@@ -145,8 +145,6 @@ export("densityHeatmap")

 export("dist2")

 export("grid.boxplot")

 export("grid.dendrogram")

-export("height")

-export("height<-")

 export("ht_global_opt")

 export("ht_opt")

 export("is_abs_unit")

@@ -165,14 +163,10 @@ export("row_anno_histogram")

 export("row_anno_link")

 export("row_anno_points")

 export("row_anno_text")

-export("size")

-export("size<-")

 export("subset_gp")

 export("subset_matrix_by_row")

 export("subset_vector")

 export("unify_mat_list")

-export("width")

-export("width<-")

 exportClasses("AdditiveUnit")

 export("AdditiveUnit")

 exportClasses("AnnotationFunction")

@@ -215,7 +209,7 @@ exportMethods("make_layout")

 exportMethods("make_row_cluster")

 exportMethods("map_to_colors")

 exportMethods("prepare")

-exportMethods("resize")

+exportMethods("re_size")

 exportMethods("row_dend")

 exportMethods("row_order")

 exportMethods("set_component_height")

@@ -2,13 +2,13 @@ setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors

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

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

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

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

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

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

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

 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('resize', function(object, ...) standardGeneric('resize'))

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

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

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

@@ -1,69 +1,24 @@

-# == title

-# Generic Method for width()

-#

-# == param

-# -x An object.

-# -... Other arguments.

-#

 width = function (x, ...) {

 	UseMethod("width", x)

 }

-# == title

-# Generic Method for height()

-#

-# == param

-# -x An object.

-# -... Other arguments.

-#

 height = function (x, ...) {

 	UseMethod("height", x)

 }

-# == title

-# Generic Method for size()

-#

-# == param

-# -x An object.

-# -... Other arguments.

-#

 size = function (x, ...) {

 	UseMethod("size", x)

 }

-# == title

-# Generic Assignment Method for width()

-#

-# == param

-# -x An object.

-# -value The value

-# -... Other arguments.

-#

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

 	UseMethod("width<-", x)

 }

-# == title

-# Generic Assignment Method for height()

-#

-# == param

-# -x An object.

-# -value The value

-# -... Other arguments.

-#

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

 	UseMethod("height<-", x)

 }

-# == title

-# Generic Assignment Method for size()

-#

-# == param

-# -x An object.

-# -value The value

-# -... Other arguments.

-#

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

 	UseMethod("size<-", x)

 }

@@ -73,13 +28,16 @@ size = function (x, ...) {

 #

 # == param

 # -x A `AnnotationFunction-class` object.

-# -... Other arguments

+# -... Other arguments.

+#

+# == detail

+# Internally used.

 #

 # == example

 # anno = anno_points(1:10)

-# width(anno)

+# ComplexHeatmap:::width(anno)

 # anno = anno_points(1:10, which = "row")

-# width(anno)

+# ComplexHeatmap:::width(anno)

 width.AnnotationFunction = function(x, ...) {

 	x@width

 }

@@ -92,6 +50,9 @@ width.AnnotationFunction = function(x, ...) {

 # -... Other arguments.

 # -value A `grid::unit` object.

 #

+# == detail

+# Internally used.

+#

 "width<-.AnnotationFunction" = function(x, ..., value) {

 	x@width = value

 	x

@@ -102,13 +63,16 @@ width.AnnotationFunction = function(x, ...) {

 #

 # == param

 # -x The `AnnotationFunction-class` object.

-# -... Other arguments

+# -... Other arguments.

+#

+# == detail

+# Internally used.

 #

 # == example

 # anno = anno_points(1:10)

-# height(anno)

+# ComplexHeatmap:::height(anno)

 # anno = anno_points(1:10, which = "row")

-# height(anno)

+# ComplexHeatmap:::height(anno)

 height.AnnotationFunction = function(x, ...) {

 	x@height

 }

@@ -121,6 +85,9 @@ height.AnnotationFunction = function(x, ...) {

 # -value A `grid::unit` object.

 # -... Other arguments.

 #

+# == detail

+# Internally used.

+#

 "height<-.AnnotationFunction" = function(x, ..., value) {

 	x@height = value

 	x

@@ -136,11 +103,13 @@ height.AnnotationFunction = function(x, ...) {

 # == detail

 # It returns the width if it is a row annotation and the height if it is a column annotation.

 #

+# Internally used.

+#

 # == example

 # anno = anno_points(1:10)

-# size(anno)

+# ComplexHeatmap:::size(anno)

 # anno = anno_points(1:10, which = "row")

-# size(anno)

+# ComplexHeatmap:::size(anno)

 size.AnnotationFunction = function(x, ...) {

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

 		x@width

@@ -160,10 +129,12 @@ size.AnnotationFunction = function(x, ...) {

 # == detail

 # It assigns to the width if it is a row annotation and the height if it is a column annotation.

 #

+# Internally used.

+#

 # == example

 # anno = anno_points(1:10)

-# size(anno) = unit(4, "cm")

-# size(anno)

+# ComplexHeatmap:::size(anno) = unit(4, "cm")

+# ComplexHeatmap:::size(anno)

 "size<-.AnnotationFunction" = function(x, ..., value) {

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

 		x@width = value

@@ -182,6 +153,9 @@ size.AnnotationFunction = function(x, ...) {

 # -x The `SingleAnnotation-class` object.

 # -... Other arguments.

 #

+# == detail

+# Internally used.

+#

 width.SingleAnnotation = function(x, ...) {

     x@width

 }

@@ -194,6 +168,9 @@ width.SingleAnnotation = function(x, ...) {

 # -value A `grid::unit` object.

 # -... Other arguments.

 #

+# == detail

+# Internally used.

+#

 "width<-.SingleAnnotation" = function(x, ..., value) {

     x@width = value

     if(inherits(x@fun, "AnnotationFunction")) {

@@ -209,6 +186,9 @@ width.SingleAnnotation = function(x, ...) {

 # -x The `SingleAnnotation-class` object.

 # -... Other arguments.

 #

+# == detail

+# Internally used.

+#

 height.SingleAnnotation = function(x, ...) {

     x@height

 }

@@ -221,6 +201,9 @@ height.SingleAnnotation = function(x, ...) {

 # -value A `grid::unit` object.

 # -... Other arguments.

 #

+# == detail

+# Internally used.

+#

 "height<-.SingleAnnotation" = function(x, ..., value) {

     x@height = value

     if(inherits(x@fun, "AnnotationFunction")) {

@@ -239,6 +222,8 @@ height.SingleAnnotation = function(x, ...) {

 # == detail

 # It returns the width if it is a row annotation and the height if it is a column annotation.

 #

+# Internally used.

+#

 size.SingleAnnotation = function(x, ...) {

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

         x@width

@@ -258,6 +243,8 @@ size.SingleAnnotation = function(x, ...) {

 # == detail

 # It assigns to the width if it is a row annotation and the height if it is a column annotation.

 #

+# Internally used.

+#

 "size<-.SingleAnnotation" = function(x, ..., value) {

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

         width(x) = value

@@ -276,6 +263,9 @@ size.SingleAnnotation = function(x, ...) {

 # -x The `HeatmapAnnotation-class` object.

 # -... Other arguments.

 #

+# == detail

+# Internally used.

+#

 width.HeatmapAnnotation = function(x, ...) {

     x@width

 }

@@ -288,6 +278,9 @@ width.HeatmapAnnotation = function(x, ...) {

 # -value A `grid::unit` object.

 # -... Other arguments.

 #

+# == detail

+# Internally used.

+#

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

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

@@ -296,7 +289,7 @@ width.HeatmapAnnotation = function(x, ...) {

     		width(x@anno_list[[i]]) = value

     	}

     } else {

-    	x = resize(x, width = value)

+    	x = re_size(x, width = value)

     }

     x

 }

@@ -309,6 +302,9 @@ width.HeatmapAnnotation = function(x, ...) {

 # -x The `HeatmapAnnotation-class` object.

 # -... Other arguments.

 #

+# == detail

+# Internally used.

+#

 height.HeatmapAnnotation = function(x, ...) {

     x@height

 }

@@ -321,6 +317,9 @@ height.HeatmapAnnotation = function(x, ...) {

 # -value A `grid::unit` object.

 # -... Other arguments.

 #

+# == detail

+# Internally used.

+#

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

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

@@ -329,7 +328,7 @@ height.HeatmapAnnotation = function(x, ...) {

     		height(x@anno_list[[i]]) = height

     	}

     } else {

-    	x = resize(x, height = value)

+    	x = re_size(x, height = value)

     }

     x

 }

@@ -344,6 +343,8 @@ height.HeatmapAnnotation = function(x, ...) {

 # == detail

 # It returns the width if it is a row annotation and the height if it is a column annotation.

 #

+# Internally used.

+#

 size.HeatmapAnnotation = function(x, ...) {

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

         x@width

@@ -363,6 +364,8 @@ size.HeatmapAnnotation = function(x, ...) {

 # == detail

 # It assigns the width if it is a row annotation and the height if it is a column annotation.

 #

+# Internally used.

+#

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

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

         width(x) = value

@@ -383,6 +386,10 @@ size.HeatmapAnnotation = function(x, ...) {

 # == value

 # The returned unit x is always in ``mm``.

 #

+# == example

+# lgd = Legend(labels = 1:10, title = "foo", gp = gpar(fill = "red"))

+# width(lgd)

+#

 width.Legends = function(x, ...) {

 	s = attr(x@grob, "width")

 	s

@@ -399,8 +406,68 @@ width.Legends = function(x, ...) {

 # == value

 # The returned unit x is always in ``mm``.

 #

+# == example

+# lgd = Legend(labels = 1:10, title = "foo", gp = gpar(fill = "red"))

+# height(lgd)

+#

 height.Legends = function(x, ...) {

 	s = attr(x@grob, "height")

 	s

 }

+

+# == title

+# Width of the Heatmap List

+#

+# == param

+# -x The `HeatmapList-class` object returned by `draw,HeatmapList-method`.

+# -... Other arguments.

+#

+width.HeatmapList = function(x, ...) {

+    if(object@layout$initialized) {

+        x@ht_list_param$width

+    } else {

+        stop_wrap("width() can only be applied to the heatmap list object returned by draw().")

+    }

+}

+

+

+# == title

+# Height of the Heatmap List

+#

+# == param

+# -x The `HeatmapList-class` object returned by `draw,HeatmapList-method`.

+# -... Other arguments.

+#

+height.HeatmapList = function(x, ...) {

+    if(object@layout$initialized) {

+        x@ht_list_param$height

+    } else {

+        stop_wrap("height() can only be applied to the heatmap list object returned by draw().")

+    }

+}

+

+

+# == title

+# Width of the Heatmap

+#

+# == param

+# -x The `HeatmapList-class` object returned by `draw,Heatmap-method`.

+# -... Other arguments.

+#

+width.Heatmap = function(x, ...) {

+    stop_wrap("width() can only be applied to the heatmap object returned by draw().")

+}

+

+

+# == title

+# Height of the Heatmap

+#

+# == param

+# -x The `HeatmapList-class` object returned by `draw,Heatmap-method`.

+# -... Other arguments.

+#

+height.Heatmap = function(x, ...) {

+    stop_wrap("height() can only be applied to the heatmap object returned by draw().")

+}

+

@@ -5,7 +5,7 @@

 # == detail 

 # This class is a super class for `Heatmap-class`, `HeatmapList-class` and

 # `HeatmapAnnotation-class` classes. It is only designed for ``+`` generic

-# method so that above three classes can be appended to each other.

+# method and the `\%v\%v` method so that above three classes can be appended to each other.

 #

 AdditiveUnit = setClass("AdditiveUnit")

@@ -1,6 +1,6 @@

 # == title

-# The AnnotationFunction class

+# The AnnotationFunction Class

 #

 # == details

 # The heatmap annotation is basically graphics aligned to the heatmap columns

@@ -550,6 +550,16 @@ validate_axis_param = function(axis_param, which) {

 	for(nm in names(axis_param)) {

 		dft[[nm]] = axis_param[[nm]]

 	}

+	if(which == "row") {

+		if(dft$side %in% c("left", "right")) {

+			stop_wrap("axis side can only be set to 'top' or 'bottom' for row annotations.")

+		}

+	}

+	if(which == "column") {

+		if(dft$side %in% c("top", "bottom")) {

+			stop_wrap("axis side can only be set to 'left' or 'right' for row annotations.")

+		}

+	}

 	return(dft)

 }

@@ -569,7 +579,6 @@ construct_axis_grob = function(axis_param, which, data_scale) {

 		axis_param$labels = axis_param$at

 	}

 	axis_grob = do.call(annotation_axis_grob, axis_param)

-	

 	return(axis_grob)

 }

@@ -1,6 +1,6 @@

 # == title

-# Draw the Heatmap Body

+# Draw Heatmap Body

 #

 # == param

 # -object A `Heatmap-class` object.

@@ -321,7 +321,7 @@ setMethod(f = "draw_dimnames",

 # -object A `Heatmap-class` object.

 # -which Is title put on the row or on the column of the heatmap?

 # -k Slice index.

-# -... Pass to `grid::viewport` which includes the complete heatmap title

+# -... Pass to `grid::viewport` which includes the complete heatmap title.

 #

 # == details

 # A viewport is created which contains heatmap title.

@@ -6,11 +6,11 @@

 # -object A `Heatmap-class` object.

 # 

 # == detail

-# The layout of the single heatmap will be established by setting the size of each heatmap components.

+# The layout of the single heatmap will be established by setting the size of each heatmap component.

 # Also how to make graphics for heatmap components will be recorded by saving as functions.

 #

 # Whether to apply row clustering or column clustering affects the layout, so clustering should be applied 

-# first before making the layout.

+# first by `prepare,Heatmap-method` before making the layout.

 #

 # This function is only for internal use.

 #

@@ -476,7 +476,7 @@ setMethod(f = "show",

 # -direction Whether the heatmap is added horizontal or vertically?

 #

 # == details

-# There is a shortcut function ``+.AdditiveUnit``.

+# Normally we directly use ``+`` for horizontal concatenation and `\%v\%` for vertical concatenation.

 #

 # == value

 # A `HeatmapList-class` object.

@@ -4,8 +4,8 @@

 #

 # == param

 # -x A `Heatmap-class` object.

-# -i Row indices

-# -j Column indices

+# -i Row indices.

+# -j Column indices.

 #

 # == details

 # This functionality is quite experimental. It should be applied before the layout is initialized.

@@ -108,12 +108,14 @@ HeatmapAnnotation = function(...,

 	) {

 	dev.null()

-	on.exit(dev.off2())

 	.ENV$current_annotation_which = NULL

 	which = match.arg(which)[1]

 	.ENV$current_annotation_which = which

-	on.exit(.ENV$current_annotation_which <- NULL)

+	on.exit({

+		.ENV$current_annotation_which <- NULL

+		dev.off2()

+	})

 	fun_args = names(as.list(environment()))

@@ -409,10 +411,10 @@ HeatmapAnnotation = function(...,

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

     if(which == "column") {

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

+	    .Object = re_size(.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, 

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

 			anno_simple_size = anno_simple_size, simple_anno_size_adjust = simple_anno_size_adjust)

 	}

@@ -744,7 +746,7 @@ nobs.HeatmapAnnotation = function(object, ...) {

 # -direction Whether it is a horizontal add or a vertical add?

 #

 # == details

-# There is a helper function ``+.AdditiveUnit`` for horizontal add or `\%v\%` for vertical add.

+# Normally we directly use ``+`` for horizontal concatenation and `\%v\%` for vertical concatenation.

 #

 # == value

 # A `HeatmapList-class` object.

@@ -984,7 +986,7 @@ length.HeatmapAnnotation = function(x) {

 #      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",

+setMethod(f = "re_size",

 	signature = "HeatmapAnnotation",

 	definition = function(object, 

 	annotation_height = NULL, 

@@ -518,8 +518,8 @@ setMethod(f = "draw",

     upViewport()

     upViewport()

-    object@ht_list_param$width = ht_list_width

-    object@ht_list_param$height = ht_list_height

+    object@ht_list_param$width = w

+    object@ht_list_param$height = h

     for(i in seq_along(object@ht_list)) {

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

@@ -1,6 +1,6 @@

 # == title

-# Adjust heatmap list

+# Adjust Heatmap List

 #

 # == param

 # -object A `HeatmapList-class` object

@@ -38,12 +38,12 @@ setMethod(f = "adjust_heatmap_list",

         for(i in ht_index) {

             if(has_component(object@ht_list[[i]], "column_anno_top")) {

                 if(verbose) qqcat("adjust height of top annotation of heamtap @{object@ht_list[[i]]@name}\n")

-                object@ht_list[[i]]@top_annotation = resize(object@ht_list[[i]]@top_annotation, height = max_top_anno_height)

+                object@ht_list[[i]]@top_annotation = re_size(object@ht_list[[i]]@top_annotation, height = max_top_anno_height)

                 object@ht_list[[i]] = set_component_height(object@ht_list[[i]], "column_anno_top", object@ht_list[[i]]@top_annotation@height + ht_opt$COLUMN_ANNO_PADDING)

             }

             if(has_component(object@ht_list[[i]], "column_anno_bottom")) {   

                 if(verbose) qqcat("adjust height of bottom annotation of heamtap @{object@ht_list[[i]]@name}\n")

-                object@ht_list[[i]]@bottom_annotation = resize(object@ht_list[[i]]@bottom_annotation, height = max_bottom_anno_height)

+                object@ht_list[[i]]@bottom_annotation = re_size(object@ht_list[[i]]@bottom_annotation, height = max_bottom_anno_height)

                 object@ht_list[[i]] = set_component_height(object@ht_list[[i]], "column_anno_bottom", object@ht_list[[i]]@bottom_annotation@height + ht_opt$COLUMN_ANNO_PADDING)

             }

         }

@@ -240,12 +240,12 @@ setMethod(f = "adjust_heatmap_list",

         for(i in ht_index) {

             if(has_component(object@ht_list[[i]], "row_anno_left")) {

                 if(verbose) qqcat("adjust width of left annotation of heamtap @{object@ht_list[[i]]@name}\n")

-                object@ht_list[[i]]@left_annotation = resize(object@ht_list[[i]]@left_annotation, width = max_left_anno_width)

+                object@ht_list[[i]]@left_annotation = re_size(object@ht_list[[i]]@left_annotation, width = max_left_anno_width)

                 object@ht_list[[i]] = set_component_width(object@ht_list[[i]], "row_anno_left", object@ht_list[[i]]@left_annotation@width + ht_opt$ROW_ANNO_PADDING)

             }

             if(has_component(object@ht_list[[i]], "row_anno_right")) {   

                 if(verbose) qqcat("adjust width of right annotation of heamtap @{object@ht_list[[i]]@name}\n")

-                object@ht_list[[i]]@right_annotation = resize(object@ht_list[[i]]@right_annotation, width = max_right_anno_width)

+                object@ht_list[[i]]@right_annotation = re_size(object@ht_list[[i]]@right_annotation, width = max_right_anno_width)

                 object@ht_list[[i]] = set_component_width(object@ht_list[[i]], "row_anno_right", object@ht_list[[i]]@right_annotation@width + ht_opt$ROW_ANNO_PADDING)

             }

         }

@@ -537,16 +537,6 @@ setMethod(f = "draw_heatmap_list",

             } else if(inherits(ht, "HeatmapAnnotation")) {

                 # calcualte the position of the heatmap body

                 pushViewport(viewport(y = max_bottom_component_height, height = unit(1, "npc") - max_top_component_height - max_bottom_component_height, just = c("bottom")))

-                # if(length(ht) == 1 & n_slice > 1) {

-                #     if(inherits(ht@anno_list[[1]], "AnnotationFunction")) {

-                #         if(identical(ht@anno_list[[1]]@fun@fun_name, "anno_mark")) {

-                #             # adjust pos_map var

-                #             fun = ht@anno_list[[1]]@fun

-                #             draw(fun, index = ht_main@row_order)

-                #             next

-                #         }

-                #     }

-                # }

                 for(j in seq_len(n_slice)) {

                     draw(ht, index = ht_main@row_order_list[[j]], y = slice_y[j], height = slice_height[j], just = slice_just[2], k = j, n = n_slice)

                 }

@@ -24,7 +24,7 @@

 # row_order(ht_list)

 setMethod(f = "row_order",

 	signature = "HeatmapList",

-	definition = function(object) {

+	definition = function(object, name = NULL) {

 	object = make_layout(object)

@@ -1,13 +1,19 @@

 # == title

-# Draw legends for all heatmaps

+# Draw legends for All Heatmaps

 #

 # == param

-# -object a `HeatmapList-class` object

-# -legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.

-# -... graphic parameters passed to `color_mapping_legend,ColorMapping-method`.

+# -object A `HeatmapList-class` object.

+# -legend_list A list of self-defined legends, should be wrapped into `grid::grob` objects. It is

+#          normally constructed by `Legend`.

+# -... Other arguments.

 #

 # == details

+# Actually we call the "heatmap legends" as the main legends.

+# For horizontal heatmap list, the legends are those from heamtap/row annotation/left/right annotation.

+# For vertical heatmap list, the legends are those from heamtap/column annotation/top/bottom annotation.

+# if ``merge_legends`` is true in `draw,HeatmapList-method`, then it contains all legends shown on the plot.

+#

 # A viewport is created which contains heatmap legends.

 #

 # This function is only for internal use.

@@ -128,14 +134,19 @@ setMethod(f = "draw_heatmap_legend",

 })

 # == title

-# Draw legends for all column annotations

+# Draw legends for All Annotations

 #

 # == param

-# -object a `HeatmapList-class` object

-# -legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.

-# -... graphic parameters passed to `color_mapping_legend,ColorMapping-method`.

+# -object A `HeatmapList-class` object.

+# -legend_list A list of self-defined legends, should be wrapped into `grid::grob` objects.

+#      It is normally constructed by `Legend`.

+# -... Other arguments.

 #

 # == details

+# We call the "annotation legends" as the secondary legends.

+# For horizontal heamtap list, the legends are those from all top/bottom annotations, and for vertical heatmap list, 

+# the legends are those from all left/right annotations.

+#

 # A viewport is created which contains annotation legends.

 #

 # This function is only for internal use.

@@ -212,14 +223,17 @@ setMethod(f = "draw_annotation_legend",

 })

 # == title

-# Size of the heatmap legend viewport

+# Size of the Heatmap Legends

 #

 # == param

-# -object a `HeatmapList-class` object

-# -legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.

-# -... graphic parameters passed to `color_mapping_legend,ColorMapping-method`.

+# -object A `HeatmapList-class` object.

+# -legend_list A list of self-defined legend, should be wrapped into `grid::grob` objects.

+#     It is normally constructed by `Legend`.

+# -... Other arguments.

 #

 # == detail

+# Internally, all heatmap legends are packed by `packLegend` as a single `grid::grob` object.

+#

 # This function is only for internal use.

 #

 # == value

@@ -301,16 +315,16 @@ setMethod(f = "heatmap_legend_size",

 })

 # == title

-# Size of the annotation legend viewport

+# Size of the Annotation Legends

 #

 # == param

 # -object a `HeatmapList-class` object.

-# -legend_list a list of self-defined legend, should be wrapped into `grid::grob` objects.

-# -... graphic parameters passed to `color_mapping_legend,ColorMapping-method`.

+# -legend_list A list of self-defined legend, should be wrapped into `grid::grob` objects.

+#     It is normally constructed by `Legend`.

+# -... Other arguments.

 #

 # == detail

-# Legends for all heatmaps or legends for all annotations will be put in one viewport. This function

-# calculates the size of such viewport. Note graphic parameters for legends will affect the size.

+# Internally, all annotation legends are packed by `packLegend` as a single `grid::grob` object.

 #

 # This function is only for internal use.

 #

@@ -1,17 +1,105 @@

 # == title

-# Grob for annotation axis

+# Grob for Annotation Axis

 #

 # == param

-# -at Break values.

+# -at Break values. If it is not specified, it is inferred from data scale in current viewport.

 # -labels Corresponding labels.

 # -labels_rot Rotations of labels.

 # -gp Graphic parameters.

-# -side side of the axis to the annotation viewport.

+# -side side of the axis of the annotation viewport.

 # -facing Facing of the axis.

 #

 # == value

 # A `grid::grob` object.

 #

+# == examples

+# gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+#     side = "left", facing = "outside")

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# grid.draw(gb)

+# grid.rect(x = unit(0, "npc"), width = grobWidth(gb), just = "right")

+# popViewport()

+#

+# gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+#     side = "left", facing = "inside")

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# grid.draw(gb)

+# grid.rect(x = unit(0, "npc"), width = grobWidth(gb), just = "left")

+# popViewport()

+#

+# gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+#     side = "right", facing = "outside")

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# grid.draw(gb)

+# grid.rect(x = unit(1, "npc"), width = grobWidth(gb), just = "left")

+# popViewport()

+#

+# gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+#     side = "right", facing = "inside")

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# grid.draw(gb)

+# grid.rect(x = unit(1, "npc"), width = grobWidth(gb), just = "right")

+# popViewport()

+#

+# gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+#     side = "top", facing = "outside")

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# grid.draw(gb)

+# grid.rect(y = unit(1, "npc"), height = grobHeight(gb), just = "bottom")

+# popViewport()

+#

+# gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 90, 

+#     side = "top", facing = "outside")

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# grid.draw(gb)

+# grid.rect(y = unit(1, "npc"), height = grobHeight(gb), just = "bottom")

+# popViewport()

+#

+# gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 45, 

+#     side = "top", facing = "outside")

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# grid.draw(gb)

+# grid.rect(y = unit(1, "npc"), height = grobHeight(gb), just = "bottom")

+# popViewport()

+#

+# gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+#     side = "top", facing = "inside")

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# grid.draw(gb)

+# grid.rect(y = unit(1, "npc"), height = grobHeight(gb), just = "top")

+# popViewport()

+#

+# gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+#     side = "bottom", facing = "outside")

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# grid.draw(gb)

+# grid.rect(y = unit(0, "npc"), height = grobHeight(gb), just = "top")

+# popViewport()

+#

+# gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+#     side = "bottom", facing = "inside")

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# grid.draw(gb)

+# grid.rect(y = unit(0, "npc"), height = grobHeight(gb), just = "bottom")

+# popViewport()

+#

+# grid.newpage()

+# pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+# gb = annotation_axis_grob(labels_rot = 0, side = "left", facing = "outside")

+# grid.draw(gb)

+# grid.rect(x = unit(0, "npc"), width = grobWidth(gb), just = "right")

+# popViewport()

+#

 annotation_axis_grob = function(at = NULL, labels = at, labels_rot = 0, gp = gpar(), 

 	side = "left", facing = "outside") {

@@ -136,20 +224,26 @@ annotation_axis_grob = function(at = NULL, labels = at, labels_rot = 0, gp = gpa

 # == title

-# Grob width for annotation_axis

+# Width for annotation_axis Grob

 #

 # == param

-# -x legend body

+# -x The ``annotation_axis`` grob returned by `annotation_axis_grob`.

+#

+# == details

+# The physical width of the grob can be get by ``convertWidth(grobWidth(axis_grob), "mm")``.

 #

 widthDetails.annotation_axis = function(x) {

 	attr(x, "width")

 }

 # == title

-# Grob width for annotation_axis

+# Height for annotation_axis Grob

 #

 # == param

-# -x legend body

+# -x The ``annotation_axis`` grob returned by `annotation_axis_grob`.

+#

+# == details

+# The physical height of the grob can be get by ``convertWidth(grobHeight(axis_grob), "mm")``.

 #

 heightDetails.annotation_axis = function(x) {