[[i]][n_breaks], x = 0, 

-					height = max_density_x - density_x[[i]][n_breaks], width = 1, 

-					just = c("left", "bottom"), default.units = "native", 

-					gp = gpar(fill = col_fun(0), col = NA))

+				if(density_x[[i]][1] - min_density_x > 0) {

+					grid.rect(y = density_x[[i]][1], x = 0, height = density_x[[i]][1] - min_density_x, 

+						width = 1, just = c("left", "top"), default.units = "native", 

+						gp = gpar(fill = col_fun(0), col = NA))

+				}

+				if(max_density_x - density_x[[i]][n_breaks] > 0) {

+					grid.rect(y = density_x[[i]][n_breaks], x = 0, 

+						height = max_density_x - density_x[[i]][n_breaks], width = 1, 

+						just = c("left", "bottom"), default.units = "native", 

+						gp = gpar(fill = col_fun(0), col = NA))

+				}

 			}

 			popViewport()

 		}

@@ -1958,6 +1958,8 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,

 # -type Type of graphics to represent density distribution. "lines" for normal density plot; "violine" for violin plot

 #       and "heatmap" for heatmap visualization of density distribution.

 # -xlim Range on x-axis.

+# -max_density Maximal density values in the plot. Normally you don't need to manually set it, but when you have multiple density annotations

+#   and you want to compare between them, you should manually set this argument to make density distributions are in a same scale.

 # -heatmap_colors A vector of colors for interpolating density values.

 # -joyplot_scale Relative height of density distribution. A value higher than 1 increases the height of the density

 #               distribution and the plot will represented as so-called "joyplot".

@@ -1986,7 +1988,7 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,

 #     heatmap_colors = c("white", "orange"))

 # draw(anno, test = "heatmap, colors")

 anno_density = function(x, which = c("column", "row"),

-	type = c("lines", "violin", "heatmap"), xlim = NULL,

+	type = c("lines", "violin", "heatmap"), xlim = NULL, max_density = NULL,

 	heatmap_colors = rev(brewer.pal(name = "RdYlBu", n = 11)), 

 	joyplot_scale = 1, border = TRUE, gp = gpar(fill = "#CCCCCC"),

 	axis = TRUE, axis_param = default_axis_param(which),

@@ -2044,16 +2046,29 @@ anno_density = function(x, which = c("column", "row"),

 	if(type == "lines") {

 		xscale = xscale + c(-0.025, 0.025)*(xscale[2] - xscale[1])

-		yscale = c(0, max(unlist(density_y)))

+		if(is.null(max_density)) {

+			yscale = c(0, max(unlist(density_y)))

+		} else {

+			yscale = c(0, max_density)

+		}

 		yscale[2] = yscale[2]*1.05

 	} else if(type == "violin") {

 		xscale = xscale + c(-0.025, 0.025)*(xscale[2] - xscale[1])

-		yscale = max(unlist(density_y))

+		if(is.null(max_density)) {

+			yscale = max(unlist(density_y))

+		} else {

+			yscale = max_density

+		}

 		yscale = c(-yscale*1.05, yscale*1.05)

 	} else if(type == "heatmap") {

 		yscale = c(0, 1)

-		min_y = min(unlist(density_y))

-		max_y = max(unlist(density_y))

+		if(is.null(max_density)) {

+			min_y = min(unlist(density_y))

+			max_y = max(unlist(density_y))

+		} else {

+			min_y = 0

+			max_y = max_density

+		}

 		col_fun = colorRamp2(seq(min_y, max_y, 

 			length.out = length(heatmap_colors)), heatmap_colors)

 	}

@@ -1300,18 +1300,18 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 		data_scale = range(rowSums(x, na.rm = TRUE), na.rm = TRUE)

 	}

-	if(data_scale[1] == data_scale[2]) data_scale[2] = data_scale[1] + 1

+	if(data_scale[1] == data_scale[2]) data_scale[2] = data_scale[1] + .Machine$double.eps*1.1

 	if(!is.null(ylim)) data_scale = ylim

 	if(baseline == "min") {

 		data_scale = data_scale + c(0, extend)*(data_scale[2] - data_scale[1])

-		baseline = min(x)

+		baseline = min(x, na.rm = TRUE)

 	} else if(baseline == "max") {

 		data_scale = data_scale + c(-extend, 0)*(data_scale[2] - data_scale[1])

-		baseline = max(x)

+		baseline = max(x, na.rm = TRUE)

 	} else {

 		if(is.numeric(baseline)) {

-			if(baseline == 0 && all(abs(rowSums(x) - 1) < 1e-6) && !beside) {

+			if(baseline == 0 && all(abs(rowSums(x, na.rm = TRUE) - 1) < 1e-6) && !beside) {

 				data_scale = c(0, 1)

 			} else if(baseline <= data_scale[1]) {

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

@@ -4314,8 +4314,8 @@ anno_customize = function(x, graphics = list(), which = c("column", "row"),

 # == param

 # -x A vector of numeric values.

 # -rg Range. A numeric vector of length two.

-# -labels_gp. Graphics parameters for labels.

-# -x_convert. A function applied on ``x``. E.g. when ``x`` contains p-values, to map ``x`` to the heights of bars, a transformation of ``-log10(x)`` 

+# -labels_gp Graphics parameters for labels.

+# -x_convert A function applied on ``x``. E.g. when ``x`` contains p-values, to map ``x`` to the heights of bars, a transformation of ``-log10(x)`` 

 #      is normally applied.

 # -labels_format A function applied on ``x``. E.g., when ``x`` is a numeric, ``labels_format`` can be set to ``function(x) sprintf("\%.2f", x)``.

 # -labels_offset Offset of labels to the left or right of bars.

@@ -4330,7 +4330,7 @@ anno_customize = function(x, graphics = list(), which = c("column", "row"),

 #

 # == example

 # m = matrix(rnorm(100), 10)

-# x = numeric(10)

+# x = rnorm(10)

 # Heatmap(m, right_annotation = rowAnnotation(numeric = anno_numeric(x)))

 anno_numeric = function(x, rg = range(x), labels_gp = gpar(), x_convert = NULL, 

 	labels_format = NULL, labels_offset = unit(4, "pt"),

@@ -4359,6 +4359,10 @@ anno_numeric = function(x, rg = range(x), labels_gp = gpar(), x_convert = NULL,

 		rg = range(x_convert(rg))

 	}

+	if(rg[1] == rg[2]) {

+		rg[2] = rg[2] + .Machine$double.eps*1.1

+	}

+

     x[x < rg[1]] = rg[1]

     x[x > rg[2]] = rg[2]

@@ -10,6 +10,7 @@

 #       and the original heatmap slices.

 # -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.

 # -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.

+# -show_name Whether to show annotation name.

 #

 # == details

 # It creates an empty annotation and holds space, later users can add graphics

@@ -46,7 +47,7 @@

 # anno = anno_empty(border = FALSE)

 # draw(anno, test = "anno_empty without border")

 anno_empty = function(which = c("column", "row"), border = TRUE, zoom = FALSE,

-	width = NULL, height = NULL) {

+	width = NULL, height = NULL, show_name = FALSE) {

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

 		which = match.arg(which)[1]

@@ -68,10 +69,10 @@ anno_empty = function(which = c("column", "row"), border = TRUE, zoom = FALSE,

 		which = which,

 		var_import = list(border, zoom),

 		subset_rule = list(),

-		subsetable = TRUE,

+		subsettable = TRUE,

 		height = anno_size$height,

 		width = anno_size$width,

-		show_name = FALSE

+		show_name = show_name

 	)

 	return(anno) 

@@ -242,10 +243,15 @@ anno_simple = function(x, col, na_col = "grey",

 			pch = pch[index, , drop = FALSE]

 			for(i in seq_len(nc)) {

-				if(color_mapping@type == "continuous") {

+				if(color_mapping@type == "continuous" || !is.null(gp$col)) {

 				    fill = map_to_colors(color_mapping, value[index, i])

-				    if(is.null(gp$col)) gp$col = fill

+				    flag = 0

+	                if(is.null(gp$col)) {

+	                	gp$col = fill

+	                	flag = 1

+	                }

 				    grid.rect(x = (i-0.5)/nc, y, height = 1/n, width = 1/nc, gp = do.call("gpar", c(list(fill = fill), gp)))

+				    if(flag) gp$col = NULL

 				} else {

 					r = rle(value[index, i])

 					fill = map_to_colors(color_mapping, r$values)

@@ -269,7 +275,7 @@ anno_simple = function(x, col, na_col = "grey",

 			    }

 			}

 	    } else {

-	    	if(color_mapping@type == "continuous") {

+	    	if(color_mapping@type == "continuous" || !is.null(gp$col)) {

 				fill = map_to_colors(color_mapping, value[index])

 				if(is.null(gp$col)) gp$col = fill

 				grid.rect(x = 0.5, y, height = 1/n, width = 1, gp = do.call("gpar", c(list(fill = fill), gp)))

@@ -308,12 +314,16 @@ anno_simple = function(x, col, na_col = "grey",

             nc = ncol(value)

 		    pch = pch[index, , drop = FALSE]

-				  

 	        for(i in seq_len(nc)) {

-	        	if(color_mapping@type == "continuous") {

+	        	if(color_mapping@type == "continuous" || !is.null(gp$col)) {

 	                fill = map_to_colors(color_mapping, value[index, i])

-	                if(is.null(gp$col)) gp$col = fill

+	                flag = 0

+	                if(is.null(gp$col)) {

+	                	gp$col = fill

+	                	flag = 1

+	                }

 	                grid.rect(x, y = (nc-i +0.5)/nc, width = 1/n, height = 1/nc, gp = do.call("gpar", c(list(fill = fill), gp)))

+	                if(flag) gp$col = NULL

 	            } else {

 	            	r = rle(value[index, i])

 					fill = map_to_colors(color_mapping, r$values)

@@ -337,7 +347,7 @@ anno_simple = function(x, col, na_col = "grey",

 				}

 		    }

         } else {

-        	if(color_mapping@type == "continuous") {

+        	if(color_mapping@type == "continuous" || !is.null(gp$col)) {

 				fill = map_to_colors(color_mapping, value[index])

 				if(is.null(gp$col)) gp$col = fill

 				grid.rect(x, y = 0.5, width = 1/n, height = 1, gp = do.call("gpar", c(list(fill = fill), gp)))

@@ -400,7 +410,7 @@ anno_simple = function(x, col, na_col = "grey",

 		}

 	}

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	return(anno)      

 }

@@ -563,7 +573,13 @@ anno_image = function(image, which = c("column", "row"), border = TRUE,

 				grid.picture(image_list[[ index[i] ]], x = (i-0.5)/n, width = width, height = height)

 			}

 		}

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

+		if(is.logical(border)) {

+			if(border) {

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

+			}

+		} else {

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

+		}

 		popViewport()

 	}

@@ -592,7 +608,13 @@ anno_image = function(image, which = c("column", "row"), border = TRUE,

 				grid.picture(image_list[[ index[i] ]], y = (n - i + 0.5)/n, width = width, height = height)

 			}

 		}

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

+		if(is.logical(border)) {

+			if(border) {

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

+			}

+		} else {

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

+		}

 		popViewport()

 	}

@@ -617,7 +639,7 @@ anno_image = function(image, which = c("column", "row"), border = TRUE,

 	anno@subset_rule$image_list = subset_vector

 	anno@subset_rule$image_class = subset_vector

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	return(anno)   

 }

@@ -914,7 +936,7 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()

 		anno@subset_rule$pch = subset_vector

 	}

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

@@ -1185,7 +1207,7 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),

 		anno@subset_rule$pch = subset_vector

 	}

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

@@ -1205,6 +1227,7 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),

 # -border Wether draw borders of the annotation region?

 # -bar_width Relative width of the bars. The value should be smaller than one.

 # -beside When ``x`` is a matrix, will bars be positioned beside each other or as stacked bars?

+# -attach When ``beside`` is ``TRUE``, it controls whether bars should be attached.

 # -gp Graphic parameters for bars. The length of each graphic parameter can be 1, length of ``x`` if ``x``

 #     is a vector, or number of columns of ``x`` is ``x`` is a matrix.

 # -ylim Data ranges. By default it is ``range(x)`` if ``x`` is a vector, or ``range(rowSums(x))`` if ``x`` is a matrix.

@@ -1233,7 +1256,8 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),

 # m = t(apply(m, 1, function(x) x/sum(x)))

 # anno = anno_barplot(m, gp = gpar(fill = 2:5), bar_width = 1, height = unit(6, "cm"))

 # draw(anno, test = "proportion matrix")

-anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6, beside = FALSE,

+anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6, 

+	beside = FALSE, attach = FALSE,

 	gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE, 

 	axis_param = default_axis_param(which), 

 	add_numbers = FALSE, numbers_gp = gpar(fontsize = 8), 

@@ -1375,13 +1399,23 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 				nr = nrow(value)

 				for(i in seq_along(index)) {

 			        for(j in 1:nbar) {

-			        	if(axis_param$direction == "normal") {

-				        	grid.rect(x = baseline, y = nr-i+0.5 + (j-0.5)/nbar, width = value[index[i], j], height = 1/nbar*bar_width, just = c("left"),

-				        		default.units = "native", gp = subset_gp(gp, j))

-				        } else {

-				        	grid.rect(x = baseline, y = nr-i+0.5 + (j-0.5)/nbar, width = value[index[i], j], height = 1/nbar*bar_width, just = c("right"),

-				        		default.units = "native", gp = subset_gp(gp, j))

-				        }

+			        	if(attach) {

+			        		if(axis_param$direction == "normal") {

+					        	grid.rect(x = baseline, y = nr-i+0.5 + (1-bar_width)/2 + (nbar - j + 0.5)/nbar*bar_width, width = value[index[i], j], height = 1/nbar*bar_width, just = c("left"),

+					        		default.units = "native", gp = subset_gp(gp, j))

+					        } else {

+					        	grid.rect(x = baseline, y = nr-i+0.5 + (1-bar_width)/2 + (nbar - j + 0.5)/nbar*bar_width, width = value[index[i], j], height = 1/nbar*bar_width, just = c("right"),

+					        		default.units = "native", gp = subset_gp(gp, j))

+					        }

+			        	} else {

+				        	if(axis_param$direction == "normal") {

+					        	grid.rect(x = baseline, y = nr-i+0.5 + (nbar - j + 0.5)/nbar, width = value[index[i], j], height = 1/nbar*bar_width, just = c("left"),

+					        		default.units = "native", gp = subset_gp(gp, j))

+					        } else {

+					        	grid.rect(x = baseline, y = nr-i+0.5 + (nbar - j + 0.5)/nbar, width = value[index[i], j], height = 1/nbar*bar_width, just = c("right"),

+					        		default.units = "native", gp = subset_gp(gp, j))

+					        }

+					    }

 			        }

 			    }

 			} else {

@@ -1440,13 +1474,23 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 				nr = nrow(value)

 				for(i in seq_along(index)) {

 			        for(j in 1:nbar) {

-			        	if(axis_param$direction == "normal") {

-				        	grid.rect(y = baseline, x = nr-i+0.5 + (j-0.5)/nbar, height = value[index[i], j], width = 1/nbar*bar_width, just = c("bottom"),

-				        		default.units = "native", gp = subset_gp(gp, j))

-				        } else {

-				        	grid.rect(y = baseline, x = nr-i+0.5 + (j-0.5)/nbar, height = value[index[i], j], width = 1/nbar*bar_width, just = c("top"),

-				        		default.units = "native", gp = subset_gp(gp, j))

-				        }

+			        	if(attach) {

+				        	if(axis_param$direction == "normal") {

+					        	grid.rect(y = baseline, x = i-0.5 + (1-bar_width)/2 + (j-0.5)/nbar*bar_width, height = value[index[i], j], width = 1/nbar*bar_width, just = c("bottom"),

+					        		default.units = "native", gp = subset_gp(gp, j))

+					        } else {

+					        	grid.rect(y = baseline, x = i-0.5 + (1-bar_width)/2 + (j-0.5)/nbar*bar_width, height = value[index[i], j], width = 1/nbar*bar_width, just = c("top"),

+					        		default.units = "native", gp = subset_gp(gp, j))

+					        }

+					    } else {

+					    	if(axis_param$direction == "normal") {

+					        	grid.rect(y = baseline, x = i-0.5 + (j-0.5)/nbar, height = value[index[i], j], width = 1/nbar*bar_width, just = c("bottom"),

+					        		default.units = "native", gp = subset_gp(gp, j))

+					        } else {

+					        	grid.rect(y = baseline, x = i-0.5 + (j-0.5)/nbar, height = value[index[i], j], width = 1/nbar*bar_width, just = c("top"),

+					        		default.units = "native", gp = subset_gp(gp, j))

+					        }

+					    }

 			        }

 			    }

 			} else {

@@ -1489,7 +1533,7 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 		height = anno_size$height,

 		n = n,

 		data_scale = data_scale,

-		var_import = list(value, gp, border, bar_width, baseline, beside, axis, axis_param, axis_grob, data_scale, add_numbers, numbers_gp, numbers_offset, numbers_rot)

+		var_import = list(value, gp, border, bar_width, baseline, beside, attach, axis, axis_param, axis_grob, data_scale, add_numbers, numbers_gp, numbers_offset, numbers_rot)

 	)

 	anno@subset_rule$value = subset_matrix_by_row

@@ -1497,7 +1541,7 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 		anno@subset_rule$gp = subset_gp

 	}

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

@@ -1734,7 +1778,7 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

 	anno@subset_rule$pch = subset_vector

 	anno@subset_rule$size = subset_vector

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

@@ -1897,7 +1941,7 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,

 	anno@subset_rule$histogram_breaks = subset_vector

 	anno@subset_rule$histogram_counts = subset_vector

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

@@ -2176,7 +2220,7 @@ anno_density = function(x, which = c("column", "row"),

 	anno@subset_rule$density_x = subset_vector

 	anno@subset_rule$density_y = subset_vector

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

@@ -2360,7 +2404,7 @@ anno_text = function(x, which = c("column", "row"), gp = gpar(),

 	anno@subset_rule$value = subset_vector

 	anno@subset_rule$gp = subset_gp

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	return(anno)

 }

@@ -2549,7 +2593,7 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000

 	anno@subset_rule$value = subset_vector

 	anno@subset_rule$gp = subset_gp

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

@@ -2733,7 +2777,7 @@ anno_horizon = function(x, which = c("column", "row"),

 	anno@subset_rule$value = subset_vector

 	anno@subset_rule$gp = subset_gp

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

@@ -3220,7 +3264,7 @@ anno_mark = function(at, labels, which = c("column", "row"),

 	anno@subset_rule$at = subset_by_intersect

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	attr(anno, "called_args") = list(

 		at = at, 

@@ -3427,7 +3471,7 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

 		show_name = FALSE

 	)

-	anno@subsetable = FALSE

+	anno@subsettable = FALSE

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

 	return(anno)

@@ -3437,6 +3481,8 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

 # Block annotation

 #

 # == param

+# -align_to If you don't want to create block annotation for all slices, you can specify a list of indices that cover continuously adjacent

+#        rows or columns.

 # -gp Graphic parameters.

 # -labels Labels put on blocks.

 # -labels_gp Graphic parameters for labels.

@@ -3447,7 +3493,7 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

 # -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.

 # -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.

 # -show_name Whether show annotatio name.

-# -graphics A self-defined function that draws graphics in each slice. It must have two arguments: 1. row/column indices for the 

+# -panel_fun A self-defined function that draws graphics in each slice. It must have two arguments: 1. row/column indices for the 

 #      current slice and 2. a vector of levels from the split variable that correspond to current slice. When ``graphics`` is set,

 #      all other graphics parameters in `anno_block` are ignored.

 #

@@ -3470,11 +3516,11 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

 #     row_km = 3)

 #

 #

-# # =============  set the graphics argument ==============

+# # =============  set the panel_fun argument ==============

 # col = c("1" = "red", "2" = "blue", "A" = "green", "B" = "orange")

 # Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 

 # rowAnnotation(foo = anno_block(

-# 	graphics = function(index, levels) {

+# 	panel_fun = function(index, levels) {

 # 		grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))

 # 		grid.text(paste(levels, collapse = ","), 0.5, 0.5, rot = 90,

 # 			gp = gpar(col = col[levels[1]]))

@@ -3483,7 +3529,7 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

 #

 # labels = c("1" = "one", "2" = "two", "A" = "Group_A", "B" = "Group_B")

 # Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 

-# rowAnnotation(foo = anno_block(graphics = function(index, levels) {

+# rowAnnotation(foo = anno_block(panel_fun = function(index, levels) {

 # 	grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))

 # 	grid.text(paste(labels[levels], collapse = ","), 0.5, 0.5, rot = 90,

 # 		gp = gpar(col = col[levels[1]]))

@@ -3491,7 +3537,7 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

 #

 # Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 

 # rowAnnotation(foo = anno_block(

-# 	graphics = function(index, levels) {

+# 	panel_fun = function(index, levels) {

 # 		grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))

 # 		txt = paste(levels, collapse = ",")

 # 		txt = paste0(txt, "\n", length(index), " rows")

@@ -3501,17 +3547,40 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0

 # 	width = unit(3, "cm")

 # ))

 #

-anno_block = function(gp = gpar(), labels = NULL, labels_gp = gpar(), 

+# # =========== set align_to ################

+# col = c("foo" = "red", "bar" = "blue")

+# Heatmap(matrix(rnorm(100), 10), cluster_rows = FALSE) +

+# rowAnnotation(foo = anno_block(

+# 	align_to = list(foo = 1:4, bar = 6:10),

+# 	panel_fun = function(index, nm) {

+# 		grid.rect(gp = gpar(fill = col[nm]))

+# 		grid.text(nm, 0.5, 0.5)

+# 	},

+# 	width = unit(2, "cm"))

+# )

+anno_block = function(align_to = NULL, gp = gpar(), labels = NULL, labels_gp = gpar(), 

 	labels_rot = ifelse(which == "row", 90, 0),

 	labels_offset = unit(0.5, "npc"), labels_just = "center",

 	which = c("column", "row"), width = NULL, height = NULL, show_name = FALSE,

-	graphics = NULL) {

+	panel_fun = NULL) {

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

 		which = match.arg(which)[1]

 	} else {

 		which = .ENV$current_annotation_which

 	}

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

+		if(is.numeric(align_to)) {

+			align_to = list(v = align_to)

+		}

+		if(!is.list(align_to)) {

+			stop_wrap("`align_to` should be a list.")

+		}

+		if(is.null(names(align_to))) {

+			stop_wrap("`align_to` should be a named list.")

+		}

+	}

+

 	if(length(labels)) {

 		if(which == "column") {

 			if(missing(height)) {

@@ -3534,10 +3603,40 @@ anno_block = function(gp = gpar(), labels = NULL, labels_gp = gpar(),

 		}

 	}

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

+		if(length(as.list(formals(panel_fun))) == 1) {

+	 		formals(panel_fun) = alist(index = , nm = NULL)

+		}

+	}

+

 	anno_size = anno_width_and_height(which, width, height, unit(5, "mm"))

 	fun = function(index, k, n) {

-		if(is.null(graphics)) {

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

+			is_in = sapply(align_to, function(x) any(x %in% index))

+			

+			ind_aln = which(is_in)

+

+			for(ai in ind_aln) {

+				ind = which(index %in% align_to[[ai]])

+				if(any(diff(ind) > 1)) {

+					stop_wrap("Indices in `align_to` should be continuously adjacent in the heatmap.")

+				}

+

+				ni = length(index)

+

+				if(which == "row") {

+					pushViewport(viewport(y = (ni - ind[length(ind)])/ni, height = length(ind)/ni, default.units = "npc", just = "bottom"))

+					panel_fun(index[ind], names(align_to)[ai])

+					popViewport()

+				} else {

+					pushViewport(viewport(x = (ind[length(ind)])/ni, width = length(ind)/ni, default.units = "npc", just = "right"))

+					panel_fun(index[ind], names(align_to)[ai])

+					popViewport()

+				}