@@ -158,7 +158,7 @@ anno_simple = function(x, col, na_col = "grey",

 	input_is_matrix = is.matrix(x)

 	anno_size = anno_width_and_height(which, width, height, 

-		ht_opt$anno_simple_row_size*ifelse(input_is_matrix, ncol(x), 1))

+		ht_opt$anno_simple_size*ifelse(input_is_matrix, ncol(x), 1))

 	if(missing(col)) {

 		col = default_col(x)

@@ -292,9 +292,9 @@ Heatmap = function(matrix, col, name,

     row_split = split,

     column_km = 1,

     column_split = NULL,

-    gap = unit(0.5, "mm"),

-    row_gap = unit(0.5, "mm"),

-    column_gap = unit(0.5, "mm"),

+    gap = unit(1, "mm"),

+    row_gap = unit(1, "mm"),

+    column_gap = unit(1, "mm"),

     width = unit(1, "npc"),

     heatmap_body_width = NULL,

@@ -350,6 +350,7 @@ Heatmap = function(matrix, col, name,

     if(is.data.frame(matrix)) {

         if(verbose) qqcat("convert data frame to matrix\n")

+        warnings("The input is a data frame, convert to the matrix.")

         matrix = as.matrix(matrix)

     }

     if(!is.matrix(matrix)) {

@@ -525,7 +526,7 @@ Heatmap = function(matrix, col, name,

     }

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

-    if(length(row_title) == 0) {

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

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

         if(is.na(row_title)) {

             row_title = character(0)

@@ -539,7 +540,7 @@ 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) == 0) {

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

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

         if(is.na(column_title)) {

             column_title = character(0)

@@ -33,13 +33,14 @@

 subset_heatmap_by_row = function(ht, ind) {

-    ht@row_order = intersect(ht@row_order, 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.")

     }

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

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

         ht@row_names_param$labels = ht@row_names_param$labels[ind]

+        ht@row_names_param$anno = ht@row_names_param$anno[ind]

     }

     ht@row_names_param$gp = subset_gp(ht@row_names_param$gp, ind)

     if(length(ht@left_annotation)) {

@@ -52,13 +53,14 @@ subset_heatmap_by_row = function(ht, ind) {

 }

 subset_heatmap_by_column = function(ht, ind) {

-    ht@column_order = intersect(ht@column_order, 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.")

     }

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

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

         ht@column_names_param$labels = ht@column_names_param$labels[ind]

+        ht@column_names_param$anno = ht@column_names_param$anno[ind]

     }

     ht@column_names_param$gp = subset_gp(ht@column_names_param$gp, ind)

     if(length(ht@top_annotation)) {

@@ -87,18 +87,23 @@ HeatmapAnnotation = function(...,

 	annotation_legend_param = list(), 

 	show_legend = TRUE, 

 	which = c("column", "row"), 

-	annotation_height = NULL, 

-	annotation_width = NULL, 

-	height = NULL,   # total height

-	width = NULL,    # total width

 	gp = gpar(col = NA),

 	border = FALSE,

 	gap = unit(0, "mm"),

+	

 	show_annotation_name = TRUE,

 	annotation_name_gp = gpar(),

 	annotation_name_offset = unit(1, "mm"),

 	annotation_name_side = ifelse(which == "column", "right", "bottom"),

-	annotation_name_rot = ifelse(which == "column", 0, 90)) {

+	annotation_name_rot = ifelse(which == "column", 0, 90),

+	

+	annotation_height = NULL, 

+	annotation_width = NULL, 

+	height = NULL,

+	width = NULL,

+	anno_simple_size = ht_opt$anno_simple_size,

+	simple_anno_size_adjust = FALSE

+	) {

 	.ENV$current_annotation_which = NULL

 	which = match.arg(which)[1]

@@ -336,26 +341,9 @@ HeatmapAnnotation = function(...,

     global_height = NULL

     global_width = NULL

     if(which == "column") {

-    	if(is.null(annotation_height)) {

-    		if(!is.null(height)) {

-    			global_height = height

-    		}

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

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

-    	} else {

-    		if(length(annotation_height) != n_total_anno) {

-    			stop(qq("Length of `annotation_height` should be @{n_total_anno}"))

-    		}

-    		if(!is.unit(annotation_height)) {

-    			stop("`annotation_height` should be unit object")

-    		}

-    		if(!all(sapply(seq_along(annotation_height), function(x) is_abs_unit(annotation_height[i])))) {

-    			stop("`annotation_height` should only contain absolute units")

-    		}

-    		anno_size = annotation_height

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

-    	}

-

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

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

+    	

     	# for width, only look at `width`

     	if(is.null(width)) {

     		width = unit(1, "npc")

@@ -365,26 +353,10 @@ HeatmapAnnotation = function(...,

     	}

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

-    	if(is.null(annotation_width)) {

-    		if(!is.null(width)) {

-    			global_width = width

-    		}

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

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

-    	} else {

-    		if(length(annotation_width) != n_total_anno) {

-    			stop(qq("Length of `annotation_width` should be @{n_total_anno}"))

-    		}

-    		if(!is.unit(annotation_width)) {

-    			stop("`annotation_width` should be unit object")

-    		}

-    		if(!all(sapply(seq_along(annotation_width), function(x) is_abs_unit(annotation_width[i])))) {

-    			stop("`annotation_width` should only contain absolute units")

-    		}

-    		anno_size = annotation_width

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

-    	}

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

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

+    	

     	if(is.null(height)) {

     		height = unit(1, "npc")

     	}

@@ -417,13 +389,14 @@ HeatmapAnnotation = function(...,

     }

     .Object@extended = extended

-    ### if global width or height was set, adjust it

-    if(!is.null(global_height)) {

-    	height(.Object) = global_height

-    }

-    if(!is.null(global_width)) {

-    	width(.Object) = global_width

-    }

+    ## adjust height/width if `width`/`annotation_width` is set

+    if(which == "column") {

+	    .Object = resize(.Object, height = height, annotation_height = annotation_height,

+	    	anno_simple_size = anno_simple_size, simple_anno_size_adjust = simple_anno_size_adjust)

+	} else {

+		.Object = resize(.Object, width = width, annotation_width = annotation_width, 

+			anno_simple_size = anno_simple_size, simple_anno_size_adjust = simple_anno_size_adjust)

+	}

     return(.Object)

 }

@@ -972,7 +945,7 @@ length.HeatmapAnnotation = function(x) {

 # -annotation_width A vector of of annotation widths in `grid::unit` class.

 # -height The height of the complete heatmap annotation.

 # -width The width of the complete heatmap annotation.

-# -anno_simple_row_size The size of one line of the simple annotation.

+# -anno_simple_size The size of one line of the simple annotation.

 # -simple_anno_size_adjust Whether adjust the size of the simple annotation?

 #

 # == details

@@ -983,10 +956,10 @@ length.HeatmapAnnotation = function(x) {

 #    ``annotation_height`` are absolute units, ``height`` is ignored.

 # 2. if ``annotation_height`` contains non-absolute units, ``height`` also need to be set and the

 #    non-absolute unit should be set in a simple form such as 1:10 or ``unit(1, "null")``.

-# 3. ``anno_simple_row_size`` is only used when ``annotation_height`` is NULL.

+# 3. ``anno_simple_size`` is only used when ``annotation_height`` is NULL.

 # 4. if only ``height`` is set, non-simple annotation is adjusted while keep simple anntation unchanged.

 # 5. if only ``height`` is set and all annotations are simple annotations, all anntations are adjusted.

-#      and ``anno_simple_row_size`` is disabled.

+#      and ``anno_simple_size`` is disabled.

 # 6. If ``simple_anno_size_adjust`` is ``FALSE``, the size of the simple annotations will not change.

 #

 setMethod(f = "resize",

@@ -996,7 +969,7 @@ setMethod(f = "resize",

 	annotation_width = NULL,

 	height = NULL, 

 	width = NULL, 

-	anno_simple_row_size = ht_opt$anno_simple_row_size,

+	anno_simple_size = ht_opt$anno_simple_size,

 	simple_anno_size_adjust = FALSE) {

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

@@ -1162,10 +1135,10 @@ setMethod(f = "resize",

 			anno_size2 = anno_size

 			# size_adjusted = convertUnitFun(size_adjusted, "mm", valueOnly = TRUE)

-			if(is.null(anno_simple_row_size)) {

-				anno_simple_row_size = 5

+			if(is.null(anno_simple_size)) {

+				anno_simple_size = 5

 			} else {

-				anno_simple_row_size = convertUnitFun(anno_simple_row_size, "mm", valueOnly = TRUE)

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

 			}

 			if(size_adjusted <= sum(gap)) {

@@ -1173,12 +1146,12 @@ setMethod(f = "resize",

 			}

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

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

+			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."))

 			}

 			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_row_size/5

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

 			size_adjusted = unit(size_adjusted, "mm")

 			anno_size2 = unit(anno_size2, "mm")

@@ -310,7 +310,8 @@ setMethod(f = "draw",

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

     padding = NULL,

     adjust_annotation_extension = TRUE,

-

+    

+    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"),

@@ -518,14 +519,14 @@ setMethod(f = "draw",

     if(is_abs_unit(ht_list_width)) {

         ht_list_width = unit(round(convertWidth(ht_list_width, "mm", valueOnly = TRUE)), "mm")

-        qqcat("Since all heatmaps/annotations have absolute units, the total width of the plot is @{ht_list_width} mm.\n")

+        qqcat("Since all heatmaps/annotations have absolute units, the total width of the plot is @{ht_list_width}\n")

         w = ht_list_width

     } else {

         w = unit(1, "npc")

     }

     if(is_abs_unit(ht_list_height)) {

         ht_list_height = unit(round(convertHeight(ht_list_height, "mm", valueOnly = TRUE)), "mm")

-        qqcat("Since all heatmaps/annotations have absolute units, the total height of the plot is @{ht_list_height} mm.\n")

+        qqcat("Since all heatmaps/annotations have absolute units, the total height of the plot is @{ht_list_height}\n")

         h = ht_list_height

     } else {

         h = unit(1, "npc")

@@ -26,7 +26,7 @@ setMethod(f = "row_order",

 	object = make_layout(object)

 	n = length(object@ht_list)

-	ht_index = sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap"))

+	ht_index = which(sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap")))

 	if(length(ht_index) == 0) {

 		return(NULL)

 	}

@@ -45,7 +45,7 @@ setMethod(f = "row_order",

 	        lt_rd = c(lt_rd, list(lt))

 	    }

 	    names(lt_rd) = names(object@ht_list)[ht_index]

-	    return(lt_rd)

+	    proper_format_lt(lt_rd)

 	}

 })

@@ -111,7 +111,7 @@ setMethod(f = "column_order",

 	object = make_layout(object)

 	n = length(object@ht_list)

-	ht_index = sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap"))

+	ht_index = which(sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap")))

 	if(length(ht_index) == 0) {

 		return(NULL)

 	}

@@ -130,8 +130,7 @@ setMethod(f = "column_order",

 	        lt_rd = c(lt_rd, list(lt))

 	    }

 	    names(lt_rd) = names(object@ht_list)[ht_index]

-	    if(length(lt_rd) == 1) lt_rd = lt_rd[[1]]

-	    return(lt_rd)

+	    proper_format_lt(lt_rd)

 	}

 })

@@ -195,7 +194,7 @@ setMethod(f = "row_dend",

 	object = make_layout(object)

 	n = length(object@ht_list)

-	ht_index = sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap"))

+	ht_index = which(sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap")))

 	if(length(ht_index) == 0) {

 		return(NULL)

 	}

@@ -214,7 +213,7 @@ setMethod(f = "row_dend",

 	        lt_rd = c(lt_rd, list(lt))

 	    }

 	    names(lt_rd) = names(object@ht_list)[ht_index]

-	    return(lt_rd)

+	    proper_format_lt(lt_rd)

 	}

 })

@@ -281,7 +280,7 @@ setMethod(f = "column_dend",

 	object = make_layout(object)

 	n = length(object@ht_list)

-	ht_index = sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap"))

+	ht_index = which(sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap")))

 	if(length(ht_index) == 0) {

 		return(NULL)

 	}

@@ -300,7 +299,7 @@ setMethod(f = "column_dend",

 	        lt_rd = c(lt_rd, list(lt))

 	    }

 	    names(lt_rd) = names(object@ht_list)[ht_index]

-	    return(lt_rd)

+	    proper_format_lt(lt_rd)

 	}

 })

@@ -338,3 +337,23 @@ setMethod(f = "column_dend",

 	}

 })

+

+

+proper_format_lt = function(lt) {

+	n_ht = length(lt)

+	# for a single heatmap 

+	if(n_ht == 1) {

+		if(length(lt[[1]]) == 1) {

+			return(lt[[1]][[1]])

+		} else {

+			return(lt[[1]])

+		}

+	} else {

+		has_splitting = sapply(lt, function(x) length(x) != 1)

+		if(has_splitting) {

+			return(lt)

+		} else {

+			return(lapply(lt, function(x) x[[1]]))

+		}

+	}

+}

@@ -110,7 +110,7 @@ ht_opt = setGlobalOptions(

 		},

 		.length = 1),

 	show_vp_border = FALSE,

-	anno_simple_row_size = unit(5, "mm")

+	anno_simple_size = unit(5, "mm")

 )

@@ -52,6 +52,8 @@ ha = HeatmapAnnotation(foo = anno_empty(), height = unit(4, "cm"))

 draw(ha, 1:10, test = "anno_empty")

 ha = HeatmapAnnotation(foo = anno_empty(), bar = 1:10, height = unit(4, "cm"))

 draw(ha, 1:10, test = "anno_empty")

+ha = HeatmapAnnotation(foo = anno_empty(), bar = 1:10, height = unit(4, "cm"))

+draw(ha, 1:10, test = "anno_empty")

 ha = HeatmapAnnotation(foo = function(index) {grid.rect()}, bar = 1:10 height = unit(4, "cm"))

 draw(ha, 1:10, test = "self-defined function")