anno_block(): allows to set width and height

NEWS

@@ -3,6 +3,7 @@ CHANGES in VERSION 2.5.4
 * fixed a bug where slice clusters were wrongly reordered.
 * `Heatmap()`: add `border_gp` argument.
 * Legends are nicely placed.
+* `anno_block()`: allows to set height and width.
 
 ========================
 

R/00_S4_generic_methods.R

@@ -1,31 +1,31 @@
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
 setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
 setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
 setGeneric('draw', function(object, ...) standardGeneric('draw'))
-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
 setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
 setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
 setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
 setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
 setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

R/AnnotationFunction-function.R

@@ -3247,11 +3247,22 @@ anno_block = function(gp = gpar(), labels = NULL, labels_gp = gpar(), labels_rot
 	}
 	if(length(labels)) {
 		if(which == "column") {
-			height = grobHeight(textGrob(labels, rot = labels_rot, gp = labels_gp))
-			height = height + unit(5, "mm")
+			if(missing(height)) {
+				height = grobHeight(textGrob(labels, rot = labels_rot, gp = labels_gp))
+				height = height + unit(5, "mm")
+			} else {
+				if(!inherits(height, "unit")) {
+					stop_wrap("Since you specified `height`, the value should be `unit` object.")
+				}
+			}
 		} else {
-			width = grobWidth(textGrob(labels, rot = labels_rot, gp = labels_gp))
-			width = width + unit(5, "mm")
+			if(missing(width)) {
+				width = grobWidth(textGrob(labels, rot = labels_rot, gp = labels_gp))
+				width = width + unit(5, "mm")
+			} else {
+				if(!inherits(width, "unit")) {
+				stop_wrap("Since you specified `width`, the value should be `unit` object.")
+			}
 		}
 	}
 

R/HeatmapList-class.R

@@ -184,6 +184,9 @@ setMethod(f = "add_heatmap",
 # -annotation_legend_side side of the annotation legends
 # -show_annotation_legend whether show annotation legends
 # -annotation_legend_list user-defined legends which are put after the annotation legends
+# -align_heatmap_legend How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". If the value is ``NULL``,
+#           it automatically picks the proper value from the three options.
+# -align_annotation_legend  How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center".
 # -gap gap between heatmaps/annotations
 # -ht_gap same as ``gap``.
 # -main_heatmap index of main heatmap. The value can be a numeric index or the heatmap name

R/HeatmapList-get_order.R

@@ -27,6 +27,10 @@ setMethod(f = "row_order",
 	signature = "HeatmapList",
 	definition = function(object, name = NULL) {
 
+	if(!object@layout$initialized) {
+		warning_wrap("The heatmap list has not been initialized. You might have different results if you repeatedly execute this function. It is more suggested to do as `ht_list = draw(ht_list); row_order(ht_list)`.")
+	}
+
 	object = make_layout(object)
 
 	if(!is.null(name)) {
@@ -82,6 +86,11 @@ setMethod(f = "row_order",
 	signature = "Heatmap",
 	definition = function(object) {
 
+	if(!object@layout$initialized) {
+		warning_wrap("The heatmap has not been initialized. You might have different results if you repeatedly execute this function. It is more suggested to do as `ht = draw(ht); row_order(ht)`.")
+	}
+
+
 	object = prepare(object)
 
 	lt = object@row_order_list
@@ -123,6 +132,10 @@ setMethod(f = "column_order",
 	signature = "HeatmapList",
 	definition = function(object, name = NULL) {
 
+	if(!object@layout$initialized) {
+		warning_wrap("The heatmap list has not been initialized. You might have different results if you repeatedly execute this function. It is more suggested to do as `ht_list = draw(ht_list); column_order(ht_list)`.")
+	}
+
 	object = make_layout(object)
 
 	if(!is.null(name)) {
@@ -177,6 +190,10 @@ setMethod(f = "column_order",
 	signature = "Heatmap",
 	definition = function(object) {
 
+	if(!object@layout$initialized) {
+		warning_wrap("The heatmap has not been initialized. You might have different results if you repeatedly execute this function. It is more suggested to do as `ht = draw(ht); column_order(ht)`.")
+	}
+
 	object = prepare(object)
 
 	lt = object@column_order_list
@@ -216,6 +233,10 @@ setMethod(f = "row_dend",
 	signature = "HeatmapList",
 	definition = function(object, name = NULL) {
 
+	if(!object@layout$initialized) {
+		warning_wrap("The heatmap list has not been initialized. You might have different results if you repeatedly execute this function. It is more suggested to do as `ht_list = draw(ht_list); row_dend(ht_list)`.")
+	}
+
 	object = make_layout(object)
 
 	if(!is.null(name)) {
@@ -272,6 +293,10 @@ setMethod(f = "row_dend",
 	signature = "Heatmap",
 	definition = function(object) {
 
+	if(!object@layout$initialized) {
+		warning_wrap("The heatmap has not been initialized. You might have different results if you repeatedly execute this function. It is more suggested to do as `ht = draw(ht); row_dend(ht)`.")
+	}
+
 	object = prepare(object)
 
 	lt = object@row_dend_list
@@ -313,6 +338,10 @@ setMethod(f = "column_dend",
 	signature = "HeatmapList",
 	definition = function(object, name = NULL) {
 
+	if(!object@layout$initialized) {
+		warning_wrap("The heatmap list has not been initialized. You might have different results if you repeatedly execute this function. It is more suggested to do as `ht_list = draw(ht_list); column_dend(ht_list)`.")
+	}
+
 	object = make_layout(object)
 
 	if(!is.null(name)) {
@@ -369,6 +398,10 @@ setMethod(f = "column_dend",
 	signature = "Heatmap",
 	definition = function(object) {
 
+	if(!object@layout$initialized) {
+		warning_wrap("The heatmap has not been initialized. You might have different results if you repeatedly execute this function. It is more suggested to do as `ht = draw(ht); column_dend(ht)`.")
+	}
+
 	object = prepare(object)
 
 	lt = object@column_dend_list

R/HeatmapList-layout.R

@@ -17,6 +17,9 @@
 # -annotation_legend_side Side of annotation legends.
 # -show_annotation_legend Whether show annotation legends.
 # -annotation_legend_list A list of self-defined legends, should be wrapped into a list of `grid::grob` objects. Normally they are constructed by `Legend`.
+# -align_heatmap_legend How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center". If the value is ``NULL``,
+#           it automatically picks the proper value from the three options.
+# -align_annotation_legend  How to align the legends to heatmap. Possible values are "heatmap_center", "heatmap_top" and "global_center".
 # -ht_gap Gap between heatmaps, should be a `grid::unit` object. It can be a vector of length 1 or the number of heamtaps/annotations.
 # -main_heatmap Name or index for the main heatmap.
 # -padding Padding of the whole plot. The four values correspond to the bottom, left, top and right paddings.