@@ -19,7 +19,7 @@ AnnotationFunction = setClass("AnnotationFunction",

 		fun_name = "character",

 		width = "ANY",

 		height = "ANY",

-		n = "numeric",

+		n = "ANY",

 		var_env = "environment",

 		fun = "function",

 		subset_rule = "list",

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

 		subset_rule = list(),

 		subsetable = FALSE,

 		data_scale = c(0, 1),

-		n = 0,

+		n = NA_integer_,

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

 		show_name = TRUE

 	)

@@ -50,7 +50,7 @@ anno_width_and_height = function(which, width = NULL, height = NULL,

 			height = default

 		} else {

 			if(!is_abs_unit(height)) {

-				stop("height can only be an absolute unit.")

+				stop_wrap("height of the annotation can only be an absolute unit.")

 			} else {

 				height = convertHeight(height, "mm")

 			}

@@ -64,7 +64,7 @@ anno_width_and_height = function(which, width = NULL, height = NULL,

 			width = default

 		} else {

 			if(!is_abs_unit(width)) {

-				stop("width can only be an absolute unit.")

+				stop_wrap("width of the annotation can only be an absolute unit.")

 			} else {

 				width = convertWidth(width, "mm")

 			}

@@ -174,7 +174,7 @@ anno_width_and_height = function(which, width = NULL, height = NULL,

 # `anno_density`, `anno_joyplot`, `anno_horizon`, `anno_text` and `anno_mark`. Thess built-in annotation functions

 # 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(), 

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

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

 	which = match.arg(which)[1]

@@ -213,7 +213,7 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),

 				anno@var_env[[nm]] = var_import[[nm]]

 			}

 		} else {

-			stop_wrap("`var_import` needs to be a character vector which contains variable names or a list of variables")

+			stop_wrap("`var_import` needs to be a character vector which contains variable names or a list of variables.")

 		}

 		environment(fun) = anno@var_env

 	} else {

@@ -275,14 +275,14 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),

 		return(x)

 	} else {

 		if(!x@subsetable) {

-			stop("This object is not subsetable.")

+			stop_wrap("This object is not subsetable.")

 		}

 		x = copy_all(x)

 		for(var in names(x@subset_rule)) {

 			oe = try(x@var_env[[var]] <- x@subset_rule[[var]](x@var_env[[var]], i), silent = TRUE)

 			if(inherits(oe, "try-error")) {

 				message(paste0("An error when subsetting ", var))

-				stop(oe)

+				stop_wrap(oe)

 			}

 		}

 		if(is.logical(i)) {

@@ -357,7 +357,7 @@ setMethod(f = "draw",

 	}

 	vp_name2 = current.viewport()$name

 	if(vp_name1 != vp_name2) {

-		stop("Viewports are not the same before and after plotting the annotation graphics.")

+		stop_wrap("Viewports should be the same before and after plotting the annotation graphics.")

 	}

 	popViewport()

@@ -443,7 +443,9 @@ setMethod(f = "show",

 # anno = anno_points(1:10)

 # nobs(anno)

 nobs.AnnotationFunction = function(object, ...) {

-	if(object@n > 0) {

+	if(is.na(object@n)) {

+		return(NA)

+	} else if(object@n > 0) {

 		object@n

 	} else {

 		NA

@@ -55,6 +55,7 @@ anno_empty = function(which = c("column", "row"), border = TRUE, width = NULL, h

 	anno = AnnotationFunction(

 		fun = fun,

+		n = NA,

 		fun_name = "anno_empty",

 		which = which,

 		var_import = list(border),

@@ -236,6 +237,7 @@ anno_simple = function(x, col, na_col = "grey",

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

                 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(!is.null(pch)) {

+                	pch = pch[index, , drop = FALSE]

 					l = !is.na(pch[, i])

 					grid.points(x[l], y = rep((nc-i +0.5)/nc, sum(l)), pch = pch[l, i], size = pt_size, gp = pt_gp)

 				}

@@ -244,6 +246,7 @@ anno_simple = function(x, col, na_col = "grey",

 			fill = map_to_colors(color_mapping, value[index])

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

 			if(!is.null(pch)) {

+				pch = pch[index]

 				l = !is.na(pch)

 				grid.points(x[l], y = rep(0.5, sum(l)), pch = pch[l], size = pt_size[l], gp = subset_gp(pt_gp, which(l)))

 			}

@@ -337,10 +340,10 @@ anno_image = function(image, which = c("column", "row"), border = TRUE,

 	if(inherits(image, "character")) { ## they are file path

 		image_type = tolower(gsub("^.*\\.(\\w+)$", "\\1", image))

 		if(! all(image_type[image_type != ""] %in% allowed_image_type)) {

-			stop("image file should be of png/svg/pdf/eps/jpeg/jpg/tiff.")

+			stop_wrap("image file should be of png/svg/pdf/eps/jpeg/jpg/tiff.")

 		}

 	} else {

-		stop("`image` should be a vector of path.")

+		stop_wrap("`image` should be a vector of path.")

 	}

 	n_image = length(image)

@@ -352,25 +355,25 @@ anno_image = function(image, which = c("column", "row"), border = TRUE,

 			image_class[i] = NA

 		} else if(image_type[i] == "png") {

 			if(!requireNamespace("png")) {

-				stop("Need png package to read png images.")

+				stop_wrap("Need png package to read png images.")

 			}

 			image_list[[i]] = png::readPNG(image[i])

 			image_class[i] = "raster"

 		} else if(image_type[i] %in% c("jpeg", "jpg")) {

 			if(!requireNamespace("jpeg")) {

-				stop("Need jpeg package to read jpeg/jpg images.")

+				stop_wrap("Need jpeg package to read jpeg/jpg images.")

 			}

 			image_list[[i]] = jpeg::readJPEG(image[i])

 			image_class[i] = "raster"

 		} else if(image_type[i] == "tiff") {

 			if(!requireNamespace("tiff")) {

-				stop("Need tiff package to read tiff images.")

+				stop_wrap("Need tiff package to read tiff images.")

 			}

 			image_list[[i]] = tiff::readTIFF(image[i])

 			image_class[i] = "raster"

 		} else if(image_type[i] %in% c("pdf", "eps")) {

 			if(!requireNamespace("grImport")) {

-				stop("Need grImport package to read pdf/eps images.")

+				stop_wrap("Need grImport package to read pdf/eps images.")

 			}

 			temp_file = tempfile()

 			getFromNamespace("PostScriptTrace", ns = "grImport")(image[[i]], temp_file)

@@ -379,10 +382,10 @@ anno_image = function(image, which = c("column", "row"), border = TRUE,

 			image_class[i] = "grImport::Picture"

 		} else if(image_type[i] == "svg") {

 			if(!requireNamespace("grImport2")) {

-				stop("Need grImport2 package to read svg images.")

+				stop_wrap("Need grImport2 package to read svg images.")

 			}

 			if(!requireNamespace("rsvg")) {

-				stop("Need rsvg package to convert svg images.")

+				stop_wrap("Need rsvg package to convert svg images.")

 			}

 			temp_file = tempfile()

 			rsvg::rsvg_svg(image[i], temp_file)

@@ -1931,13 +1934,13 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000

 					value[[i]] = cbind(seq_along(x[[i]]), x[[i]])

 				}

 			} else {

-				stop("Since x is a list, x need to be a list of two-column matrices.")

+				stop_wrap("Since x is a list, x need to be a list of two-column matrices.")

 			}

 		} else {

 			value = x

 		}

 	} else {

-		stop("The input should be a list of two-column matrices or a matrix/data frame.")

+		stop_wrap("The input should be a list of two-column matrices or a matrix/data frame.")

 	}

 	xscale = range(lapply(value, function(x) x[, 1]), na.rm = TRUE)

@@ -2124,13 +2127,13 @@ anno_horizon = function(x, which = c("column", "row"),

 					value[[i]] = cbind(seq_along(x[[i]]), x[[i]])

 				}

 			} else {

-				stop("Since x is a list, x need to be a list of two-column matrices.")

+				stop_wrap("Since x is a list, x need to be a list of two-column matrices.")

 			}

 		} else {

 			value = x

 		}

 	} else {

-		stop("The input should be a list of two-column matrices or a matrix/data frame.")

+		stop_wrap("The input should be a list of two-column matrices or a matrix/data frame.")

 	}

 	if(is.null(gp$pos_fill)) gp$pos_fill = "#D73027"

@@ -2148,7 +2151,7 @@ anno_horizon = function(x, which = c("column", "row"),

 	}

 	if(which == "column") {

-		stop("anno_horizon() does not support column annotation. If you want, please email me.")

+		stop_wrap("anno_horizon() does not support column annotation. If you want, please email me.")

 	}

 	if(normalize) {

@@ -2323,7 +2326,7 @@ split_vec_by_NA = function(x) {

 #

 row_anno_points = function(...) {

 	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {

-		message("From this version of ComplexHeatmap, you can directly use `anno_points()` for row annotation if you call it in `rowAnnotation()`.")

+		message_wrap("From this version of ComplexHeatmap, you can directly use `anno_points()` for row annotation if you call it in `rowAnnotation()`.")

 	}

 	anno_points(..., which = "row")

 }

@@ -2345,7 +2348,7 @@ row_anno_points = function(...) {

 #

 row_anno_barplot = function(...) {

 	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {

-		message("From this version of ComplexHeatmap, you can directly use `anno_barplot()` for row annotation if you call it in `rowAnnotation()`.")

+		message_wrap("From this version of ComplexHeatmap, you can directly use `anno_barplot()` for row annotation if you call it in `rowAnnotation()`.")

 	}

 	anno_barplot(..., which = "row")

 }

@@ -2367,7 +2370,7 @@ row_anno_barplot = function(...) {

 #

 row_anno_boxplot = function(...) {

 	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {

-		message("From this version of ComplexHeatmap, you can directly use `anno_boxplot()` for row annotation if you call it in `rowAnnotation()`.")

+		message_wrap("From this version of ComplexHeatmap, you can directly use `anno_boxplot()` for row annotation if you call it in `rowAnnotation()`.")

 	}

 	anno_boxplot(..., which = "row")

 }

@@ -2388,7 +2391,7 @@ row_anno_boxplot = function(...) {

 #

 row_anno_histogram = function(...) {

 	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {

-		message("From this version of ComplexHeatmap, you can directly use `anno_histogram()` for row annotation if you call it in `rowAnnotation()`.")

+		message_wrap("From this version of ComplexHeatmap, you can directly use `anno_histogram()` for row annotation if you call it in `rowAnnotation()`.")

 	}

 	anno_histogram(..., which = "row")

 }

@@ -2409,7 +2412,7 @@ row_anno_histogram = function(...) {

 #

 row_anno_density = function(...) {

 	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {

-		message("From this version of ComplexHeatmap, you can directly use `anno_density()` for row annotation if you call it in `rowAnnotation()`.")

+		message_wrap("From this version of ComplexHeatmap, you can directly use `anno_density()` for row annotation if you call it in `rowAnnotation()`.")

 	}

 	anno_density(..., which = "row")

 }

@@ -2430,7 +2433,7 @@ row_anno_density = function(...) {

 #

 row_anno_text = function(...) {

 	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {

-		message("From this version of ComplexHeatmap, you can directly use `anno_text()` for row annotation if you call it in `rowAnnotation()`.")

+		message_wrap("From this version of ComplexHeatmap, you can directly use `anno_text()` for row annotation if you call it in `rowAnnotation()`.")

 	}

 	anno_text(..., which = "row")

 }

@@ -2482,7 +2485,7 @@ anno_mark = function(at, labels, which = c("column", "row"),

 	}

 	if(!is.numeric(at)) {

-		stop(paste0("`at` should be numeric ", which, " index corresponding to the matrix."))

+		stop_wrap(paste0("`at` should be numeric ", which, " index corresponding to the matrix."))

 	}

 	n = length(at)

@@ -2623,7 +2626,7 @@ subset_by_intersect = function(x, i) {

 # `anno_link` is deprecated, please use `anno_mark` instead.

 #

 anno_link = function(...) {

-	warning("anno_link() is deprecated, please use anno_mark() instead.")

+	warning_wrap("anno_link() is deprecated, please use anno_mark() instead.")

 	anno_mark(...)

 }

@@ -2644,7 +2647,7 @@ anno_link = function(...) {

 #

 row_anno_link = function(...) {

 	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {

-		message("From this version of ComplexHeatmap, you can directly use `anno_mark()` for row annotation if you call it in `rowAnnotation()`.")

+		message_wrap("From this version of ComplexHeatmap, you can directly use `anno_mark()` for row annotation if you call it in `rowAnnotation()`.")

 	}

 	anno_link(..., which = "row")

 }

@@ -2659,7 +2662,7 @@ anno_summarize = function(which = c("column", "row"),

 	}

 	if(which == "column") {

-		stop("`anno_summarize()` is only allowed as a column annotation.")

+		stop_wrap("`anno_summarize()` is only allowed as a column annotation.")

 	}

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

@@ -482,25 +482,6 @@ Heatmap = function(matrix, col, name,

     .Object@matrix_param$cell_fun = cell_fun

     .Object@matrix_param$layer_fun = layer_fun

-    if(!missing(width)) {

-        if(is_abs_unit(width)) {

-            heatmap_width = unit(1, "npc") # since width is a relative unit and all components are absolute, it will be refit

-        }

-    }

-    if(!missing(height)) {

-        if(is_abs_unit(height)) {

-            heatmap_height = unit(1, "npc")

-        }

-    }

-    if(is.null(width)) {

-        width = unit(ncol(matrix), "null")

-    }

-    if(is.null(height)) {

-        height = unit(nrow(matrix), "null")

-    }

-    .Object@matrix_param$width = width

-    .Object@matrix_param$height = height

-

     ### color for main matrix #########

     if(ncol(matrix) > 0 && nrow(matrix) > 0) {

         if(missing(col)) {

@@ -522,7 +503,7 @@ Heatmap = function(matrix, col, name,

                     .Object@matrix_color_mapping = ColorMapping(col_fun = col, name = name, na_col = na_col)

                     if(verbose) qqcat("input color is a vector with no names, treat it as continuous color mapping\n")

                 } else {

-                    stop("`col` should have names to map to values in `mat`.")

+                    stop_wrap("`col` should have names to map to values in `mat`.")

                 }

             } else {

                 col = col[intersect(c(names(col), "_NA_"), as.character(matrix))]

@@ -534,13 +515,8 @@ Heatmap = function(matrix, col, name,

     }

     ##### titles, should also consider titles after row splitting #####

-    if(length(row_title) != 1) {

-    } else if(!inherits(row_title, c("expression", "call"))) {

-        if(is.na(row_title)) {

-            row_title = character(0)

-        } else if(row_title == "") {

-            row_title = character(0)

-        }

+    if(identical(row_title, NA) || identical(row_title, "")) {

+        row_title = character(0)

     }

     .Object@row_title = row_title

     .Object@row_title_param$rot = row_title_rot %% 360

@@ -548,13 +524,8 @@ Heatmap = function(matrix, col, name,

     .Object@row_title_param$gp = check_gp(row_title_gp)  # if the number of settings is same as number of row-splits, gp will be adjusted by `make_row_dend`

     .Object@row_title_param$just = get_text_just(rot = row_title_rot, side = .Object@row_title_param$side)

-    if(length(column_title) != 1) {

-    } else if(!inherits(column_title, c("expression", "call"))) {

-        if(is.na(column_title)) {

-            column_title = character(0)

-        } else if(column_title == "") {

-            column_title = character(0)

-        }

+    if(identical(column_title, NA) || identical(column_title, "")) {

+        column_title = character(0)

     }

     .Object@column_title = column_title

     .Object@column_title_param$rot = column_title_rot %% 360

@@ -574,6 +545,9 @@ Heatmap = function(matrix, col, name,

     .Object@row_names_param$max_width = row_names_max_width + unit(2, "mm")

     # we use anno_text to draw row/column names because it already takes care of text rotation

     if(length(row_labels)) {

+        if(length(row_labels) != nrow(matrix)) {

+            stop_wrap("Length of `row_labels` should be the same as the nrow of matrix.")

+        }

         row_names_anno = anno_text(row_labels, which = "row", gp = row_names_gp, rot = row_names_rot,

             location = ifelse(.Object@row_names_param$side == "left", 1, 0), 

             just = ifelse(.Object@row_names_param$side == "left", "right", "left"))

@@ -590,6 +564,9 @@ Heatmap = function(matrix, col, name,

     .Object@column_names_param$rot = column_names_rot

     .Object@column_names_param$max_height = column_names_max_height + unit(2, "mm")

     if(length(column_labels)) {

+        if(length(column_labels) != ncol(matrix)) {

+            stop_wrap("Length of `column_labels` should be the same as the ncol of matrix.")

+        }

         column_names_anno = anno_text(column_labels, which = "column", gp = column_names_gp, rot = column_names_rot,

             location = ifelse(.Object@column_names_param$side == "top", 0, 1), 

             just = ifelse(.Object@column_names_param$side == "top", 

@@ -683,13 +660,13 @@ Heatmap = function(matrix, col, name,

     if(!is.null(top_annotation)) {

         if(length(top_annotation) > 0) {

             if(!.Object@top_annotation@which == "column") {

-                stop("`which` in `top_annotation` should only be `column`.")

+                stop_wrap("`which` in `top_annotation` should only be `column`.")

             }

         }

         nb = nobs(top_annotation)

         if(!is.na(nb)) {

             if(nb != ncol(.Object@matrix)) {

-                stop("number of items in top anntotion should be same as number of columns of the matrix.")

+                stop_wrap("number of observations in top annotation should be as same as ncol of the matrix.")

             }

         }

     }

@@ -703,13 +680,13 @@ Heatmap = function(matrix, col, name,

     if(!is.null(bottom_annotation)) {

         if(length(bottom_annotation) > 0) {

             if(!.Object@bottom_annotation@which == "column") {

-                stop("`which` in `bottom_annotation` should only be `column`.")

+                stop_wrap("`which` in `bottom_annotation` should only be `column`.")

             }

         }

         nb = nobs(bottom_annotation)

         if(!is.na(nb)) {

             if(nb != ncol(.Object@matrix)) {

-                stop("number of items in bottom anntotion should be same as number of columns of the matrix.")

+                stop_wrap("number of observations in bottom anntotion should be as same as ncol of the matrix.")

             }

         }

     }

@@ -723,13 +700,13 @@ Heatmap = function(matrix, col, name,

     if(!is.null(left_annotation)) {

         if(length(left_annotation) > 0) {

             if(!.Object@left_annotation@which == "row") {

-                stop("`which` in `left_annotation` should only be `row`, or consider using `rowAnnotation()`.")

+                stop_wrap("`which` in `left_annotation` should only be `row`, or consider using `rowAnnotation()`.")

             }

         }

         nb = nobs(left_annotation)

         if(!is.na(nb)) {

             if(nb != nrow(.Object@matrix)) {

-                stop("number of items in left anntotion should be same as number of rows of the matrix.")

+                stop_wrap("number of observations in left anntotion should be same as nrow of the matrix.")

             }

         }

     }

@@ -743,13 +720,13 @@ Heatmap = function(matrix, col, name,

     if(!is.null(right_annotation)) {

         if(length(right_annotation) > 0) {

             if(!.Object@right_annotation@which == "row") {

-                stop("`which` in `right_annotation` should only be `row`, or consider using `rowAnnotation()`.")

+                stop_wrap("`which` in `right_annotation` should only be `row`, or consider using `rowAnnotation()`.")

             }

         }

         nb = nobs(right_annotation)

         if(!is.na(nb)) {

             if(nb != nrow(.Object@matrix)) {

-                stop("number of items in right anntotion should be same as number of rows of the matrix.")

+                stop_wrap("number of observations in right anntotion should be same as nrow of the matrix.")

             }

         }

     }

@@ -780,6 +757,36 @@ Heatmap = function(matrix, col, name,

         initialized = FALSE

     )

+    if(is.null(width)) {

+        width = unit(ncol(matrix), "null")

+    } else if(is.numeric(width) && !inherits(width, "unit")) {

+        width = unit(width, "null")

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

+        stop_wrap("`width` should be a `unit` object or a single number.")

+    }

+

+    if(is.null(height)) {

+        height = unit(nrow(matrix), "null")

+    } else if(is.numeric(height) && !inherits(height, "unit")) {

+        height = unit(height, "null")

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

+        stop_wrap("`height` should be a `unit` object or a single number.")

+    }

+

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

+        if(is_abs_unit(width) && is_abs_unit(heatmap_width)) {

+            stop_wrap("`heatmap_width` and `width` should not all be the absolute units.")

+        }

+    }

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

+        if(is_abs_unit(height) && is_abs_unit(heatmap_height)) {

+            stop_wrap("`heatmap_height` and `width` should not all be the absolute units.")

+        }

+    }

+    

+    .Object@matrix_param$width = width

+    .Object@matrix_param$height = height

+

     .Object@heatmap_param$width = heatmap_width

     .Object@heatmap_param$height = heatmap_height

     .Object@heatmap_param$show_heatmap_legend = show_heatmap_legend

@@ -791,11 +798,9 @@ Heatmap = function(matrix, col, name,

     .Object@heatmap_param$post_fun = post_fun

     if(nrow(matrix) == 0) {

-        .Object@heatmap_param$height = unit(0, "mm")

         .Object@matrix_param$height = unit(0, "mm")

     }

     if(ncol(matrix) == 0) {

-        .Object@heatmap_param$width = unit(0, "mm")

         .Object@matrix_param$width = unit(0, "mm")

     }

@@ -827,7 +832,13 @@ setMethod(f = "make_row_cluster",

     signature = "Heatmap",

     definition = function(object) {

-    make_cluster(object, "row")

+    object = make_cluster(object, "row")

+    if(length(object@row_title) > 1) {

+        if(length(object@row_title) != length(object@row_order_list)) {

+            stop_wrap("If `row_title` is set with length > 1, the length should be as same as the number of row slices.")

+        }

+    }

+    return(object)  

 })

 # == title

@@ -853,7 +864,13 @@ setMethod(f = "make_column_cluster",

     signature = "Heatmap",

     definition = function(object) {

-    make_cluster(object, "column")

+    object = make_cluster(object, "column")

+    if(length(object@column_title) > 1) {

+        if(length(object@column_title) != length(object@column_order_list)) {

+            stop_wrap("If `column_title` is set with length > 1, the length should be as same as the number of column slices.")

+        }

+    }

+    return(object)

 })

 make_cluster = function(object, which = c("row", "column")) {

@@ -902,7 +919,7 @@ make_cluster = function(object, which = c("row", "column")) {

         if(!is.null(dend_param$obj)) {

             if(km > 1) {

-                stop("You can not make k-means partition since you have already specified a clustering object.")

+                stop_wrap("You can not perform k-means clustering since you have already specified a clustering object.")

             }

             if(inherits(dend_param$obj, "hclust")) {

@@ -916,10 +933,10 @@ make_cluster = function(object, which = c("row", "column")) {

                 if(verbose) qqcat("since you provided a clustering object and @{which}_split is null, the entrie clustering object is taken as an one-element list.\n")

             } else {

                 if(length(split) > 1 || !is.numeric(split)) {

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

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

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

                 }

                 ct = cut_dendrogram(dend_param$obj, split)

@@ -959,11 +976,11 @@ make_cluster = function(object, which = c("row", "column")) {

                 if(which == "row") {

                     if(length(reorder) != nrow(mat)) {

-                        stop("weight of reordering should have same length as number of rows.\n")

+                        stop_wrap("weight of reordering should have same length as number of rows.\n")

                     }

                 } else {

                     if(length(reorder) != ncol(mat)) {

-                        stop("weight of reordering should have same length as number of columns\n")

+                        stop_wrap("weight of reordering should have same length as number of columns\n")

                     }

                 }

@@ -1010,9 +1027,9 @@ make_cluster = function(object, which = c("row", "column")) {

                 } else if(length(gap) == n_slice - 1) {

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

                 } else if(length(gap) != n_slice) {

-                    stop(qq("Length of `gap` should be 1 or number of @{which} slices."))

+                    stop_wrap(qq("Length of `gap` should be 1 or number of @{which} slices."))

                 }

-                object@matrix_param[[ paste0(which, "_gap") ]] = gap# adjust title

+                object@matrix_param[[ paste0(which, "_gap") ]] = gap # adjust title

                 title = slot(object, paste0(which, "_title"))

                 if(!is.null(split)) {

@@ -1032,7 +1049,7 @@ make_cluster = function(object, which = c("row", "column")) {

                             })

                         } else if(grepl("\\{.+\\}", title)) {

                             if(!requireNamespace("glue")) {

-                                stop("You need to install glue package.")

+                                stop_wrap("You need to install glue package.")

                             }

                             title = apply(unique(split), 1, function(x) {

                                 x = x

@@ -1097,7 +1114,7 @@ make_cluster = function(object, which = c("row", "column")) {

         order_list[[1]] = order

     } else {

-        if(verbose) qqcat("process `split` data frame\n")

+        if(verbose) cat("process `split` data frame\n")

         if(is.null(ncol(split))) split = data.frame(split)

         if(is.matrix(split)) split = as.data.frame(split)

@@ -1147,7 +1164,7 @@ make_cluster = function(object, which = c("row", "column")) {

                     } else {

                         oe = try(obj <- as.dendrogram(obj), silent = TRUE)

                         if(inherits(oe, "try-error")) {

-                            stop("the clustering function must return a `dendrogram` object or a object that can be coerced to `dendrogram` class.")

+                            stop_wrap("the clustering function must return a `dendrogram` object or a object that can be coerced to `dendrogram` class.")

                         }

                         dend_list[[i]] = obj

                     }

@@ -1201,11 +1218,11 @@ make_cluster = function(object, which = c("row", "column")) {

             if(which == "row") {

                 if(length(reorder) != nrow(mat)) {

-                    stop("weight of reordering should have same length as number of rows\n")

+                    stop_wrap("weight of reordering should have same length as number of rows\n")

                 }

             } else {

                 if(length(reorder) != ncol(mat)) {

-                    stop("weight of reordering should have same length as number of columns\n")

+                    stop_wrap("weight of reordering should have same length as number of columns\n")

                 }

             }

             for(i in seq_along(dend_list)) {

@@ -1240,11 +1257,11 @@ make_cluster = function(object, which = c("row", "column")) {

     if(which == "row") {

         if(nrow(mat) != length(order)) {

-            stop(qq("Number of rows in the matrix are not the same as the length of the cluster or the @{which} orders."))

+            stop_wrap(qq("Number of rows in the matrix are not the same as the length of the cluster or the @{which} orders."))

         }

     } else {

         if(ncol(mat) != length(order)) {

-            stop(qq("Number of columns in the matrix are not the same as the length of the cluster or the @{which} orders."))

+            stop_wrap(qq("Number of columns in the matrix are not the same as the length of the cluster or the @{which} orders."))

         }

     }

@@ -1269,7 +1286,7 @@ make_cluster = function(object, which = c("row", "column")) {

     } else if(length(gap) == n_slice - 1) {

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

     } else if(length(gap) != n_slice) {

-        stop(qq("Length of `gap` should be 1 or number of @{which} slices."))

+        stop_wrap(qq("Length of `gap` should be 1 or number of @{which} slices."))

     }

     object@matrix_param[[ paste0(which, "_gap") ]] = gap

@@ -1292,7 +1309,7 @@ make_cluster = function(object, which = c("row", "column")) {

                 })

             } else if(grepl("\\{.+\\}", title)) {

                 if(!requireNamespace("glue")) {

-                    stop("You need to install glue package.")

+                    stop_wrap("You need to install glue package.")

                 }

                 title = apply(unique(split), 1, function(x) {

                     x = x

@@ -1371,7 +1388,7 @@ setMethod(f = "draw",

             upViewport()

         } else {

             if(ncol(object@matrix) == 0) {

-                stop("Single heatmap should contains a matrix with at least one column. Zero-column matrix can only be appended to the heatmap list.")

+                stop_wrap("Single heatmap should contains a matrix with at least one column. Zero-column matrix can only be appended to the heatmap list.")

             }

             ht_list = new("HeatmapList")

             ht_list = add_heatmap(ht_list, object)

@@ -399,9 +399,6 @@ setMethod(f = "make_layout",

             object@heatmap_param$width = object@heatmap_param$width + sum(row_gap[seq_len(nr_slice-1)])

         }

     } else {

-        if(!is.unit(object@heatmap_param$width)) {

-            warning("width of the heatmap can only be set as an absolute unit.")

-        }

         object@heatmap_param$width = unit(1, "npc")

     }

@@ -145,12 +145,12 @@ HeatmapAnnotation = function(...,

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

     if("df" %in% called_args) {

     	if(is.matrix(df)) {

-    		warning("`df` should be a data frame while not a matrix. Convert it to data frame.")

+    		warning_wrap("`df` should be a data frame while not a matrix. Convert it to data frame.")

     		df = as.data.frame(df)

     	} else if(!is.data.frame(df)) {

     		oe = try(df <- as.data.frame(df), silent = TRUE)

     		if(inherits(oe, "try-errir")) {

-    			stop("`df` should be a data frame.")

+    			stop_wrap("`df` should be a data frame.")

     		}

     	}

     }

@@ -158,7 +158,7 @@ HeatmapAnnotation = function(...,

     anno_arg_list = list(...)

 	if("df" %in% called_args && length(anno_arg_list)) {

 		if(any(duplicated(c(names(df), names(anno_arg_list))))) {

-			stop("Annotation names are duplicated. Check the column names of `df`.")

+			stop_wrap("Annotation names are duplicated. Check the column names of `df`.")

 		}

 	}

@@ -190,12 +190,12 @@ HeatmapAnnotation = function(...,

 		if(all(sapply(annotation_legend_param, inherits, "list"))) {  # if it is a list of lists

 			nl = length(annotation_legend_param)

 			if(nl > n_simple_anno) {

-				stop("Amount of legend params is larger than the number of simple annotations.")

+				stop_wrap("Amount of legend params is larger than the number of simple annotations.")

 			}

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

 				names(annotation_legend_param) = simple_anno_name[seq_len(nl)]

 			} else if(length(setdiff(names(annotation_legend_param), simple_anno_name))) {

-				stop("Some names in 'annotation_legend_param' are not in names of simple annotations.")

+				stop_wrap("Some names in 'annotation_legend_param' are not in names of simple annotations.")

 			} else {

 				annotation_legend_param = annotation_legend_param[ intersect(simple_anno_name, names(annotation_legend_param)) ]

 			}

@@ -539,8 +539,8 @@ setMethod(f = "draw",

     if(test2) {

     	grid.newpage()

-    	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))

+    	if(which == "column") pushViewport(viewport(width = unit(1, "npc") - unit(3, "cm"), height = object@height))

+    	if(which == "row") pushViewport(viewport(height = unit(1, "npc") - unit(3, "cm"), width = object@width))

     } else {

 		pushViewport(viewport(...))

 	}

@@ -571,7 +571,7 @@ setMethod(f = "draw",

 			oe = try(draw(object@anno_list[[i]], index, k, n))

 			if(inherits(oe, "try-error")) {

 				cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")

-				stop(oe)

+				stop_wrap(oe)

 			}

 			upViewport()

 		}

@@ -581,7 +581,7 @@ setMethod(f = "draw",

 			oe = try(draw(object@anno_list[[i]], index, k, n))

 			if(inherits(oe, "try-error")) {

 				cat("Error when drawing annotation '", object@anno_list[[i]]@name, "'\n", sep = "")

-				stop(oe)

+				stop_wrap(oe)

 			}

 			upViewport()

 		}

@@ -653,7 +653,11 @@ setMethod(f = "show",

 				paste0(object@anno_list[[i]]@color_mapping@type, " vector")

 			}

 		} else if(inherits(object@anno_list[[i]]@fun, "AnnotationFunction")) {

-			"AnnotationFunction"

+			if(object@anno_list[[i]]@fun@fun_name != "") {

+				paste0(object@anno_list[[i]]@fun@fun_name, "()")

+			} else {

+				"AnnotationFunction"

+			}

 		} else if(inherits(object@anno_list[[i]]@fun, "function")) {

 			"function"

 		} else {

@@ -416,6 +416,7 @@ setMethod(f = "draw",

         main_heatmap = main_heatmap,

         padding = padding,

+        auto_adjust = auto_adjust,

         row_dend_side = row_dend_side,

         row_sub_title_side = row_sub_title_side,

         column_dend_side = column_dend_side,

@@ -86,6 +86,7 @@ setMethod(f = "make_layout",

     main_heatmap = which(sapply(object@ht_list, inherits, "Heatmap"))[1],

     padding = NULL,

+    auto_adjust = TRUE,

     row_dend_side = c("original", "left", "right"),

     row_sub_title_side = c("original", "left", "right"),

     column_dend_side = c("original", "top", "bottom"),

@@ -423,6 +424,7 @@ setMethod(f = "make_layout",

         }

     }

     object@ht_list_param$padding = padding

+    object@ht_list_param$auto_adjust = auto_adjust

     ## orders of other heatmaps should be changed

     if(direction == "horizontal") {

@@ -446,6 +448,30 @@ setMethod(f = "make_layout",

         }

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

     }

+

+    if(auto_adjust) {

+        if(direction == "horizontal") {

+            for(i in seq_len(n_ht)) {

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

+                    if(i == 1 && !is.null(object@ht_list[[i]]@row_names_param$anno) && object@ht_list[[i]]@row_names_param$side == "left") {

+                    } else if(i == n_ht && !is.null(object@ht_list[[i]]@row_names_param$anno) && object@ht_list[[i]]@row_names_param$side == "right") {

+                    } else {

+                        object@ht_list[[i]]@row_names_param$anno = NULL

+                        object@ht_list[[i]]@row_names_param$show = FALSE

+                    }

+                }

+            }

+        } else {

+            for(i in seq_len(n_ht)) {

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

+                    object@ht_list[[i]]@column_order_list = ht_main@column_order_list

+                    object@ht_list[[i]]@column_order = ht_main@column_order

+                    object@ht_list[[i]]@column_dend_param$show = FALSE

+                    object@ht_list[[i]]@column_dend_param$cluster = FALSE  # don't do clustering because cluster was already done

+                }

+            }

+        }   

+    }

     if(direction == "horizontal") {

         # update other heatmaps' row titles

@@ -187,7 +187,7 @@ SingleAnnotation = function(name, value, col, fun,

     .Object@name = name

     if(!name_rot %in% c(0, 90, 180, 270)) {

-        stop("`name_rot` can only take values in c(0, 90, 180, 270)")

+        stop_wrap("@{name}: `name_rot` can only take values in c(0, 90, 180, 270)")

     }

     if(verbose) qqcat("create a SingleAnnotation with name '@{name}'\n")

@@ -242,7 +242,7 @@ SingleAnnotation = function(name, value, col, fun,

     if(which == "column") {

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

     	if(!name_side %in% c("left", "right")) {

-    		stop("`name_side` should be 'left' or 'right' when it is a column annotation.")

+    		stop_wrap("@{name}: `name_side` should be 'left' or 'right' when it is a column annotation.")

     	}

         if(verbose) qqcat("@{name}: adjust positions of annotation names\n")

     	if(name_side == "left") {

@@ -305,7 +305,7 @@ SingleAnnotation = function(name, value, col, fun,

     } else if(which == "row") {

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

     	if(!name_side %in% c("top", "bottom")) {

-    		stop("`name_side` should be 'left' or 'right' when it is a column annotation.")

+    		stop_wrap("@{name}: `name_side` should be 'left' or 'right' when it is a column annotation.")

     	}

         if(verbose) qqcat("@{name}: adjust positions of annotation names\n")

     	if(name_side == "top") {

@@ -413,7 +413,7 @@ SingleAnnotation = function(name, value, col, fun,

     gp = check_gp(gp)

     if(!is.null(gp$fill)) {

-    	stop("You should not set `fill`.")

+    	stop_wrap("@{name}: You should not set `fill`.")

     }

     if(missing(fun)) {

@@ -479,7 +479,7 @@ SingleAnnotation = function(name, value, col, fun,

     	if(!is.null(f_which)) {

     		fun_name = fun@fun_name

     		if(f_which != which) {

-    			stop(paste0("You are putting ", fun_name, "() as ", which, " annotations, you need to set 'which' argument to '", which, "' as well,\nor use the helper function ", which, "_", fun_name, "()."))

+    			stop_wrap("You are putting @{fun_name} as @{which} annotations, you need to set 'which' argument to '@{which}' as well, or use the helper function @{which}_@{fun_name}().")

     		}

         }

@@ -545,7 +545,7 @@ setMethod(f = "draw",

     if(missing(index)) {

         if(has_AnnotationFunction(object)) {

             if(object@fun@n == 0) {

-                stop("Cannot infer the number of Observations in the annotation function, you need to provide `index`.")

+                stop_wrap("Cannot infer the number of Observations in the annotation function, you need to provide `index`.")

             }

             index = seq_len(object@fun@n)

         }

@@ -737,7 +737,7 @@ has_AnnotationFunction = function(single_anno) {

                 return(x2)

             }

         }

-        stop("This SingleAnnotation object is not allowed for subsetting.")

+        stop_wrap("This SingleAnnotation object is not allowed for subsetting.")

     } else if(nargs() == 1) {

         return(x)

@@ -141,8 +141,8 @@ ht_global_opt = ht_opt

 DENDROGRAM_PADDING = unit(0.5, "mm")

 DIMNAME_PADDING = unit(1, "mm")

 TITLE_PADDING = unit(2.5, "mm")

-COLUMN_ANNO_PADDING = unit(0.5, "mm")

-ROW_ANNO_PADDING = unit(0.5, "mm")

+COLUMN_ANNO_PADDING = unit(1, "mm")

+ROW_ANNO_PADDING = unit(1, "mm")

 GLOBAL_PADDING = unit(c(2, 2, 2, 2), "mm")

@@ -364,19 +364,19 @@ dev.null = function(...) {

 }

 stop_wrap = function (...) {

-    x = paste0(...)

+    x = qq(paste0(...))

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

     stop(x, call. = FALSE)

 }

 warning_wrap = function (...) {

-    x = paste0(...)

+    x = qq(paste0(...))

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

     warning(x, call. = FALSE)

 }

 message_wrap = function (...) {