@@ -25,7 +25,8 @@ AnnotationFunction = setClass("AnnotationFunction",

 		subset_rule = "list",

 		subsetable = "logical",

 		data_scale = "numeric",

-		extended = "ANY"

+		extended = "ANY",

+		show_name = "logical"

 	),

 	prototype = list(

 		fun_name = "",

@@ -35,7 +36,8 @@ AnnotationFunction = setClass("AnnotationFunction",

 		subsetable = FALSE,

 		data_scale = c(0, 1),

 		n = 0,

-		extended = unit(c(0, 0, 0, 0), "mm")

+		extended = unit(c(0, 0, 0, 0), "mm"),

+		show_name = TRUE

 	)

 )

@@ -173,7 +175,7 @@ anno_width_and_height = function(which, width = NULL, height = NULL,

 # are all subsettable.

 AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"), 

 	var_import = list(), n = 0, data_scale = c(0, 1), subset_rule = list(), 

-	subsetable = FALSE, width = NULL, height = NULL) {

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

 	which = match.arg(which)[1]

@@ -190,6 +192,8 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),

 	anno@width = anno_size$width

 	anno@height = anno_size$height

+	anno@show_name = show_name

+

 	anno@n = n

 	anno@data_scale = data_scale

@@ -61,7 +61,8 @@ anno_empty = function(which = c("column", "row"), border = TRUE, width = NULL, h

 		subset_rule = list(),

 		subsetable = TRUE,

 		height = anno_size$height,

-		width = anno_size$width

+		width = anno_size$width,

+		show_name = FALSE

 	)

 	return(anno) 

 }

@@ -762,7 +763,7 @@ update_anno_extend = function(anno, axis_grob, axis_param) {

 # 	add_points = TRUE, pt_gp = gpar(col = 5:6), pch = c(1, 16))

 # draw(anno, test = "matrix")

 anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(), 

-	add_points = FALSE, pch = 16, size = unit(2, "mm"), pt_gp = gpar(), ylim = NULL, 

+	add_points = FALSE, smooth = FALSE, pch = 16, size = unit(2, "mm"), pt_gp = gpar(), ylim = NULL, 

 	extend = 0.05, axis = TRUE, axis_param = default_axis_param(which),

 	width = NULL, height = NULL) {

@@ -822,18 +823,34 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),

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

 		if(is.matrix(value)) {

 			for(i in seq_len(ncol(value))) {

-				grid.lines(value[index, i], n - seq_along(index) + 1, gp = subset_gp(gp, i), 

-					default.units = "native")

+				x = n - seq_along(index) + 1

+				y = value[index, i]

+				if(smooth) {

+					fit = loess(y ~ x)

+					x2 = seq(x[1], x[length(x)], length = 100)

+					y2 = predict(fit, x2)

+					grid.lines(y2, x2, gp = subset_gp(gp, i), default.units = "native")

+				} else {

+					grid.lines(y, x, gp = subset_gp(gp, i), default.units = "native")

+				}

 				if(add_points) {

-					grid.points(value[index, i], n - seq_along(index) + 1, gp = subset_gp(pt_gp, i), 

+					grid.points(y, x, gp = subset_gp(pt_gp, i), 

 						default.units = "native", pch = pch[i], size = size[i])

 				}

 			}

 		} else {

-			grid.lines(value[index, i], n - seq_along(index) + 1, gp = gp, 

-				default.units = "native")

+			x = n - seq_along(index) + 1

+			y = value[index]

+			if(smooth) {

+				fit = loess(y ~ x)

+				x2 = seq(x[1], x[length(x)], length = 100)

+				y2 = predict(fit, x2)

+				grid.lines(y2, x2, gp = gp, default.units = "native")

+			} else {

+				grid.lines(y, x, gp = gp, default.units = "native")

+			}

 			if(add_points) {

-				grid.points(value[index], n - seq_along(index) + 1, gp = gp, default.units = "native", 

+				grid.points(y, x, gp = gp, default.units = "native", 

 					pch = pch[index], size = size[index])

 			}

 		}

@@ -853,15 +870,32 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),

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

 		if(is.matrix(value)) {

 			for(i in seq_len(ncol(value))) {

-				grid.lines(seq_along(index), value[index, i], gp = subset_gp(gp, i), 

-					default.units = "native")

+				x = seq_along(index)

+				y = value[index, i]

+				if(smooth) {

+					fit = loess(y ~ x)

+					x2 = seq(x[1], x[length(x)], length = 100)

+					y2 = predict(fit, x2)

+					grid.lines(x2, y2, gp = subset_gp(gp, i), default.units = "native")

+				} else {

+					grid.lines(x, y, gp = subset_gp(gp, i), default.units = "native")

+				}

 				if(add_points) {

-					grid.points(seq_along(index), value[index, i], gp = subset_gp(pt_gp, i), 

+					grid.points(x, y, gp = subset_gp(pt_gp, i), 

 						default.units = "native", pch = pch[i], size = size[i])

 				}

 			}

 		} else {

-			grid.lines(seq_along(index), value[index], gp = gp, default.units = "native")

+			x = seq_along(index)

+			y = value[index]

+			if(smooth) {

+				fit = loess(y ~ x)

+				x2 = seq(x[1], x[length(x)], length = 100)

+				y2 = predict(fit, x2)

+				grid.lines(x2, y2, gp = gp, default.units = "native")

+			} else {

+				grid.lines(x, y, gp = gp, default.units = "native")

+			}

 			if(add_points) {

 				grid.points(seq_along(index), value[index], gp = pt_gp, default.units = "native", 

 					pch = pch[index], size = size[index])

@@ -891,7 +925,8 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),

 		height = anno_size$height,

 		n = n,

 		data_scale = data_scale,

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

+		var_import = list(value, gp, border, pch, size, pt_gp, axis, axis_param, 

+			axis_grob, data_scale, add_points, smooth)

 	)

 	anno@subset_rule$gp = subset_vector

@@ -968,15 +1003,17 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 	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)

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

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

+		baseline = max(x)

 	} else {

 		if(is.numeric(baseline)) {

 			if(baseline == 0 && all(rowSums(x) == 1)) {

 				data_scale = c(0, 1)

 			} else if(baseline <= min(x)) {

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

-			} else if(baseline >= rowSums(x)) {

+			} else if(baseline >= max(x)) {

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

 			} else {

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

@@ -1824,7 +1861,8 @@ anno_text = function(x, which = c("column", "row"), gp = gpar(),

 		width = width,

 		height = height,

 		n = n,

-		var_import = list(value, gp, just, rot, location)

+		var_import = list(value, gp, just, rot, location),

+		show_name = FALSE

 	)

 	anno@subset_rule$value = subset_vector

@@ -2465,6 +2503,8 @@ anno_mark = function(at, labels, which = c("column", "row"),

 		width = unit(1, "npc")

 	}

+	# a map between row index and positions

+	# pos_map = 

 	row_fun = function(index) {

 		n = length(index)

 		# adjust at and labels

@@ -2558,7 +2598,9 @@ 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, padding, side, link_width, extend)

+		var_import = list(at, labels2index, at2labels, link_gp, labels_gp, padding, 

+			side, link_width, extend),

+		show_name = FALSE

 	)

 	anno@subset_rule$at = subset_by_intersect

@@ -767,7 +767,8 @@ Heatmap = function(matrix, col, name,

         ),

         layout_index = NULL,

-        graphic_fun_list = list()

+        graphic_fun_list = list(),

+        initialized = FALSE

     )

     .Object@heatmap_param$width = width

@@ -1397,6 +1398,10 @@ setMethod(f = "prepare",

     signature = "Heatmap",

     definition = function(object, process_rows = TRUE, process_columns = TRUE) {

+    if(object@layout$initialized) {

+        return(object)

+    }

+    

     if(process_rows) {

         object = make_row_cluster(object)

     }

@@ -24,6 +24,10 @@ setMethod(f = "make_layout",

     signature = "Heatmap",

     definition = function(object) {

+    if(object@layout$initialized) {

+        return(object)

+    }

+

     # position of each row-slice

     row_gap = object@matrix_param$row_gap

     column_gap = object@matrix_param$column_gap

@@ -432,6 +436,8 @@ setMethod(f = "make_layout",

     object@heatmap_param$width_is_absolute_unit = is_abs_unit(object@heatmap_param$width) 

     object@heatmap_param$height_is_absolute_unit = is_abs_unit(object@heatmap_param$height) 

+    object@layout$initialized = TRUE

+

     return(object)

 })

@@ -133,6 +133,9 @@ HeatmapAnnotation = function(...,

     called_args = names(arg_list)

     anno_args = setdiff(called_args, fun_args)

     if(any(anno_args == "")) stop("annotations should have names.")

+    if(is.null(called_args)) {

+    	stop_wrap("It seems you are putting only one argument to the function. If it is a simple vector annotation, specify it as HeatmapAnnotation(name = value). If it is a data frame annotation, specify it as HeatmapAnnotation(df = value)")

+    }

     ##### pull all annotation to `anno_value_list`####

     if("df" %in% called_args) {

@@ -563,8 +566,8 @@ setMethod(f = "draw",

     if(test2) {

     	grid.newpage()

-    	if(which == "column") pushViewport(viewport(width = unit(1, "npc") - unit(4, "cm"), height = object@height))

-    	if(which == "row") pushViewport(viewport(height = unit(1, "npc") - unit(4, "cm"), width = object@width))

+    	if(which == "column") pushViewport(viewport(width = unit(1, "npc") - unit(2, "cm"), height = object@height))

+    	if(which == "row") pushViewport(viewport(height = unit(1, "npc") - unit(2, "cm"), width = object@width))

     } else {

 		pushViewport(viewport(...))

 	}

@@ -579,7 +582,12 @@ setMethod(f = "draw",

 			}

 		})

 		len = len[!is.na(len)]

-		if(length(len)) index = seq_len(len[1])

+		if(length(len)) {

+			index = seq_len(len[1])

+		} 

+		if(!length(index)) {

+			stop("Cannot infer the number of observations of the annotation.")

+		}

     }

 	if(which == "column") {

@@ -607,10 +615,10 @@ setMethod(f = "draw",

 	}

 	if(test2) {

         grid.text(test, y = unit(1, "npc") + unit(2, "mm"), just = "bottom")

-        grid.rect(unit(0, "npc") - object@extended[2], unit(0, "npc") - object@extended[1], 

-            width = unit(1, "npc") + object@extended[2] + object@extended[4],

-            height = unit(1, "npc") + object@extended[1] + object@extended[3],

-            just = c("left", "bottom"), gp = gpar(fill = "transparent", col = "red", lty = 2))

+        # grid.rect(unit(0, "npc") - object@extended[2], unit(0, "npc") - object@extended[1], 

+        #     width = unit(1, "npc") + object@extended[2] + object@extended[4],

+        #     height = unit(1, "npc") + object@extended[1] + object@extended[3],

+        #     just = c("left", "bottom"), gp = gpar(fill = "transparent", col = "red", lty = 2))

     }

 	upViewport()

 })

@@ -523,6 +523,16 @@ setMethod(f = "draw_heatmap_list",

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

                 # calcualte the position of the heatmap body

                 pushViewport(viewport(y = max_bottom_component_height, height = unit(1, "npc") - max_top_component_height - max_bottom_component_height, just = c("bottom")))

+                # if(length(ht) == 1 & n_slice > 1) {

+                #     if(inherits(ht@anno_list[[1]], "AnnotationFunction")) {

+                #         if(identical(ht@anno_list[[1]]@fun@fun_name, "anno_mark")) {

+                #             # adjust pos_map var

+                #             fun = ht@anno_list[[1]]@fun

+                #             draw(fun, index = ht_main@row_order)

+                #             next

+                #         }

+                #     }

+                # }

                 for(j in seq_len(n_slice)) {

                     draw(ht, index = ht_main@row_order_list[[j]], y = slice_y[j], height = slice_height[j], just = slice_just[2], k = j, n = n_slice)

                 }

@@ -229,6 +229,8 @@ SingleAnnotation = function(name, value, col, fun,

         if(inherits(fun, "AnnotationFunction")) {

             anno_fun_extend = fun@extended

             if(verbose) qqcat("@{name}: annotation is a AnnotationFunction object\n")

+

+            show_name = fun@show_name

         } else {

             fun = AnnotationFunction(fun = fun)

             anno_fun_extend = fun@extended

@@ -752,7 +752,7 @@ horizontal_continuous_legend_body = function(at, labels = at, col_fun,

 # draw(pd, test = "two legends")

 # pd = packLegend(lgd1, lgd2, direction = "horizontal")

 # draw(pd, test = "two legends packed horizontally")

-packLegend = function(..., row_gap = unit(2, "mm"), column_gap = unit(2, "mm"),

+packLegend = function(...,gap = unit(2, "mm"), row_gap = unit(2, "mm"), column_gap = unit(2, "mm"),

 	direction = c("vertical", "horizontal"),

 	max_width = NULL, max_height = NULL, list = NULL) {

@@ -771,6 +771,16 @@ packLegend = function(..., row_gap = unit(2, "mm"), column_gap = unit(2, "mm"),

 		lgd

 	})

 	direction = match.arg(direction)

+	if(direction == "vertical") {

+		if(missing(row_gap)) {

+			row_gap = gap

+		}

+	}

+	if(direction == "horizontal") {

+		if(missing(column_gap)) {

+			column_gap = gap

+		}

+	}

 	if(length(row_gap) != 1) {

 		stop("Length of `row_gap` must be one.")

 	}

@@ -279,7 +279,12 @@ rep.list = function(x, n) {

 list_component = function() {

-    vp_name = grid.ls(viewports = TRUE, grobs = FALSE, print = FALSE)$name

+    vp = grid.ls(viewports = TRUE, grob = FALSE, flatten = FALSE, print = FALSE)

+    vp = unlist(vp)

+    attributes(vp) = NULL

+    vp = vp[!grepl("^\\d+$", vp)]

+    vp = vp[!grepl("GRID.VP", vp)]

+    unique(vp)

 }

 # == title

@@ -361,13 +366,13 @@ dev.null = function(...) {

 stop_wrap = function (...) {

     x = paste0(...)

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

-    stop(x)

+    stop(x, call. = FALSE)

 }

 warning_wrap = function (...) {

     x = paste0(...)

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

-    warning(x)

+    warning(x, call. = FALSE)

 }

 message_wrap = function (...) {

@@ -123,6 +123,18 @@ draw(anno, test = "matrix")

 anno = anno_lines(cbind(c(1:5, 1:5), c(5:1, 5:1)), gp = gpar(col = 2:3),

 	add_points = TRUE, pt_gp = gpar(col = 5:6), pch = c(1, 16))

 draw(anno, test = "matrix")

+anno = anno_lines(sort(rnorm(10)), height = unit(2, "cm"), smooth = TRUE, add_points = TRUE)

+draw(anno, test = "anno_lines, smooth")

+anno = anno_lines(cbind(sort(rnorm(10)), sort(rnorm(10), decreasing = TRUE)), 

+	height = unit(2, "cm"), smooth = TRUE, add_points = TRUE, gp = gpar(col = 2:3))

+draw(anno, test = "anno_lines, smooth, matrix")

+

+anno = anno_lines(sort(rnorm(10)), width = unit(2, "cm"), smooth = TRUE, add_points = TRUE, which = "row")

+draw(anno, test = "anno_lines, smooth, by row")

+anno = anno_lines(cbind(sort(rnorm(10)), sort(rnorm(10), decreasing = TRUE)), 

+	width = unit(2, "cm"), smooth = TRUE, add_points = TRUE, gp = gpar(col = 2:3), which = "row")

+draw(anno, test = "anno_lines, smooth, matrix, by row")

+

 ###### test anno_text #######

@@ -246,4 +258,5 @@ anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which =

 Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)

 Heatmap(m) + rowAnnotation(mark = anno)

-

+ht_list = Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)

+draw(ht_list, row_split = c(rep("a", 95), rep("b", 5)))

@@ -64,3 +64,8 @@ draw(ha, test = "complex annotations on row")

 ## test row annotation with no heatmap

 rowAnnotation(foo = 1:10, bar = anno_points(10:1))

+

+

+HeatmapAnnotation(1:10)

+

+HeatmapAnnotation(data.frame(1:10))