add show_name in anno_empty()

DESCRIPTION

@@ -6,7 +6,7 @@ Date: 2021-11-08
 Author: Zuguang Gu
 Maintainer: Zuguang Gu <[email protected]>
 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, 

NAMESPACE

@@ -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")

NEWS

@@ -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()`.
 
 =========================
 

R/00_S4_generic_methods.R

@@ -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'))

R/AnnotationFunction-class.R

@@ -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
@@ -133,15 +133,15 @@ 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)
 # Heatmap(m, top_annotation = HeatmapAnnotation(foo = anno1))
 # 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])) {