add numbers to the barplot annotations

NAMESPACE

@@ -221,6 +221,7 @@ export("subset_matrix_by_row")
 export("subset_vector")
 export("test_alter_fun")
 export("unify_mat_list")
+export("upset_left_annotation")
 export("upset_right_annotation")
 export("upset_top_annotation")
 exportClasses("AdditiveUnit")

NEWS

@@ -7,6 +7,7 @@ CHANGES in VERSION 2.9.3
 * legends: fixed a bug of the grid heights were not correctedly calculated.
 * discrete annotations: neighbour grids are merged into one single grid if they have the 
   same values.
+* `anno_barplot()`: allows to add numbers on top of bars.
 
 =========================
 

R/00_S4_generic_methods.R

@@ -1,32 +1,32 @@
-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
 setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
 setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
 setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
 setGeneric('draw', function(object, ...) standardGeneric('draw'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
 setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
 setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
 setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
 setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

R/AnnotationFunction-function.R

@@ -1189,6 +1189,10 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),
 # -extend The extension to both side of ``ylim``. The value is a percent value corresponding to ``ylim[2] - ylim[1]``.
 # -axis Whether to add axis?
 # -axis_param parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters.
+# -add_numbers Whether to add numbers to the bars. It only works when ``x`` is a simple vector.
+# -numbers_gp Graphics parameters for the numbers.
+# -numbers_rot Rotation of numbers.
+# -numbers_offset Offset to the default positions (1mm away the top of the bars).
 # -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.
 # -... Other arguments.
@@ -1209,7 +1213,9 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),
 # draw(anno, test = "proportion matrix")
 anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6,
 	gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE, 
-	axis_param = default_axis_param(which),
+	axis_param = default_axis_param(which), 
+	add_numbers = FALSE, numbers_gp = gpar(fontsize = 8), 
+	numbers_rot = ifelse(which == "column", 45, 0), numbers_offset = unit(2, "mm"),
 	width = NULL, height = NULL, ...) {
 
 	other_args = list(...)
@@ -1282,6 +1288,19 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
 	}
 
 	value = x
+
+	if(ncol(value) == 1) {
+		if(add_numbers) {
+			if(which == "column") {
+				extend = convertHeight(sin(numbers_rot/180*pi)*max_text_width(value, gp = numbers_gp) + numbers_offset + unit(4, "mm"), "mm", valueOnly = TRUE)/convertHeight(anno_size$height, "mm", valueOnly = TRUE)*(data_scale[2] - data_scale[1])
+				data_scale[2] = data_scale[2] + extend
+			} else if(which == "row") {
+				extend = convertWidth(cos(numbers_rot/180*pi)*max_text_width(value, gp = numbers_gp) + numbers_offset + unit(4, "mm"), "mm", valueOnly = TRUE)/convertWidth(anno_size$width, "mm", valueOnly = TRUE)*(data_scale[2] - data_scale[1])
+				data_scale[2] = data_scale[2] + extend
+			}
+		}
+	}
+
 	axis_param = validate_axis_param(axis_param, which)
 	axis_grob = if(axis) construct_axis_grob(axis_param, which, data_scale) else NULL
 
@@ -1299,6 +1318,13 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
 			width = value[index] - baseline
 			x_coor = width/2+baseline
 			grid.rect(x = x_coor, y = n - seq_along(index) + 1, width = abs(width), height = 1*bar_width, default.units = "native", gp = subset_gp(gp, index))
+			if(add_numbers) {
+				if(axis_param$direction == "normal") {
+					grid.text(value[index], x = unit(baseline + width, "native") + numbers_offset, y = n - seq_along(index) + 1, default.units = "native", gp = subset_gp(numbers_gp, index), just = c("left"), rot = numbers_rot)
+				} else {
+					grid.text(value_origin[index], x = unit(baseline + width, "native") - numbers_offset, y = n - seq_along(index) + 1, default.units = "native", gp = subset_gp(numbers_gp, index), just = c("right"), rot = numbers_rot)
+				}
+			}
 		} else {
 			for(i in seq_len(ncol(value))) {
 				if(axis_param$direction == "normal") {
@@ -1336,6 +1362,9 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
 			height = value[index] - baseline
 			y_coor = height/2+baseline
 			grid.rect(y = y_coor, x = seq_along(index), height = abs(height), width = 1*bar_width, default.units = "native", gp = subset_gp(gp, index))
+			if(add_numbers) {
+				grid.text(value[index], x = seq_along(index), y = unit(baseline + height, "native") + numbers_offset, default.units = "native", gp = subset_gp(numbers_gp, index), just = c("left"), rot = numbers_rot)
+			}
 		} else {
 			for(i in seq_len(ncol(value))) {
 				if(axis_param$direction == "normal") {
@@ -1375,7 +1404,7 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
 		height = anno_size$height,
 		n = n,
 		data_scale = data_scale,
-		var_import = list(value, gp, border, bar_width, baseline, axis, axis_param, axis_grob, data_scale)
+		var_import = list(value, gp, border, bar_width, baseline, axis, axis_param, axis_grob, data_scale, add_numbers, numbers_gp, numbers_offset, numbers_rot)
 	)
 
 	anno@subset_rule$value = subset_matrix_by_row

R/HeatmapList-draw_component.R

@@ -445,6 +445,7 @@ setMethod(f = "adjust_heatmap_list",
     padding = unit(c(0, 0, 0, 0), "mm")
     if(is.null(adjust_annotation_extension)) {
         if(direction == "horizontal") {
+            # right side
             if(inherits(object@ht_list[[n]], "Heatmap")) {
                 # if the last heatmap has nothing on the right while something on the right of heatmap list
                 if(!(has_component(object@ht_list[[n]], "row_anno_right") ||
@@ -459,6 +460,7 @@ setMethod(f = "adjust_heatmap_list",
                     }
                 }
             }
+            # left side
             if(inherits(object@ht_list[[1]], "Heatmap")) {
                 if(!(has_component(object@ht_list[[1]], "row_anno_left") ||
                      has_component(object@ht_list[[1]], "row_names_left") ||
@@ -472,6 +474,21 @@ setMethod(f = "adjust_heatmap_list",
                     }
                 }
             }
+            # bottom side
+            if(has_heatmap_list_component(object, "column_title_bottom") || 
+               has_heatmap_list_component(object, "heatmap_legend_bottom") || 
+               has_heatmap_list_component(object, "annotation_legend_bottom")) {
+                object@layout$row_anno_max_bottom_extended = unit(0, "mm")
+                adjust_annotation_extension = TRUE
+            }
+
+            if(has_heatmap_list_component(object, "column_title_top") || 
+               has_heatmap_list_component(object, "heatmap_legend_top") || 
+               has_heatmap_list_component(object, "annotation_legend_top")) {
+                object@layout$row_anno_max_top_extended = unit(0, "mm")
+                adjust_annotation_extension = TRUE
+            }
+
         } else {
             if(inherits(object@ht_list[[n]], "Heatmap")) {
                 # if the last heatmap has nothing on the right while something on the right of heatmap list
@@ -500,6 +517,20 @@ setMethod(f = "adjust_heatmap_list",
                     }
                 }
             }
+
+            if(has_heatmap_list_component(object, "column_title_bottom") || 
+               has_heatmap_list_component(object, "heatmap_legend_bottom") || 
+               has_heatmap_list_component(object, "annotation_legend_bottom")) {
+                object@layout$row_anno_max_bottom_extended = unit(0, "mm")
+                adjust_annotation_extension = TRUE
+            }
+
+            if(has_heatmap_list_component(object, "column_title_top") || 
+               has_heatmap_list_component(object, "heatmap_legend_top") || 
+               has_heatmap_list_component(object, "annotation_legend_top")) {
+                object@layout$row_anno_max_top_extended = unit(0, "mm")
+                adjust_annotation_extension = TRUE
+            }
         }
     }
 

R/HeatmapList-layout.R

@@ -345,7 +345,6 @@ setMethod(f = "make_layout",
             object@ht_list[[i_main]]@row_order = row_order
             if(verbose) qqcat("set row_order to main heatmap\n")
         }
-
 
         if(!is.null(height) && !is.null(heatmap_height)) {
             stop_wrap("You can only specify one of `height` and `heatmap_height` in draw().")

R/HeatmapList-legends.R

@@ -140,7 +140,7 @@ setMethod(f = "draw_heatmap_legend",
                 y = max(y1, y2)
                 pushViewport(viewport(name = "heatmap_legend", x = unit(0.5, "npc"), y = y, width = size[1], height = size[2], just = c("center", "top")))           
             } else {
-                x1 = unit(0.5, "npc") - size[1]*0.5  # top of heatmap legend
+                x1 = unit(0.5, "npc") - size[1]*0.5  # left of heatmap legend
                 x2 = unit(0.5, "npc") - annotation_legend_size[1]*0.5
                 x = min(x1, x2)
                 pushViewport(viewport(name = "heatmap_legend", x = x, y = unit(0.5, "npc"), width = size[1], height = size[2], just = c("left", "center")))           

R/Upset.R

@@ -1250,6 +1250,7 @@ print.comb_mat = function(x, ...) {
 # -set_order The order of sets.
 # -comb_order The order of combination sets.
 # -top_annotation A `HeatmapAnnotation` object on top of the combination matrix.
+# -left_annotation A `HeatmapAnnotation` object on top of the combination matrix.
 # -right_annotation A `HeatmapAnnotation` object on the right of the combination matrix.
 # -row_names_side The side of row names.
 # -... Other arguments passed to `Heatmap`.
@@ -1350,6 +1351,7 @@ UpSet = function(m,
 		},
 	top_annotation = upset_top_annotation(m),
 	right_annotation = upset_right_annotation(m),
+	left_annotation = NULL,
 	row_names_side = "left",
 	...) {
 
@@ -1364,6 +1366,15 @@ UpSet = function(m,
 	pt_size = pt_size
 	lwd = lwd
 
+	if(!is.null(left_annotation)) {
+		if(missing(right_annotation)) {
+			right_annotation = NULL
+		}
+		if(missing(row_names_side)) {
+			row_names_side = "right"
+		}
+	}
+
 	if(set_on_rows) {
 		n_comb = ncol(m)
 		if(length(comb_col == 1)) comb_col = rep(comb_col, n_comb)
@@ -1409,7 +1420,7 @@ UpSet = function(m,
 		ht = Heatmap(m2, cluster_rows = FALSE, cluster_columns = FALSE, rect_gp = gpar(type = "none"),
 			layer_fun = layer_fun, show_heatmap_legend = FALSE,
 			top_annotation = ra,
-			right_annotation = right_annotation,
+			right_annotation = right_annotation, left_annotation = left_annotation,
 			row_names_side = row_names_side, col = c("0" = bg_pt_col, "1" = comb_col[1]),
 			row_order = set_order, column_order = comb_order, ...)
 	} else {
@@ -1451,10 +1462,21 @@ UpSet = function(m,
 				}
 			}
 		}
+		la = left_annotation
+		if(length(la) == 1) {
+			ta_call = substitute(top_annotation)
+			ta_call = as.list(ta_call)
+			if(as.character(ta_call[[1]]) == "upset_left_annotation") {
+				if(!"gp" %in% names(as.list(ta_call))) {
+					la@anno_list[[1]]@fun@var_env$gp$fill = comb_col
+					la@anno_list[[1]]@fun@var_env$gp$col = comb_col
+				}
+			}
+		}
 		ht = Heatmap(m2, cluster_rows = FALSE, cluster_columns = FALSE, rect_gp = gpar(type = "none"),
 			layer_fun = layer_fun, show_heatmap_legend = FALSE,
 			top_annotation = top_annotation,
-			right_annotation = ra, col = c("0" = bg_pt_col, "1" = comb_col[1]),
+			right_annotation = ra, left_annotation = la, col = c("0" = bg_pt_col, "1" = comb_col[1]),
 			row_order = comb_order, column_order = set_order, ...)
 	}
 	ht@heatmap_param$type = "UpSet"
@@ -1495,6 +1517,8 @@ order.comb_mat = function(m, decreasing = TRUE, on = "comb_set") {
 	}
 }
 
+
+
 # == title
 # Default UpSet Top Annotation
 #
@@ -1573,7 +1597,7 @@ upset_top_annotation = function(m,
 # -annotation_name_offset Offset to the annotation name, a `grid::unit` object.
 # -annotation_name_side Side of the annotation name.
 # -annotation_name_rot Rotation of the annotation name, it can only take values in ``c(00, 90, 180, 270)``.
-# -... Passed to `anno_barplot`.
+# -... Passed to `anno_barplot`, e.g. to set ``add_numbers``.
 #
 # == details
 # The default right annotation is actually barplot implemented by `anno_barplot`. For
@@ -1627,6 +1651,70 @@ upset_right_annotation = function(m,
 	return(ha)
 }
 
+# == title
+# UpSet Left Annotation
+#
+# == param
+# -m A combination matrix which is as same as the one for `UpSet`.
+# -gp Graphic parameters for bars.
+# -axis_param Parameters for axis.
+# -width Width of the left annotation.
+# -show_annotation_name Whether show annotation names?
+# -annotation_name_gp Graphic parameters for anntation names.
+# -annotation_name_offset Offset to the annotation name, a `grid::unit` object.
+# -annotation_name_side Side of the annotation name.
+# -annotation_name_rot Rotation of the annotation name, it can only take values in ``c(00, 90, 180, 270)``.
+# -... Passed to `anno_barplot`, e.g. to set ``add_numbers``.
+#
+upset_left_annotation = function(m,
+	gp = gpar(fill = "black"),  
+	axis_param = list(direction = "reverse"),
+	width = unit(ifelse(set_on_rows, 2, 3), "cm"),
+	show_annotation_name = TRUE,
+	annotation_name_gp = gpar(),
+	annotation_name_offset = NULL,
+	annotation_name_side = "bottom",
+	annotation_name_rot = NULL,
+	...) {
+
+	set_on_rows = attr(m, "param")$set_on_rows
+
+	if(!"direction" %in% names(axis_param)) {
+		axis_param$direction = "reverse"
+	}
+
+	if(set_on_rows) {
+		ha = rowAnnotation("set_size" = anno_barplot(set_size(m), border = FALSE, 
+					gp = gp, width = width, axis_param = axis_param, ...),
+				show_annotation_name = show_annotation_name,
+				annotation_name_gp = annotation_name_gp,
+				annotation_name_offset = annotation_name_offset,
+				annotation_name_side = annotation_name_side,
+				annotation_name_rot = annotation_name_rot,
+				annotation_label = "Set size")
+	} else {
+		ha = rowAnnotation("intersection_size" = anno_barplot(comb_size(m), 
+					border = FALSE, gp = gp, width = width, axis_param = axis_param, ...),
+				show_annotation_name = show_annotation_name,
+				annotation_name_gp = annotation_name_gp,
+				annotation_name_offset = annotation_name_offset,
+				annotation_name_side = annotation_name_side,
+				annotation_name_rot = annotation_name_rot,
+				annotation_label = "Intersection\nsize")
+	}
+
+	mode = attr(m, "param")$mode
+	if(!set_on_rows) {
+		if(mode %in% c("distinct", "intersect")) {
+			# names(ha) = "intersection_size"
+		} else {
+			names(ha) = "union_size"
+			ha@anno_list[[1]]@label = "Union size"
+		}
+	}
+	return(ha)
+}
+
 # == title
 # Normalize a list of combination matrice
 #

man/UpSet.Rd

@@ -19,6 +19,7 @@ UpSet(m,
     },
     top_annotation = upset_top_annotation(m),
     right_annotation = upset_right_annotation(m),
+    left_annotation = NULL,
     row_names_side = "left",
     ...)
 }
@@ -33,6 +34,7 @@ UpSet(m,
   \item{set_order}{The order of sets.}
   \item{comb_order}{The order of combination sets.}
   \item{top_annotation}{A \code{\link{HeatmapAnnotation}} object on top of the combination matrix.}
+  \item{left_annotation}{A \code{\link{HeatmapAnnotation}} object on top of the combination matrix.}
   \item{right_annotation}{A \code{\link{HeatmapAnnotation}} object on the right of the combination matrix.}
   \item{row_names_side}{The side of row names.}
   \item{...}{Other arguments passed to \code{\link{Heatmap}}.}