@@ -6,7 +6,7 @@ Date: 2021-11-08

 Author: Zuguang Gu

 Maintainer: Zuguang Gu <z.gu@dkfz.de>

 Depends: R (>= 3.5.0), methods, grid, graphics, stats, grDevices

-Imports: circlize (>= 0.4.5), GetoptLong, colorspace, clue,

+Imports: circlize (>= 0.4.14), GetoptLong, colorspace, clue,

     RColorBrewer, GlobalOptions (>= 0.1.0), png,

     digest, IRanges, matrixStats, foreach, doParallel

 Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, 

@@ -48,6 +48,8 @@ S3method("heightDetails", "legend_body")

 export("heightDetails.legend_body")

 S3method("heightDetails", "packed_legends")

 export("heightDetails.packed_legends")

+S3method("heightDetails", "text_box")

+export("heightDetails.text_box")

 S3method("length", "HeatmapAnnotation")

 export("length.HeatmapAnnotation")

 S3method("length", "HeatmapList")

@@ -122,6 +124,8 @@ S3method("widthDetails", "legend_body")

 export("widthDetails.legend_body")

 S3method("widthDetails", "packed_legends")

 export("widthDetails.packed_legends")

+S3method("widthDetails", "text_box")

+export("widthDetails.text_box")

 export("%v%")

 export("AdditiveUnit")

 export("AnnotationFunction")

@@ -149,11 +153,13 @@ export("anno_joyplot")

 export("anno_lines")

 export("anno_link")

 export("anno_mark")

+export("anno_numeric")

 export("anno_oncoprint_barplot")

 export("anno_points")

 export("anno_simple")

 export("anno_summary")

 export("anno_text")

+export("anno_text_box")

 export("anno_zoom")

 export("annotation_axis_grob")

 export("bar3D")

@@ -193,6 +199,7 @@ export("getXY_in_parent_vp")

 export("grid.annotation_axis")

 export("grid.boxplot")

 export("grid.dendrogram")

+export("grid.text_box")

 export("gt_render")

 export("ht_global_opt")

 export("ht_opt")

@@ -228,6 +235,7 @@ export("subset_matrix_by_row")

 export("subset_no")

 export("subset_vector")

 export("test_alter_fun")

+export("text_box_grob")

 export("unify_mat_list")

 export("upset_left_annotation")

 export("upset_right_annotation")

@@ -3,6 +3,9 @@ CHANGES in VERSION 2.11.1

 * add a global option `ht_opt$COLOR` to control colors for continuous color mapping.

 * `annotation_label` can be an `expression` object.

 * `recycle_gp()`: now consider when n = 0.

+* `anno_block()`: add `align_to` argument.

+* add `anno_text_box()` and `grid.text_box()`.

+* add `show_name` argument in `anno_empty()`.

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

@@ -1,32 +1,32 @@

+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))

+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))

+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))

+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))

+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

 setGeneric('draw', function(object, ...) standardGeneric('draw'))

-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))

+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))

 setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))

-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))

+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

 setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))

+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))

 setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))

-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))

-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))

-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))

-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))

-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))

 setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))

-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))

-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))

-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))

-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))

-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))

-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))

-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

 setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))

-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))

-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))

+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))

+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

 setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))

+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))

+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

 setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))

+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))

+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))

+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))

+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))

+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

@@ -24,7 +24,7 @@ AnnotationFunction = setClass("AnnotationFunction",

 		var_env = "environment",

 		fun = "function",

 		subset_rule = "list",

-		subsetable = "logical",

+		subsettable = "logical",

 		data_scale = "numeric",

 		extended = "ANY",

 		show_name = "logical"

@@ -34,7 +34,7 @@ AnnotationFunction = setClass("AnnotationFunction",

 		width = unit(1, "npc"),

 		height = unit(1, "npc"),

 		subset_rule = list(),

-		subsetable = FALSE,

+		subsettable = FALSE,

 		data_scale = c(0, 1),

 		n = NA_integer_,

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

@@ -92,8 +92,8 @@ anno_width_and_height = function(which, width = NULL, height = NULL,

 # -data_scale The data scale on the data axis (y-axis for column annotation and x-axis for row annotation). It is only used

 #             when `decorate_annotation` is used with "native" unit coordinates.

 # -subset_rule The rule of subsetting variables in ``var_import``. It should be set when users want the final object to

-#              be subsetable. See **Details** section.

-# -subsetable Whether the object is subsetable?

+#              be subsettable. See **Details** section.

+# -subsettable Whether the object is subsettable?

 # -show_name It is used to turn off the drawing of annotation names in `HeatmapAnnotation`. Annotations always have names

 #        associated and normally they will be drawn beside the annotation graphics to tell what the annotation is about.

 #        e.g. the annotation names put beside the points annotation graphics. However, for some of the annotations, the names

@@ -133,7 +133,7 @@ anno_width_and_height = function(which, width = NULL, height = NULL,

 #     },

 #     var_import = list(x = x),

 #     n = 10,

-#     subsetable = TRUE,

+#     subsettable = TRUE,

 #     height = unit(2, "cm")

 # )

 # m = rbind(1:10, 11:20)

@@ -141,7 +141,7 @@ anno_width_and_height = function(which, width = NULL, height = NULL,

 # Heatmap(m, top_annotation = HeatmapAnnotation(foo = anno1), column_km = 2)

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

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

-	subsetable = length(subset_rule) > 0, show_name = TRUE, width = NULL, height = NULL) {

+	subsettable = length(subset_rule) > 0, show_name = TRUE, width = NULL, height = NULL) {

 	which = match.arg(which)[1]

@@ -183,7 +183,7 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"), ce

 				}

 			}

 		}

-		subsetable = TRUE

+		subsettable = TRUE

 	}

 	if(length(var_import)) {

@@ -232,13 +232,13 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"), ce

 		}

 	}

-	if(missing(subsetable)) {

+	if(missing(subsettable)) {

 		# is user defined subset rule

 		if(length(anno@subset_rule)) {

-			anno@subsetable = TRUE

+			anno@subsettable = TRUE

 		}

 	} else {

-		anno@subsetable = subsetable

+		anno@subsettable = subsettable

 	}

 	return(anno)

@@ -263,8 +263,8 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"), ce

 	if(nargs() == 1) {

 		return(x)

 	} else {

-		if(!x@subsetable) {

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

+		if(!x@subsettable) {

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

 		}

 		x = copy_all(x)

 		if(x@fun_name == "anno_mark") {

@@ -425,12 +425,12 @@ setMethod(f = "show",

 	var_imported = names(object@var_env)

 	if(length(var_imported)) {

 		cat("  imported variable:", paste(var_imported, collapse = ", "), "\n")

-		var_subsetable = names(object@subset_rule)

-		if(length(var_subsetable)) {

-			cat("  subsetable variable:", paste(var_subsetable, collapse = ", "), "\n")

+		var_subsettable = names(object@subset_rule)

+		if(length(var_subsettable)) {

+			cat("  subsettable variable:", paste(var_subsettable, collapse = ", "), "\n")

 		}

 	}

-	cat("  this object is ", ifelse(object@subsetable, "", "not "), "subsetable\n", sep = "")

+	cat("  this object is ", ifelse(object@subsettable, "", "not "), "subsettable\n", sep = "")

 	dirt = c("bottom", "left", "top", "right")

 	for(i in 1:4) {

 		if(!identical(unit(0, "mm"), object@extended[i])) {

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

 #       and the original heatmap slices.

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

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

+# -show_name Whether to show annotation name.

 #

 # == details

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

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

 # anno = anno_empty(border = FALSE)

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

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

-	width = NULL, height = NULL) {

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

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

 		which = match.arg(which)[1]

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

 		which = which,

 		var_import = list(border, zoom),

 		subset_rule = list(),

-		subsetable = TRUE,

+		subsettable = TRUE,

 		height = anno_size$height,

 		width = anno_size$width,

-		show_name = FALSE

+		show_name = show_name

 	)

 	return(anno) 

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

 			pch = pch[index, , drop = FALSE]

 			for(i in seq_len(nc)) {

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

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

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

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

+				    flag = 0

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

+	                	gp$col = fill

+	                	flag = 1

+	                }

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

+				    if(flag) gp$col = NULL

 				} else {

 					r = rle(value[index, i])

 					fill = map_to_colors(color_mapping, r$values)

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

 			    }

 			}

 	    } else {

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

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

 				fill = map_to_colors(color_mapping, value[index])

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

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

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

             nc = ncol(value)

 		    pch = pch[index, , drop = FALSE]

-				  

 	        for(i in seq_len(nc)) {

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

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

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

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

+	                flag = 0

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

+	                	gp$col = fill

+	                	flag = 1

+	                }

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

+	                if(flag) gp$col = NULL

 	            } else {

 	            	r = rle(value[index, i])

 					fill = map_to_colors(color_mapping, r$values)

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

 				}

 		    }

         } else {

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

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

 				fill = map_to_colors(color_mapping, value[index])

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

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

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

 		}

 	}

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	return(anno)      

 }

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

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

 			}

 		}

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

+		if(is.logical(border)) {

+			if(border) {

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

+			}

+		} else {

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

+		}

 		popViewport()

 	}

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

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

 			}

 		}

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

+		if(is.logical(border)) {

+			if(border) {

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

+			}

+		} else {

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

+		}

 		popViewport()

 	}

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

 	anno@subset_rule$image_list = subset_vector

 	anno@subset_rule$image_class = subset_vector

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	return(anno)   

 }

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

 		anno@subset_rule$pch = subset_vector

 	}

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

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

 		anno@subset_rule$pch = subset_vector

 	}

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

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

 # -border Wether draw borders of the annotation region?

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

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

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

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

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

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

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

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

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

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

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

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

+	beside = FALSE, attach = FALSE,

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

 	axis_param = default_axis_param(which), 

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

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

 				nr = nrow(value)

 				for(i in seq_along(index)) {

 			        for(j in 1:nbar) {

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

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

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

-				        } else {

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

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

-				        }

+			        	if(attach) {

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

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

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

+					        } else {

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

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

+					        }

+			        	} else {

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

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

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

+					        } else {

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

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

+					        }

+					    }

 			        }

 			    }

 			} else {

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

 				nr = nrow(value)

 				for(i in seq_along(index)) {

 			        for(j in 1:nbar) {

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

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

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

-				        } else {

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

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

-				        }

+			        	if(attach) {

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

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

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

+					        } else {

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

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

+					        }

+					    } else {

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

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

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

+					        } else {

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

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

+					        }

+					    }

 			        }

 			    }

 			} else {

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

 		height = anno_size$height,

 		n = n,

 		data_scale = data_scale,

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

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

 	)

 	anno@subset_rule$value = subset_matrix_by_row

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

 		anno@subset_rule$gp = subset_gp

 	}

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

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

 	anno@subset_rule$pch = subset_vector

 	anno@subset_rule$size = subset_vector

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

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

 	anno@subset_rule$histogram_breaks = subset_vector

 	anno@subset_rule$histogram_counts = subset_vector

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

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

 	anno@subset_rule$density_x = subset_vector

 	anno@subset_rule$density_y = subset_vector

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

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

 	anno@subset_rule$value = subset_vector

 	anno@subset_rule$gp = subset_gp

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	return(anno)

 }

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

 	anno@subset_rule$value = subset_vector

 	anno@subset_rule$gp = subset_gp

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

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

 	anno@subset_rule$value = subset_vector

 	anno@subset_rule$gp = subset_gp

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

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

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

 	anno@subset_rule$at = subset_by_intersect

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	attr(anno, "called_args") = list(

 		at = at, 

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

 		show_name = FALSE

 	)

-	anno@subsetable = FALSE

+	anno@subsettable = FALSE

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

 	return(anno)

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

 # Block annotation

 #

 # == param

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

+#        rows or columns.

 # -gp Graphic parameters.

 # -labels Labels put on blocks.

 # -labels_gp Graphic parameters for labels.

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

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

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

 # -show_name Whether show annotatio name.

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

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

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

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

 #

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

 #     row_km = 3)

 #

 #

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

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

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

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

 # rowAnnotation(foo = anno_block(

-# 	graphics = function(index, levels) {

+# 	panel_fun = function(index, levels) {

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

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

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

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

 #

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

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

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

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

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

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

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

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

 #

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

 # rowAnnotation(foo = anno_block(

-# 	graphics = function(index, levels) {

+# 	panel_fun = function(index, levels) {

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

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

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

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

 # 	width = unit(3, "cm")

 # ))

 #

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

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

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

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

+# rowAnnotation(foo = anno_block(

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

+# 	panel_fun = function(index, nm) {

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

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

+# 	},

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

+# )

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

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

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

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

-	graphics = NULL) {

+	panel_fun = NULL) {

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

 		which = match.arg(which)[1]

 	} else {

 		which = .ENV$current_annotation_which

 	}

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

+		if(is.numeric(align_to)) {

+			align_to = list(v = align_to)

+		}

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

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

+		}

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

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

+		}

+	}

+

 	if(length(labels)) {

 		if(which == "column") {

 			if(missing(height)) {

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

 		}

 	}

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

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

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

+		}

+	}

+

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

 	fun = function(index, k, n) {

-		if(is.null(graphics)) {

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

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

+			

+			ind_aln = which(is_in)

+

+			for(ai in ind_aln) {

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

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

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

+				}

+

+				ni = length(index)

+

+				if(which == "row") {

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

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

+					popViewport()

+				} else {

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

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

+					popViewport()

+				}

+			}

+

+		} else if(is.null(panel_fun)) {

 			gp = subset_gp(recycle_gp(gp, n), k)

 			grid.rect(gp = gp)

 			if(length(labels)) {

@@ -3551,7 +3650,7 @@ anno_block = function(gp = gpar(), labels = NULL, labels_gp = gpar(),

 				if(which == "row") x = labels_offset

 				grid.text(label, x = x, y = y, gp = labels_gp, rot = labels_rot, just = labels_just)

 			}

-		} else {

+		} else  {

 			for(ifa in 1:30) {

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

@@ -3568,9 +3667,9 @@ anno_block = function(gp = gpar(), labels = NULL, labels_gp = gpar(),

 				order_list = ht@column_order_list

 			}

 			if(is.null(split)) {

-				graphics(index, NULL)

+				panel_fun(index, NULL)

 			} else {

-				graphics(index, unlist(split[order_list[[k]][1], ]))

+				panel_fun(index, unlist(split[order_list[[k]][1], ]))

 			}

 		}

 	}

@@ -3580,9 +3679,9 @@ anno_block = function(gp = gpar(), labels = NULL, labels_gp = gpar(),

 		n = NA,

 		fun_name = "anno_block",

 		which = which,

-		var_import = list(gp, labels, labels_gp, labels_rot, labels_offset, labels_just, graphics, which),

+		var_import = list(gp, labels, labels_gp, labels_rot, labels_offset, labels_just, panel_fun, which, align_to),

 		subset_rule = list(),

-		subsetable = TRUE,

+		subsettable = TRUE,

 		height = anno_size$height,

 		width = anno_size$width,

 		show_name = show_name

@@ -4087,7 +4186,7 @@ anno_zoom = function(align_to, panel_fun = function(index, nm = NULL) { grid.rec

 		}

 	}

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	return(anno)

 }

@@ -4202,8 +4301,147 @@ anno_customize = function(x, graphics = list(), which = c("column", "row"),

 	anno@subset_rule$value = subset_vector

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	return(anno) 

 }

+

+

+# == title

+# Numeric labels annotation

+#

+# == param

+# -x A vector of numeric values.

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

+# -labels_gp. Graphics parameters for labels.

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

+#      is normally applied.

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

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

+# -bg_gp Graphics parameters for the background bars.

+# -bar_width Width of bars. Note it corresponds to the vertical direction.

+# -round_corners Whether to draw bars with round corners?

+# -r Radius of the round corners.

+# -which Row or column. Currently it only supports row annotation.

+# -align_to Which side bars as well as the labels are aligned to. Values can be "left" or "right". If ``x`` contains both positive and negative values,

+#       ``align_to`` can also be set to 0 so that bars are aligned to ``pos = 0``.

+# -width Width of the annotation.

+#

+# == example

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

+# x = numeric(10)

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

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

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

+	bg_gp = gpar(fill = "#8080FF", col = "#8080FF"), 

+	bar_width = unit(1, "npc") - unit(4, "pt"),

+	round_corners = TRUE, r = unit(0.05, "snpc"), 

+    which = c("row", "column"), align_to = "left", width = NULL) {

+

+	which = match.arg(which)[1]

+	if(which == "column") {

+		stop_wrap("`anno_numeric()` can only be used as row annotation.")

+	}

+

+	if(!is.numeric(x)) {

+		stop_wrap("Input for `anno_numeric()` should be a numeric vector.")

+	}

+

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

+    	labels = labels_format(x)

+    } else {

+    	labels = x

+    }

+

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

+		x = x_convert(x)

+		rg = range(x_convert(rg))

+	}

+

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

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

+

+    if(missing(align_to) && (any(x > 0) & any(x < 0))) {

+    	align_to = 0

+    }

+

+    cell_fun_pct = function(i) {

+

+    	min_x = rg[1]

+    	max_x = rg[2]

+        pushViewport(viewport(xscale = rg))

+        if(align_to == "right") {

+        	if(round_corners) {

+	            grid.roundrect(x = unit(1, "npc"), 

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

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

+	        } else {

+	        	grid.rect(x = unit(1, "npc"), 

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

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

+	        }

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

+        } else if(align_to == "left") {

+        	if(round_corners) {

+	            grid.roundrect(x = unit(0, "npc"), 

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

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

+	        } else {

+	        	grid.rect(x = unit(0, "npc"), 

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

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

+	        }

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

+        } else if(align_to == 0) {

+        	if(x[i] <= 0) {

+        		if(round_corners) {

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

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

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

+		        } else {

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

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

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

+		        }

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

+	        } else {

+	        	if(round_corners) {

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

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

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

+		        } else {

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

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

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

+		        }

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

+	        }

+        }

+        popViewport()

+    }

+

+    if(is.null(width)) {

+    	if(align_to == "left" || align_to == "right") {

+        	width = convertWidth(max(unit.c(unit(2, "cm"), max_text_width(labels, gp = labels_gp) + labels_offset*2)), "mm")

+        } else {

+        	l1 = x >= 0

+        	l2 = x < 0

+        	if(any(l1) && any(l2)) {

+        		w1 = max_text_width(labels[l1], gp = subset_gp(labels_gp, l1)) + labels_offset*2

+        		w2 = max_text_width(labels[l2], gp = subset_gp(labels_gp, l2)) + labels_offset*2

+				width = convertWidth(max(unit.c(unit(2, "cm"), w1 + w2)), "mm")

+        		

+        	} else {

+        		width = convertWidth(max(unit.c(unit(2, "cm"), max_text_width(labels, gp = labels_gp) + labels_offset*2)), "mm")

+        	}

+        }

+    }

+    AnnotationFunction(

+        cell_fun = cell_fun_pct,

+        var_import = list(rg, labels, x, labels_gp, align_to, bg_gp, bar_width, labels_offset, round_corners, r), 

+        which = "row",

+        width = width

+    )

+}

+

@@ -974,7 +974,17 @@ Heatmap = function(matrix, col, name,

     .Object@heatmap_param$height = heatmap_height

     .Object@heatmap_param$show_heatmap_legend = show_heatmap_legend

     .Object@heatmap_param$use_raster = use_raster

-    .Object@heatmap_param$raster_device = match.arg(raster_device)[1]

+

+    if(missing(raster_device)) {

+        if(requireNamespace("Cairo", quietly = TRUE)) {

+            raster_device = "CairoPNG"

+        } else {

+            raster_device = "png"

+        }