Browse code

add 'graphics' argument in 'anno_block()'

Zuguang Gu authored on 11/03/2021 09:41:22
Showing14 changed files

... ...
@@ -1,6 +1,7 @@
1 1
 CHANGES in VERSION 2.7.8
2 2
 
3 3
 * add `cluster_between_groups()`.
4
+* add `graphics` argument in `anno_block()`.
4 5
 
5 6
 CHANGES in VERSION 2.7.7
6 7
 
... ...
@@ -1,32 +1,32 @@
1
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
2
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
3 1
 setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
4
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
2
+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
3
+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
5 4
 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
6
-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
7
-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
8
-setGeneric('draw', function(object, ...) standardGeneric('draw'))
9
-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
10
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
11
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
12
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
13
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
5
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
6
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
14 7
 setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
15
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
8
+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
16 9
 setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
10
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
17 11
 setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
12
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
13
+setGeneric('draw', function(object, ...) standardGeneric('draw'))
14
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
15
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
18 16
 setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
19
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
20
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
21
-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
22 17
 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
23
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
24
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
18
+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
19
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
25 20
 setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
21
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
26 22
 setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
27
-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
28
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
29
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
30
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
23
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
24
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
31 25
 setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
32 26
 setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
27
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
28
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
29
+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
30
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
31
+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
32
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
... ...
@@ -3271,6 +3271,9 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0
3271 3271
 # -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.
3272 3272
 # -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.
3273 3273
 # -show_name Whether show annotatio name.
3274
+# -graphics A self-defined function that draws graphics in each slice. It must have two arguments: 1. row/column indices for the 
3275
+#      current slice and a vector of levels from the split variable that correspond to current slice. When ``graphics`` is set,
3276
+#      all other graphics parameters in `anno_block` are ignored.
3274 3277
 #
3275 3278
 # == details
3276 3279
 # The block annotation is used for representing slices. The length of all arguments should be 1 or the number of slices.
... ...
@@ -3289,10 +3292,44 @@ anno_summary = function(which = c("column", "row"), border = TRUE, bar_width = 0
3289 3292
 #     left_annotation = rowAnnotation(foo = anno_block(gp = gpar(fill = 2:4),
3290 3293
 #         labels = c("group1", "group2", "group3"), labels_gp = gpar(col = "white"))),
3291 3294
 #     row_km = 3)
3295
+#
3296
+#
3297
+# # =============  set the graphics argument ==============
3298
+# col = c("1" = "red", "2" = "blue", "A" = "green", "B" = "orange")
3299
+# Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 
3300
+# rowAnnotation(foo = anno_block(
3301
+# 	graphics = function(index, levels) {
3302
+# 		grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))
3303
+# 		grid.text(paste(levels, collapse = ","), 0.5, 0.5, rot = 90,
3304
+# 			gp = gpar(col = col[levels[1]]))
3305
+# 	}
3306
+# ))
3307
+#
3308
+# labels = c("1" = "one", "2" = "two", "A" = "Group_A", "B" = "Group_B")
3309
+# Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 
3310
+# rowAnnotation(foo = anno_block(graphics = function(index, levels) {
3311
+# 	grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))
3312
+# 	grid.text(paste(labels[levels], collapse = ","), 0.5, 0.5, rot = 90,
3313
+# 		gp = gpar(col = col[levels[1]]))
3314
+# }))
3315
+#
3316
+# Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 
3317
+# rowAnnotation(foo = anno_block(
3318
+# 	graphics = function(index, levels) {
3319
+# 		grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))
3320
+# 		txt = paste(levels, collapse = ",")
3321
+# 		txt = paste0(txt, "\n", length(index), " rows")
3322
+# 		grid.text(txt, 0.5, 0.5, rot = 0,
3323
+# 			gp = gpar(col = col[levels[1]]))
3324
+# 	},
3325
+# 	width = unit(3, "cm")
3326
+# ))
3327
+#
3292 3328
 anno_block = function(gp = gpar(), labels = NULL, labels_gp = gpar(), 
3293 3329
 	labels_rot = ifelse(which == "row", 90, 0),
3294 3330
 	labels_offset = unit(0.5, "npc"), labels_just = "center",
3295
-	which = c("column", "row"), width = NULL, height = NULL, show_name = FALSE) {
3331
+	which = c("column", "row"), width = NULL, height = NULL, show_name = FALSE,
3332
+	graphics = NULL) {
3296 3333
 
3297 3334
 	if(is.null(.ENV$current_annotation_which)) {
3298 3335
 		which = match.arg(which)[1]
... ...
@@ -3324,19 +3361,41 @@ anno_block = function(gp = gpar(), labels = NULL, labels_gp = gpar(),
3324 3361
 	anno_size = anno_width_and_height(which, width, height, unit(5, "mm"))
3325 3362
 	
3326 3363
 	fun = function(index, k, n) {
3327
-		gp = subset_gp(recycle_gp(gp, n), k)
3328
-		
3329
-		grid.rect(gp = gp)
3330
-		if(length(labels)) {
3331
-			if(length(labels) != n) {
3332
-				stop_wrap("Length of `labels` should be as same as number of slices.")
3364
+		if(is.null(graphics)) {
3365
+			gp = subset_gp(recycle_gp(gp, n), k)
3366
+			grid.rect(gp = gp)
3367
+			if(length(labels)) {
3368
+				if(length(labels) != n) {
3369
+					stop_wrap("Length of `labels` should be as same as number of slices.")
3370
+				}
3371
+				label = labels[k]
3372
+				labels_gp = subset_gp(recycle_gp(labels_gp, n), k)
3373
+				x = y = unit(0.5, "npc")
3374
+				if(which == "column") y = labels_offset
3375
+				if(which == "row") x = labels_offset
3376
+				grid.text(label, x = x, y = y, gp = labels_gp, rot = labels_rot, just = labels_just)
3377
+			}
3378
+		} else {
3379
+
3380
+			for(ifa in 1:30) {
3381
+				if(exists("ht_main", envir = parent.frame(ifa))) {
3382
+					ht = get("ht_main", envir = parent.frame(ifa))
3383
+					break
3384
+				}
3385
+			}
3386
+			
3387
+			if(which == "row") {
3388
+				split = ht@matrix_param$row_split
3389
+				order_list = ht@row_order_list
3390
+			} else {
3391
+				split = ht@matrix_param$column_split
3392
+				order_list = ht@column_order_list
3393
+			}
3394
+			if(is.null(split)) {
3395
+				graphics(index, NULL)
3396
+			} else {
3397
+				graphics(index, unlist(split[order_list[[k]][1], ]))
3333 3398
 			}
3334
-			label = labels[k]
3335
-			labels_gp = subset_gp(recycle_gp(labels_gp, n), k)
3336
-			x = y = unit(0.5, "npc")
3337
-			if(which == "column") y = labels_offset
3338
-			if(which == "row") x = labels_offset
3339
-			grid.text(label, x = x, y = y, gp = labels_gp, rot = labels_rot, just = labels_just)
3340 3399
 		}
3341 3400
 	}
3342 3401
 
... ...
@@ -3345,7 +3404,7 @@ anno_block = function(gp = gpar(), labels = NULL, labels_gp = gpar(),
3345 3404
 		n = NA,
3346 3405
 		fun_name = "anno_block",
3347 3406
 		which = which,
3348
-		var_import = list(gp, labels, labels_gp, labels_rot, labels_offset, labels_just, which),
3407
+		var_import = list(gp, labels, labels_gp, labels_rot, labels_offset, labels_just, graphics, which),
3349 3408
 		subset_rule = list(),
3350 3409
 		subsetable = TRUE,
3351 3410
 		height = anno_size$height,
... ...
@@ -179,7 +179,7 @@ Heatmap = setClass("Heatmap",
179 179
 # -use_raster Whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. If number of rows or columns is more than 2000, it is by default turned on. Note if ``cell_fun``
180 180
 #       is set, ``use_raster`` is enforced to be ``FALSE``.
181 181
 # -raster_device Graphic device which is used to generate the raster image.
182
-# -raster_quality Ignored now.
182
+# -raster_quality A value larger than 1.
183 183
 # -raster_device_param A list of further parameters for the selected graphic device. For raster image support, please check https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image .
184 184
 # -raster_resize_mat Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image?
185 185
 #          The value can be logical. If it is ``TRUE``, `base::mean` is used to summarize the sub matrix which corresponds to a single pixel.
... ...
@@ -294,7 +294,7 @@ Heatmap = function(matrix, col, name,
294 294
 
295 295
     use_raster = NULL, 
296 296
     raster_device = c("CairoPNG", "CairoJPEG", "CairoTIFF", "png", "jpeg", "tiff", "agg_png"),
297
-    raster_quality = 2,
297
+    raster_quality = 1,
298 298
     raster_device_param = list(),
299 299
     raster_resize_mat = FALSE,
300 300
     raster_by_magick = requireNamespace("magick", quietly = TRUE),
... ...
@@ -555,7 +555,11 @@ SingleAnnotation = function(name, value, col, fun,
555 555
     	if(!is.null(f_which)) {
556 556
     		fun_name = fun@fun_name
557 557
     		if(f_which != which) {
558
-    			stop_wrap(qq("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}()."))
558
+                if(fun_name %in% c("anno_barplot", "anno_boxplot", "anno_density", "anno_histogram", "anno_points", "anno_text")) {
559
+                    stop_wrap(qq("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}()."))
560
+                } else {
561
+                    stop_wrap(qq("You are putting @{fun_name} as @{which} annotations, you need to set 'which' argument to '@{which}' as well."))
562
+                }
559 563
     		}
560 564
         }
561 565
         
... ...
@@ -91,7 +91,7 @@ Heatmap(matrix, col, name,
91 91
     
92 92
     use_raster = NULL,
93 93
     raster_device = c("CairoPNG", "CairoJPEG", "CairoTIFF", "png", "jpeg", "tiff", "agg_png"),
94
-    raster_quality = 2,
94
+    raster_quality = 1,
95 95
     raster_device_param = list(),
96 96
     raster_resize_mat = FALSE,
97 97
     raster_by_magick = requireNamespace("magick", quietly = TRUE),
... ...
@@ -178,11 +178,11 @@ Heatmap(matrix, col, name,
178 178
   \item{heatmap_legend_param}{A list contains parameters for the heatmap legends. See \code{\link{color_mapping_legend,ColorMapping-method}} for all available parameters.}
179 179
   \item{use_raster}{Whether render the heatmap body as a raster image. It helps to reduce file size when the matrix is huge. If number of rows or columns is more than 2000, it is by default turned on. Note if \code{cell_fun} is set, \code{use_raster} is enforced to be \code{FALSE}.}
180 180
   \item{raster_device}{Graphic device which is used to generate the raster image.}
181
-  \item{raster_quality}{Ignored now.}
181
+  \item{raster_quality}{A value larger than 1.}
182 182
   \item{raster_device_param}{A list of further parameters for the selected graphic device. For raster image support, please check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image} .}
183 183
   \item{raster_resize_mat}{Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image? The value can be logical. If it is \code{TRUE}, \code{\link[base]{mean}} is used to summarize the sub matrix which corresponds to a single pixel. The value can also be a summary function, e.g. \code{\link[base:Extremes]{max}}.}
184
-  \item{raster_by_magick}{Whether to use \code{\link[magick]{image_resize}} to scale the image.}
185
-  \item{raster_magick_filter}{Pass to \code{filter} argument of \code{\link[magick]{image_resize}}. A character scalar and all possible values are in \code{\link[magick]{filter_types}}. The default is \code{"Lanczos"}.}
184
+  \item{raster_by_magick}{Whether to use \code{\link[magick:transform]{image_resize}} to scale the image.}
185
+  \item{raster_magick_filter}{Pass to \code{filter} argument of \code{\link[magick:transform]{image_resize}}. A character scalar and all possible values are in \code{\link[magick:options]{filter_types}}. The default is \code{"Lanczos"}.}
186 186
   \item{post_fun}{A function which will be executed after the heatmap list is drawn.}
187 187
 
188 188
 }
... ...
@@ -11,8 +11,8 @@ Method dispatch page for \code{add_heatmap}.
11 11
 
12 12
 \itemize{
13 13
 \item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method
14
-\item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
15 14
 \item \code{\link{add_heatmap,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
15
+\item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
16 16
 }
17 17
 }
18 18
 \examples{
... ...
@@ -10,7 +10,8 @@ Block annotation
10 10
 anno_block(gp = gpar(), labels = NULL, labels_gp = gpar(),
11 11
     labels_rot = ifelse(which == "row", 90, 0),
12 12
     labels_offset = unit(0.5, "npc"), labels_just = "center",
13
-    which = c("column", "row"), width = NULL, height = NULL, show_name = FALSE)
13
+    which = c("column", "row"), width = NULL, height = NULL, show_name = FALSE,
14
+    graphics = NULL)
14 15
 }
15 16
 \arguments{
16 17
 
... ...
@@ -24,6 +25,7 @@ anno_block(gp = gpar(), labels = NULL, labels_gp = gpar(),
24 25
   \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}
25 26
   \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}
26 27
   \item{show_name}{Whether show annotatio name.}
28
+  \item{graphics}{A self-defined function that draws graphics in each slice. It must have two arguments: 1. row/column indices for the  current slice and a vector of levels from the split variable that correspond to current slice. When \code{graphics} is set, all other graphics parameters in \code{\link{anno_block}} are ignored.}
27 29
 
28 30
 }
29 31
 \details{
... ...
@@ -43,4 +45,35 @@ Heatmap(matrix(rnorm(100), 10),
43 45
     left_annotation = rowAnnotation(foo = anno_block(gp = gpar(fill = 2:4),
44 46
         labels = c("group1", "group2", "group3"), labels_gp = gpar(col = "white"))),
45 47
     row_km = 3)
48
+
49
+# =============  set the graphics argument ==============
50
+col = c("1" = "red", "2" = "blue", "A" = "green", "B" = "orange")
51
+Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 
52
+rowAnnotation(foo = anno_block(
53
+	graphics = function(index, levels) {
54
+		grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))
55
+		grid.text(paste(levels, collapse = ","), 0.5, 0.5, rot = 90,
56
+			gp = gpar(col = col[levels[1]]))
57
+	}
58
+))
59
+
60
+labels = c("1" = "one", "2" = "two", "A" = "Group_A", "B" = "Group_B")
61
+Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 
62
+rowAnnotation(foo = anno_block(graphics = function(index, levels) {
63
+	grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))
64
+	grid.text(paste(labels[levels], collapse = ","), 0.5, 0.5, rot = 90,
65
+		gp = gpar(col = col[levels[1]]))
66
+}))
67
+
68
+Heatmap(matrix(rnorm(100), 10), row_km = 2, row_split = sample(c("A", "B"), 10, replace = TRUE)) + 
69
+rowAnnotation(foo = anno_block(
70
+	graphics = function(index, levels) {
71
+		grid.rect(gp = gpar(fill = col[levels[2]], col = "black"))
72
+		txt = paste(levels, collapse = ",")
73
+		txt = paste0(txt, "\n", length(index), " rows")
74
+		grid.text(txt, 0.5, 0.5, rot = 0,
75
+			gp = gpar(col = col[levels[1]]))
76
+	},
77
+	width = unit(3, "cm")
78
+))
46 79
 }
... ...
@@ -10,8 +10,8 @@ Method dispatch page for \code{column_order}.
10 10
 \code{column_order} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method
14 13
 \item \code{\link{column_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
14
+\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 15
 }
16 16
 }
17 17
 \examples{
... ...
@@ -10,8 +10,8 @@ Method dispatch page for \code{component_height}.
10 10
 \code{component_height} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
14 13
 \item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method
14
+\item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
15 15
 }
16 16
 }
17 17
 \examples{
... ...
@@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}.
10 10
 \code{component_width} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method
14 13
 \item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
14
+\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 15
 }
16 16
 }
17 17
 \examples{
... ...
@@ -10,12 +10,12 @@ Method dispatch page for \code{draw}.
10 10
 \code{draw} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
14
-\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method
13
+\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 14
 \item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
16 15
 \item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
16
+\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method
17
+\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
17 18
 \item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
18
-\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
19 19
 }
20 20
 }
21 21
 \examples{
... ...
@@ -10,8 +10,8 @@ Method dispatch page for \code{row_dend}.
10 10
 \code{row_dend} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method
14 13
 \item \code{\link{row_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
14
+\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method
15 15
 }
16 16
 }
17 17
 \examples{
... ...
@@ -10,12 +10,12 @@ Method dispatch page for \code{show}.
10 10
 \code{show} can be dispatched on following classes:
11 11
 
12 12
 \itemize{
13
-\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
14
-\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
15 13
 \item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method
16 14
 \item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
17
-\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
15
+\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
18 16
 \item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
17
+\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
18
+\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
19 19
 }
20 20
 }
21 21
 \examples{