@@ -4,6 +4,7 @@ This a major update of the package. The main changes are:

 * support column split

 * support align heatmaps vertically

 * add a naive `AnnotationFunction` class to handle annotation functions

+* add more annotation functions

 =======================

@@ -60,12 +60,12 @@ AdditiveUnit = function(...) {

 "+.AdditiveUnit" = function(x, y) {

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

     	if(x@which != "row") {

-    		stop("You should specify `which` to `row` or use `rowAnnotation()` directly if you want to add row annotations.")

+    		stop_wrap("You should specify `which = row` or use `rowAnnotation()` directly if you want to add row annotations horizontally.")

     	}

     }

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

     	if(y@which != "row") {

-            stop("You should specify `which` to `row` or use `rowAnnotation()` directly if you want to add row annotations.")

+            stop_wrap("You should specify `which = row` or use `rowAnnotation()` directly if you want to add row annotations horizontally.")

     	}

     }

     if(is.null(x)) {

@@ -112,12 +112,12 @@ AdditiveUnit = function(...) {

 "%v%" = function(x, y) {

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

         if(x@which != "column") {

-            stop("You should specify `which` to `column` or use `columnAnnotation()` directly if you want to add column annotations vertically.")

+            stop_wrap("You should specify `which = column` or use `columnAnnotation()` directly if you want to add column annotations vertically.")

         }

     }

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

         if(y@which != "column") {

-            stop("You should specify `which` to `column` or use `columnAnnotation()` directly if you want to add column annotations vertically.")

+            stop_wrap("You should specify `which = column` or use `columnAnnotation()` directly if you want to add column annotations vertically.")

         }

     }

     if(is.null(x)) {

@@ -1856,7 +1856,7 @@ anno_text = function(x, which = c("column", "row"), gp = gpar(),

 	rot = rot[1] %% 360

 	just = just[1]

 	if(!missing(offset)) {

-		warning("`offset` is deprecated, use `location` instead.")

+		warning_wrap("`offset` is deprecated, use `location` instead.")

 		if(missing(location)) {

 			location = offset

 		}

@@ -73,12 +73,12 @@ ColorMapping = function(name, colors = NULL, levels = NULL,

 	if(!is.null(colors)) {

 		if(is.null(levels)) {

 			if(is.null(names(colors))) {

-				stop("either provide `levels` or provide named `colors`.\n")

+				stop_wrap("either provide `levels` or provide named `colors`.\n")

 			}

 			levels = names(colors)

 		}

 		if(length(colors) != length(levels)) {

-			stop("length of colors and length of levels should be the same.\n")

+			stop_wrap("length of colors and length of levels should be the same.\n")

 		}

 		colors = t(col2rgb(colors, alpha = TRUE))

 		colors = rgb(colors[, 1:3, drop = FALSE], alpha = colors[, 4], maxColorValue = 255)

@@ -95,7 +95,7 @@ ColorMapping = function(name, colors = NULL, levels = NULL,

 		if(is.null(breaks)) {

 			breaks = attr(col_fun, "breaks")

 			if(is.null(breaks)) {

-				stop("You should provide breaks.\n")

+				stop_wrap("You should provide breaks.\n")

 			}

@@ -115,7 +115,7 @@ ColorMapping = function(name, colors = NULL, levels = NULL,

 		.Object@col_fun = col_fun

 		.Object@type = "continuous"

 	} else {

-		stop("initialization failed. Either specify `colors` + `levels` or `col_fun` + `breaks`\n")

+		stop_wrap("initialization failed. Either specify `colors` + `levels` or `col_fun` + `breaks`\n")

 	}

 	.Object@name = name

@@ -204,7 +204,7 @@ setMethod(f = "map_to_colors",

 		if(is.numeric(x)) x = as.character(x)

 		if(any(! x[!lna] %in% object@levels)) {

 			msg = paste0(object@name, ": cannot map colors to some of the levels:\n", paste(setdiff(x[!lna], object@levels), sep = ", ", collapse = ", "))

-			stop(msg)

+			stop_wrap(msg)

 		}

 		x2[lna] = object@na_col

@@ -293,12 +293,12 @@ setMethod(f = "color_mapping_legend",

 	labels_gp = check_gp(labels_gp)

 	if(object@type == "discrete" && color_bar == "continuous") {

-		stop("'color_bar' can only be set to 'discrete' only if the color mapping is discrete")

+		stop_wrap("'color_bar' can only be set to 'discrete' only if the color mapping is discrete")

 	}

 	# get labels

 	if(length(at) != length(labels)) {

-		stop("Length of 'at' should be same as length of 'labels'.")

+		stop_wrap("Length of 'at' should be same as length of 'labels'.")

 	}

 	# if it is character color mapping, remove items in `at` which are not in the available optinos

 	if(color_bar == "discrete" && is.character(at)) {

@@ -426,7 +426,7 @@ Heatmap = function(matrix, col, name,

             } else {

                 if(!is.data.frame(column_split)) column_split = data.frame(column_split)

                 if(nrow(column_split) != ncol(matrix)) {

-                    stop("Length or ncol of `column_split` should be same as ncol of `matrix`.")

+                    stop_wrap("Length or ncol of `column_split` should be same as ncol of `matrix`.")

                 }

             }

         }

@@ -868,6 +868,8 @@ make_cluster = function(object, which = c("row", "column")) {

     names_param = slot(object, paste0(which, "_names_param"))

+    dend_param$split_by_cutree = FALSE

+

     if(cluster) {

         if(is.numeric(split) && length(split) == 1) {

@@ -900,8 +902,9 @@ make_cluster = function(object, which = c("row", "column")) {

                     stop_wrap(qq("Since you specified a clustering object, you can only split @{which}s by providing a number (number of @{which} slices)."))

                 }

                 if(split < 2) {

-                    stop_wrap("Here `split` should be equal or larger than 2.")

+                    stop_wrap(qq("`@{which}_split` should be >= 2."))

                 }

+                dend_param$split_by_cutree = TRUE

                 ct = cut_dendrogram(dend_param$obj, split)

                 dend_list = ct$lower

@@ -67,16 +67,16 @@ setMethod(f = "draw_heatmap_body",

             CairoTIFF = c("Cairo", "tiff", "readTIFF")

         )

         if(!requireNamespace(device_info[1])) {

-            stop(paste0("Need ", device_info[1], " package to write image."))

+            stop_wrap(paste0("Need ", device_info[1], " package to write image."))

         }

         if(!requireNamespace(device_info[2])) {

-            stop(paste0("Need ", device_info[2], " package to read image."))

+            stop_wrap(paste0("Need ", device_info[2], " package to read image."))

         }

         # can we get the size of the heatmap body?

         heatmap_width = convertWidth(unit(1, "npc"), "bigpts", valueOnly = TRUE)

         heatmap_height = convertHeight(unit(1, "npc"), "bigpts", valueOnly = TRUE)

         if(heatmap_width <= 0 || heatmap_height <= 0) {

-            stop("The width or height of the raster image is zero, maybe you forget to turn off the previous graphic device or it was corrupted. Run `dev.off()` to close it.")

+            stop_wrap("The width or height of the raster image is zero, maybe you forget to turn off the previous graphic device or it was corrupted. Run `dev.off()` to close it.")

         }

         temp_dir = tempdir()

@@ -163,7 +163,11 @@ setMethod(f = "make_layout",

             object@layout$layout_size$row_dend_right_width = row_dend_width

             object@layout$layout_index = rbind(object@layout$layout_index, row_dend_right = heatmap_layout_index("row_dend_right"))

         }

-        row_dend_max_height = dend_heights(row_dend_slice) + max(dend_heights(object@row_dend_list))

+        if(object@row_dend_param$split_by_cutree) {

+            row_dend_max_height = dend_heights(row_dend_slice)

+        } else {

+            row_dend_max_height = dend_heights(row_dend_slice) + max(dend_heights(object@row_dend_list))

+        }

         object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {

             if(row_dend_side == "left") {

@@ -192,9 +196,27 @@ setMethod(f = "make_layout",

                 for(i in seq_len(nr_slice)) {

                     slice_leaf_pos[i] = slice_leaf_pos[i] - slice_height[i]*p[i]

                 }

-                row_dend_slice = merge_dendrogram(row_dend_slice, object@row_dend_list, only_parent = TRUE)

+                if(!object@row_dend_param$split_by_cutree) {

+                    row_dend_slice = merge_dendrogram(row_dend_slice, object@row_dend_list, only_parent = TRUE)

+                }

                 row_dend_slice = adjust_dend_by_x(row_dend_slice, slice_leaf_pos)

-                grid.dendrogram(row_dend_slice, facing = ifelse(row_dend_side == "left", "right", "left"))

+                grid.dendrogram(row_dend_slice, facing = ifelse(row_dend_side == "left", "right", "left"), gp = object@row_dend_param$gp)

+                if(!object@row_dend_param$split_by_cutree) {

+                    dh = dend_heights(object@row_dend_list)

+                    if(row_dend_side == "left") {

+                        grid.segments(unit(row_dend_max_height - max(dh), "native") - unit(0.5, "mm"), 

+                            slice_leaf_pos[1] + unit(5, "mm"), 

+                            unit(row_dend_max_height - max(dh), "native") - unit(0.5, "mm"), 

+                            slice_leaf_pos[length(slice_leaf_pos)] - unit(5, "mm"),

+                            gp = gpar(lty = 3, col = "#666666"))

+                    } else {

+                        grid.segments(unit(max(dh), "native") + unit(0.5, "mm"), 

+                            slice_leaf_pos[1] + unit(5, "mm"), 

+                            unit(max(dh), "native") + unit(0.5, "mm"), 

+                            slice_leaf_pos[length(slice_leaf_pos)] - unit(5, "mm"),

+                            gp = gpar(lty = 3, col = "#666666"))

+                    }

+                }

                 popViewport()

             }

             upViewport()

@@ -215,7 +237,11 @@ setMethod(f = "make_layout",

             object@layout$layout_size$column_dend_bottom_height = column_dend_height

             object@layout$layout_index = rbind(object@layout$layout_index, column_dend_bottom = heatmap_layout_index("column_dend_bottom"))

         }

-        column_dend_max_height = dend_heights(column_dend_slice) + max(dend_heights(object@column_dend_list))

+        if(object@column_dend_param$split_by_cutree) {

+            column_dend_max_height = dend_heights(column_dend_slice)

+        } else {

+            column_dend_max_height = dend_heights(column_dend_slice) + max(dend_heights(object@column_dend_list))

+        }

         object@layout$graphic_fun_list = c(object@layout$graphic_fun_list, function(object) {

             if(column_dend_side == "top") {

                 pushViewport(viewport(y = ht_opt$DENDROGRAM_PADDING, height = unit(1, "npc") - ht_opt$DENDROGRAM_PADDING, just = "bottom"))

@@ -243,9 +269,27 @@ setMethod(f = "make_layout",

                 for(i in seq_len(nc_slice)) {

                     slice_leaf_pos[i] = slice_leaf_pos[i] + slice_width[i]*p[i]

                 }

-                column_dend_slice = merge_dendrogram(column_dend_slice, object@column_dend_list, only_parent = TRUE)

+                if(!object@column_dend_param$split_by_cutree) {

+                    column_dend_slice = merge_dendrogram(column_dend_slice, object@column_dend_list, only_parent = TRUE)

+                }

                 column_dend_slice = adjust_dend_by_x(column_dend_slice, slice_leaf_pos)

-                grid.dendrogram(column_dend_slice, facing = ifelse(column_dend_side == "top", "bottom", "top"))

+                grid.dendrogram(column_dend_slice, facing = ifelse(column_dend_side == "top", "bottom", "top"), gp = object@column_dend_param$gp)

+                if(!object@column_dend_param$split_by_cutree) {

+                    dh = dend_heights(object@column_dend_list)

+                    if(row_dend_side == "bottom") {

+                        grid.segments(slice_leaf_pos[1] - unit(5, "mm"), 

+                            unit(column_dend_max_height - max(dh), "native") - unit(0.5, "mm"), 

+                            slice_leaf_pos[length(slice_leaf_pos)] + unit(5, "mm"),

+                            unit(column_dend_max_height - max(dh), "native") - unit(0.5, "mm"), 

+                            gp = gpar(lty = 3, col = "#666666"))

+                    } else {

+                        grid.segments(slice_leaf_pos[1] - unit(5, "mm"), 

+                            unit(max(dh), "native") + unit(0.5, "mm"), 

+                            slice_leaf_pos[length(slice_leaf_pos)] + unit(5, "mm"),

+                            unit(max(dh), "native") + unit(0.5, "mm"), 

+                            gp = gpar(lty = 3, col = "#666666"))

+                    }

+                }

                 popViewport()

             }

             upViewport()

@@ -38,7 +38,7 @@

 subset_heatmap_by_row = function(ht, ind) {

     ht@row_order = order(intersect(ht@row_order, ind))

     if(!is.null(ht@row_dend_param$obj)) {

-        stop("row dend is specified as a clustering object, cannot do subsetting.")

+        stop_wrap("row dend is specified as a clustering object, cannot do subsetting.")

     }

     ht@matrix = ht@matrix[ind, , drop = FALSE]

     if(!is.null(ht@row_names_param$labels)) {

@@ -58,7 +58,7 @@ subset_heatmap_by_row = function(ht, ind) {

 subset_heatmap_by_column = function(ht, ind) {

     ht@column_order = order(intersect(ht@column_order, ind))

     if(!is.null(ht@column_dend_param$obj)) {

-        stop("column dend is specified as a clustering object, cannot do subsetting.")

+        stop_wrap("column dend is specified as a clustering object, cannot do subsetting.")

     }

     ht@matrix = ht@matrix[, ind, drop = FALSE]

     if(!is.null(ht@column_names_param$labels)) {

@@ -159,7 +159,7 @@ HeatmapAnnotation = function(...,

     called_args = names(arg_list)

     anno_args = setdiff(called_args, fun_args)

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

+    if(any(anno_args == "")) stop_wrap("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 or a function annotation (e.g. anno_*()), specify it as HeatmapAnnotation(name = value). If it is a data frame annotation, specify it as HeatmapAnnotation(df = value)")

     }

@@ -368,7 +368,9 @@ HeatmapAnnotation = function(...,

     global_width = NULL

     if(which == "column") {

 		anno_size = do.call("unit.c", lapply(anno_list, height))

-		height = sum(anno_size) + sum(gap) - gap[n_total_anno]

+		if(is.null(height)) {

+			height = sum(anno_size) + sum(gap) - gap[n_total_anno]

+    	}

     	# for width, only look at `width`

     	if(is.null(width)) {

@@ -587,7 +589,7 @@ setMethod(f = "draw",

 			index = seq_len(len[1])

 		} 

 		if(!length(index)) {

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

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

 		}

     }

@@ -803,7 +805,7 @@ c.HeatmapAnnotation = function(..., gap = unit(0, "mm")) {

 	anno_list = list(...)

 	n = length(anno_list)

 	if(length(unique(sapply(anno_list, function(x) x@which))) != 1) {

-		stop("All annotations should be all row annotation or all column annotation.")

+		stop_wrap("All annotations should be all row annotation or all column annotation.")

 	}

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

 	if(length(gap) == n - 1) gap = unit.c(gap, unit(0, "mm"))

@@ -830,7 +832,7 @@ c.HeatmapAnnotation = function(..., gap = unit(0, "mm")) {

 	ld = duplicated(nm)

 	if(any(ld)) {

 		dup = unique(nm[ld])

-		warning(paste0("Following annotation names are duplicated:\n  ", paste(dup, collapse = ", ")))

+		warning_wrap(paste0("Following annotation names are duplicated:\n  ", paste(dup, collapse = ", ")))

 		nm2 = nm

 		nm2[unlist(split(seq_along(nm), nm))] = unlist(lapply(split(nm, nm), seq_along))

 		l = nm %in% dup

@@ -875,10 +877,10 @@ names.HeatmapAnnotation = function(x) {

 # names(ha)

 "names<-.HeatmapAnnotation" = function(x, value) {

 	if(length(value) != length(x@anno_list)) {

-		stop("Length of `value` should be same as number of annotations.")

+		stop_wrap("Length of `value` should be same as number of annotations.")

 	}

 	if(any(duplicated(value))) {

-		stop("Annotation names should be unique.")

+		stop_wrap("Annotation names should be unique.")

 	}

 	names(x@anno_list) = value

 	for(i in seq_along(value)) {

@@ -1011,12 +1013,12 @@ setMethod(f = "re_size",

 	if(object@which == "column") {

 		if(!missing(width) || !missing(annotation_width)) {

-			stop("Please use width() directly")

+			stop_wrap("Please use ComplexHeatmap:::width() directly")

 		}

 	}

 	if(object@which == "colrowumn") {

 		if(!missing(height) || !missing(annotation_height)) {

-			stop("Please use height() directly")

+			stop_wrap("Please use ComplexHeatmap:::height() directly")

 		}

 	}

@@ -1032,10 +1034,10 @@ setMethod(f = "re_size",

 			is_size_set = FALSE

 		} else {

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

-				stop("`height` should be a `unit` object")

+				stop_wrap("`height` should be a `unit` object")

 			}

 			if(!is_abs_unit(height)) {

-				stop("`height` should be an absolute unit.")

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

 			}

 			is_size_set = TRUE

 		}

@@ -1052,10 +1054,10 @@ setMethod(f = "re_size",

 			is_size_set = FALSE

 		} else {

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

-				stop("`width` should be a `unit` object")

+				stop_wrap("`width` should be a `unit` object")

 			}

 			if(!is_abs_unit(width)) {

-				stop("`width` should be an absolute unit.")

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

 			}

 			is_size_set = TRUE

 		}

@@ -1096,7 +1098,7 @@ setMethod(f = "re_size",

 			annotation_size_adjusted = rep(1, n)

 		}

 		if(length(annotation_size_adjusted) != n) {

-			stop(paste0("Length of annotation_", size_name, " should be same as number of annotations.", sep = ""))

+			stop_wrap(paste0("Length of annotation_", size_name, " should be same as number of annotations.", sep = ""))

 		}

 		if(!inherits(annotation_size_adjusted, "unit")) {

@@ -1111,10 +1113,10 @@ setMethod(f = "re_size",

 					rel_num = sapply(which(l_rel_unit), function(i) {

 						if(identical(class(annotation_size_adjusted[i]), "unit")) {

 							if(attr(annotation_size_adjusted[i], "unit") != "null") {

-								stop("relative unit should be defined as `unit(..., 'null')")

+								stop_wrap("relative unit should be defined as `unit(..., 'null')")

 							}

 						} else {

-							stop("relative unit should be defined as `unit(..., 'null')")

+							stop_wrap("relative unit should be defined as `unit(..., 'null')")

 						}

 						annotation_size_adjusted[i][[1]]

 					})

@@ -1125,17 +1127,17 @@ setMethod(f = "re_size",

 						ts = size_adjusted - sum(gap)

 					}

 					if(convertUnitFun(ts, "mm", valueOnly = TRUE) <= 0) {

-						stop(paste0(size_name, "is too small."))

+						stop_wrap(paste0(size_name, "is too small."))

 					}

 					ind = which(l_rel_unit)

 					for(i in seq_along(ind)) {

 						annotation_size_adjusted[ ind[i] ] = ts*rel_num[i]

 					}

 				} else {

-					stop(paste0("Since annotation_", size_name, " contains relative units, ", size_name, " must be set as an absolute unit."))

+					stop_wrap(paste0("Since annotation_", size_name, " contains relative units, ", size_name, " must be set as an absolute unit."))

 				}

 			} else {

-				stop(paste0("Since annotation_", size_name, " contains relative units, ", size_name, " must be set."))

+				stop_wrap(paste0("Since annotation_", size_name, " contains relative units, ", size_name, " must be set."))

 			}

 		}

 	}

@@ -1177,13 +1179,13 @@ setMethod(f = "re_size",

 				anno_simple_size = convertUnitFun(anno_simple_size, "mm", valueOnly = TRUE)

 			}

 			if(size_adjusted <= sum(gap)) {

-				stop(paste0(size_name, " you set is smaller than sum of gaps."))

+				stop_wrap(paste0(size_name, " you set is smaller than sum of gaps."))

 			}

 			## fix the size of simple annotation and zoom function annotations

 			ts = size_adjusted - sum(gap) - sum(anno_size[l_simple_anno]*anno_simple_size/5)

 			if(ts < 0) {

-				stop(paste0(size_name, " you set is too small."))

+				stop_wrap(paste0(size_name, " you set is too small."))

 			}

 			anno_size2[!l_simple_anno] = anno_size[!l_simple_anno]/sum(anno_size[!l_simple_anno]) * ts

 			anno_size2[l_simple_anno] = anno_size[l_simple_anno]*anno_simple_size/5

@@ -131,7 +131,7 @@ setMethod(f = "add_heatmap",

     ht_name = names(object@ht_list)

     which_duplicated = duplicated(ht_name)

     if(any(which_duplicated)) {

-        warning(paste0("Heatmap/annotation names are duplicated: ", paste(ht_name[which_duplicated], collapse = ", ")))

+        warning_wrap(paste0("Heatmap/annotation names are duplicated: ", paste(ht_name[which_duplicated], collapse = ", ")))

     }

     l = which(sapply(object@ht_list, inherits, "Heatmap"))

@@ -113,7 +113,7 @@ setMethod(f = "adjust_heatmap_list",

             total_fixed_width = total_fixed_width + sum(ht_gap[seq_len(n-1)])

         }

         if(!all(sapply(total_null_units_lt, is.unit))) {

-            warning("Since some of the heatmap_body_width is numeric, all heatmaps should explicitly specify heatmap_body_width as null units or numeric, or else the numeric width is treated as number of columns and will be normalized to other heatmaps.")

+            warning_wrap("Since some of the heatmap_body_width is numeric, all heatmaps should explicitly specify heatmap_body_width as null units or numeric, or else the numeric width is treated as number of columns and will be normalized to other heatmaps.")

         }

         total_null_units = sum(unlist(total_null_units_lt))

         if(total_null_units == 0) {

@@ -314,7 +314,7 @@ setMethod(f = "adjust_heatmap_list",

             total_fixed_height = total_fixed_height + sum(ht_gap[seq_len(n-1)])

         }

         if(!all(sapply(total_null_units_lt, is.unit))) {

-            warning("Since some of the heatmap_body_height is numeric, all heatmaps should explicitly specify heatmap_body_height as null units or numeric, or else the numeric height is treated as number of rows and will be normalized to other heatmaps.")

+            warning_wrap("Since some of the heatmap_body_height is numeric, all heatmaps should explicitly specify heatmap_body_height as null units or numeric, or else the numeric height is treated as number of rows and will be normalized to other heatmaps.")

         }

         total_null_units = sum(unlist(total_null_units_lt))

         if(total_null_units == 0) {

@@ -172,11 +172,11 @@ setMethod(f = "make_layout",

         } else if(length(ht_gap) == n_ht - 1) {

             ht_gap = unit.c(ht_gap, unit(0, "mm"))

         } else if(length(ht_gap) > n_ht) {

-            stop(paste0("length of `ht_gap` can only be 1 or ", n_ht-1, "."))

+            stop_wrap(paste0("length of `ht_gap` can only be 1 or ", n_ht-1, "."))

         }

     } else {

         if(!is.unit(ht_gap)) {

-            warning("`ht_gap` should be a unit object, reset it to unit(0, 'mm').")

+            warning_wrap("`ht_gap` should be a unit object, reset it to unit(0, 'mm').")

             ht_gap = unit(rep(0, n_ht), "mm")    

         }

     }

@@ -521,7 +521,7 @@ setMethod(f = "make_layout",

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

             padding = rep(padding, 2)

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

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

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

         }

     }

     object@ht_list_param$padding = padding

@@ -955,7 +955,7 @@ setMethod(f = "make_layout",

                         # if same set but different order

                         if(setequal(main_matrix_rn, matrix_rn)) {

                             if(!identical(main_matrix_rn, matrix_rn)) {

-                                warning("Row names of heatmap ", i, " is not consistent as the main heatmap (", i_main, ")", sep = "")

+                                warning_wrap("Row names of heatmap ", i, " is not consistent as the main heatmap (", i_main, ")", sep = "")

                             }

                         }

                     }

@@ -973,7 +973,7 @@ setMethod(f = "make_layout",

                         # if same set but different order

                         if(setequal(main_matrix_cn, matrix_cn)) {

                             if(!identical(main_matrix_cn, matrix_cn)) {

-                                warning("Column names of heatmap ", i, " is not consistent as the main heatmap (", i_main, ")", sep = "")

+                                warning_wrap("Column names of heatmap ", i, " is not consistent as the main heatmap (", i_main, ")", sep = "")

                             }

                         }

                     }

@@ -102,7 +102,7 @@ densityHeatmap = function(data,

 	density_param$na.rm = TRUE

 	if(!is.matrix(data) && !is.data.frame(data) && !is.list(data)) {

-		stop("only matrix and list are allowed.")

+		stop_wrap("only matrix and list are allowed.")

 	}

 	if(is.matrix(data)) {

 		data2 = as.list(as.data.frame(data))

@@ -214,13 +214,22 @@ densityHeatmap = function(data,

 		decorate_heatmap_body(paste0("density_", random_str), {

 			n = length(column_order[[n_slice]])

-			pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(min_x, max_x), clip = FALSE))

+			

+			lq = !apply(quantile_list, 1, function(x) all(x > max_x) || all(x < min_x))

+			lq = c(lq, !(all(mean_value > max_x) || all(mean_value < min_x)))

+			if(sum(lq) == 0) {

+				return(NULL)

+			}

 			labels = c(rownames(quantile_list), "mean")

 			y = c(quantile_list[, column_order[[n_slice]][n] ], mean_value[ column_order[[n_slice]][n] ])

+			labels = labels[lq]

+			y = y[lq]

 			od = order(y)

 			y = y[od]

 			labels = labels[od]

+			

+			pushViewport(viewport(xscale = c(0.5, n + 0.5), yscale = c(min_x, max_x), clip = FALSE))

 			text_height = convertHeight(grobHeight(textGrob(labels[1])) * (1 + 0.2), "native", valueOnly = TRUE)

 	        h1 = y - text_height*0.5

 	        h2 = y + text_height*0.5

@@ -230,10 +239,12 @@ densityHeatmap = function(data,

 	        n2 = length(labels)

 	        grid.text(labels, unit(1, "npc") + rep(link_width, n2), h, default.units = "native", just = "left", gp = quantile_gp)

 	        link_width = link_width - unit(1, "mm")

-	        grid.segments(unit(rep(1, n2), "npc"), y, unit(1, "npc") + rep(link_width * (1/3), n2), y, default.units = "native")

-	        grid.segments(unit(1, "npc") + rep(link_width * (1/3), n2), y, unit(1, "npc") + rep(link_width * (2/3), n2), h, default.units = "native")

-	        grid.segments(unit(1, "npc") + rep(link_width * (2/3), n2), h, unit(1, "npc") + rep(link_width, n2), h, default.units = "native")

-

+	        ly = y <= max_x & y >= min_x

+	        if(sum(ly)) {

+		        grid.segments(unit(rep(1, n2), "npc")[ly], y[ly], unit(1, "npc") + rep(link_width * (1/3), n2)[ly], y[ly], default.units = "native")

+		        grid.segments(unit(1, "npc") + rep(link_width * (1/3), n2)[ly], y[ly], unit(1, "npc") + rep(link_width * (2/3), n2)[ly], h[ly], default.units = "native")

+		        grid.segments(unit(1, "npc") + rep(link_width * (2/3), n2)[ly], h[ly], unit(1, "npc") + rep(link_width, n2)[ly], h[ly], default.units = "native")

+		    }

 			upViewport()

 		}, column_slice = n_slice)

 	}

@@ -133,7 +133,7 @@ Legend = function(at, labels = at, col_fun, nrow = NULL, ncol = 1, by_row = FALS

 		if(!missing(col_fun) && missing(at)) {

 			breaks = attr(col_fun, "breaks")

 			if(is.null(breaks)) {

-				stop("You should provide `at` for color mapping function\n")

+				stop_wrap("You should provide `at` for color mapping function\n")

 			}

 			le1 = grid.pretty(range(breaks))

@@ -191,12 +191,12 @@ Legend = function(at, labels = at, col_fun, nrow = NULL, ncol = 1, by_row = FALS

 	if(!missing(col_fun)) {

 		if(direction == "vertical") {

 			if(title_position %in% c("leftcenter", "lefttop")) {

-				stop("'topleft', 'topcenter', 'leftcenter-rot' and 'lefttop-rot' are only allowd for vertical continuous legend")

+				stop_wrap("'topleft', 'topcenter', 'leftcenter-rot' and 'lefttop-rot' are only allowd for vertical continuous legend")

 			}

 		}

 		if(direction == "horizontal") {

 			if(title_position %in% c('leftcenter-rot', 'lefttop-rot')) {

-				stop("'topleft', 'topcenter', 'lefttop' and 'leftcenter' are only allowd for horizontal continuous legend")

+				stop_wrap("'topleft', 'topcenter', 'lefttop' and 'leftcenter' are only allowd for horizontal continuous legend")

 			}

 		}

 	}

@@ -451,7 +451,7 @@ vertical_continuous_legend_body = function(at, labels = at, col_fun,

 	min_legend_height = length(at)*(grid_height)

 	if(is.null(legend_height)) legend_height = min_legend_height

 	if(convertHeight(legend_height, "mm", valueOnly = TRUE) < convertHeight(min_legend_height, "mm", valueOnly = TRUE)) {

-		warning("`legend_height` you specified is too small, use the default minimal height.")

+		warning_wrap("`legend_height` you specified is too small, use the default minimal height.")

 		legend_height = min_legend_height

 	}

@@ -797,10 +797,10 @@ packLegend = function(...,gap = unit(2, "mm"), row_gap = unit(2, "mm"), column_g

 		}

 	}

 	if(length(row_gap) != 1) {

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

+		stop_wrap("Length of `row_gap` must be one.")

 	}

 	if(length(column_gap) != 1) {

-		stop("Length of `column_gap` must be one.")

+		stop_wrap("Length of `column_gap` must be one.")

 	}

     n_lgd = length(legend_list)

     if(direction == "vertical") {

@@ -997,13 +997,13 @@ valid_just = function(just) {

 			c("center", "center"))

 	}

 	if(length(just) != 2) {

-		stop("`just` should be a single character or a vector of length 2.")

+		stop_wrap("`just` should be a single character or a vector of length 2.")

 	}

 	j = c("center" = 0.5, "left" = 0, "right" = 1, "top" = 1, "bottom" = 0)

 	if(is.character(just)) {

 		just = j[just]

 	} else if(!is.numeric(just)) {

-		stop("`just` can only be character or numeric.")

+		stop_wrap("`just` can only be character or numeric.")

 	}

 	return(unname(just))

 }

@@ -35,7 +35,7 @@ adjust_dend_by_x = function(dend, leaf_pos = 1:nobs(dend)-0.5) {

     n = nobs(dend)

     if(length(leaf_pos) != n) {

-        stop("`leaf_pos` should be a vector with same length as `dend`.")

+        stop_wrap("`leaf_pos` should be a vector with same length as `dend`.")

     }

     dend_order = order.dendrogram(dend)

@@ -341,7 +341,7 @@ merge_dendrogram = function(x, y, only_parent = FALSE, ...) {

     n = nobs(parent)

     if(n != length(children)) {

-        stop("Number of children dendrograms should be same as leaves in parent.")

+        stop_wrap("Number of children dendrograms should be same as leaves in parent.")

     }

     # adjust height of parent dendrogram

@@ -101,7 +101,7 @@ oncoPrint = function(mat,

 		all_type = names(mat_list)

 		mat_list = lapply(mat_list, function(x) {

 				if(!is.matrix(x)) {

-					stop("Expect a list of matrix (not data frames).")

+					stop_wrap("Expect a list of matrix (not data frames).")

 				}

 				oattr = attributes(x)

 				x = as.logical(x)

@@ -110,14 +110,14 @@ oncoPrint = function(mat,

 			})

 		if(length(unique(sapply(mat_list, nrow))) > 1) {

-			stop("All matrix in 'mat_list' should have same number of rows.")

+			stop_wrap("All matrix in 'mat_list' should have same number of rows.")

 		}

 		if(length(unique(sapply(mat_list, ncol))) > 1) {

-			stop("All matrix in 'mat_list' should have same number of columns.")

+			stop_wrap("All matrix in 'mat_list' should have same number of columns.")

 		}

 	} else {

-		stop("Incorrect type of 'mat'")

+		stop_wrap("Incorrect type of 'mat'")

 	}

 	cat("All mutation types:", paste(all_type, collapse = ", "), "\n")

@@ -176,10 +176,10 @@ oncoPrint = function(mat,

 			names(af) = c("background", names(mat_list))

 			col = c("red", "blue")

 		} else {

-			stop("`alter_fun` should be specified.")

+			stop_wrap("`alter_fun` should be specified.")

 		}

 		names(col) = names(mat_list)

-		warning("Using default `alter_fun` graphics and reset `col`.")

+		warning_wrap("Using default `alter_fun` graphics and reset `col`.")

 	}

 	if(is.list(alter_fun)) {

@@ -188,7 +188,7 @@ oncoPrint = function(mat,

 		if(is.null(alter_fun$background)) alter_fun$background = function(x, y, w, h) grid.rect(x, y, w, h, gp = gpar(fill = "#CCCCCC", col = NA))

 		sdf = setdiff(all_type, names(alter_fun))

 		if(length(sdf) > 0) {

-			stop(paste0("You should define graphic function for: ", paste(sdf, collapse = ", ")))

+			stop_wrap(paste0("You should define graphic function for: ", paste(sdf, collapse = ", ")))

 		}

 		alter_fun = alter_fun[unique(c("background", intersect(names(alter_fun), all_type)))]

@@ -246,7 +246,7 @@ oncoPrint = function(mat,

 			}

 		}

 	} else {

-		stop("You need to set `alter_fun`.")

+		stop_wrap("You need to set `alter_fun`.")

 	}

 	col = col[intersect(names(col), all_type)]

@@ -281,7 +281,7 @@ oncoPrint = function(mat,

 	# validate col

 	sdf = setdiff(all_type, names(col))

 	if(length(sdf) > 0) {

-		stop(paste0("You should define colors for:", paste(sdf, collapse = ", ")))

+		stop_wrap(paste0("You should define colors for:", paste(sdf, collapse = ", ")))

 	}

 	# for each gene, percent of samples that have alterations

@@ -296,7 +296,7 @@ oncoPrint = function(mat,

 	right_annotation = eval(substitute(right_annotation))

 	if("left_annotation" %in% arg_names) {

-		stop("'left_annotation' are not allowed to specify, you can add...")

+		stop_wrap("'left_annotation' are not allowed to specify, you can add...")

 	}

 	left_annotation = NULL

 	if(show_pct) {

@@ -317,7 +317,7 @@ oncoPrint = function(mat,

 	if(length(arg_list)) {

 		if(any(arg_names %in% c("rect_gp", "cluster_rows", "cluster_columns", "cell_fun"))) {

-			stop("'rect_gp', 'cluster_rows', 'cluster_columns', 'cell_fun' are not allowed to use in `oncoPrint()`.")

+			stop_wrap("'rect_gp', 'cluster_rows', 'cluster_columns', 'cell_fun' are not allowed to use in `oncoPrint()`.")

 		}

 	}

@@ -163,7 +163,7 @@ get_dist = function(matrix, method) {

         } else if(nargs == 3) {

             dst = dist2(matrix, method)

         } else {

-            stop("Since your distance method is a funciton, it can only accept one or two arguments.")

+            stop_wrap("Since your distance method is a funciton, it can only accept one or two arguments.")

         }

     } else if(method %in% c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski")) {

         # if(any(is.na(matrix))) {

@@ -185,7 +185,7 @@ get_dist = function(matrix, method) {

                     y = y[!l]

                     1 - cor(x, y, method = method)

                 })

-            warning("NA exists in the matrix, calculating distance by removing NA values.")

+            warning_wrap("NA exists in the matrix, calculating distance by removing NA values.")

         } else {

             dst = switch(method,

                          pearson = as.dist(1 - cor(t(matrix), method = "pearson")),

@@ -212,7 +212,7 @@ recycle_gp = function(gp, n = 1) {

 check_gp = function(gp) {

     if(!inherits(gp, "gpar")) {

-        stop("Graphic parameters should be specified by `gpar()`.")

+        stop_wrap("Graphic parameters should be specified by `gpar()`.")

     }

     return(gp)

 }

@@ -244,7 +244,7 @@ subset_gp = function(gp, i) {

 get_text_just = function(rot, side) {

     rot = rot %% 360

     if(! rot %in% c(0, 90, 270)) {

-        stop("Only support horizontal or vertical rotations for text.\n")

+        stop_wrap("Only support horizontal or vertical rotations for text.\n")

     }

     if(side == "left") {

         if(rot == 0) {

@@ -416,7 +416,7 @@ message_wrap = function (...) {

 generate_param_list_fun = function(default) {

     if(!is.list(default)) {

-        stop("`default` needs to be a list.")

+        stop_wrap("`default` needs to be a list.")

     }

     lt = default

     function(..., list = NULL) {

@@ -475,20 +475,20 @@ unit.c = function(...) {

 ">.unit" = function(x, y) {

     if(!identical(attr(x, "unit"), "mm")) {

-        stop("x should be in mm unit")

+        stop_wrap("x should be in mm unit")

     }

     if(!identical(attr(y, "unit"), "mm")) {

-        stop("y should be in mm unit")

+        stop_wrap("y should be in mm unit")

     }

     x[[1]] > y[[1]]

 }

 "<.unit" = function(x, y) {

     if(!identical(attr(x, "unit"), "mm")) {

-        stop("x should be in mm unit")

+        stop_wrap("x should be in mm unit")

     }

     if(!identical(attr(y, "unit"), "mm")) {

-        stop("y should be in mm unit")

+        stop_wrap("y should be in mm unit")

     }

     x[[1]] < y[[1]]

 }

@@ -96,3 +96,8 @@ fun = function(index) {

 	grid.rect()

 }

 ha = HeatmapAnnotation(fun = fun, height = unit(4, "cm"))

+draw(ha, 1:10, test = TRUE)

+

+ha = rowAnnotation(fun = fun, width = unit(4, "cm"))

+draw(ha, 1:10, test = TRUE)

+