various improvements

NAMESPACE

@@ -238,6 +238,7 @@ export("SingleAnnotation")
 exportMethods("add_heatmap")
 exportMethods("adjust_heatmap_list")
 exportMethods("annotation_legend_size")
+exportMethods("attach_annotation")
 exportMethods("color_mapping_legend")
 exportMethods("column_dend")
 exportMethods("column_order")

NEWS

@@ -8,7 +8,10 @@ CHANGES in VERSION 2.5.6
   can set `at` that are not all in the matrix but are in the `col`.
 * padding of the whole plot and spaces of column titles are adjusted to fit ggplot2 
 * add `row_gap` and `column_gap` in `Legend()`.
-* `oncoPrint()`: now draw legends as `alter_fun`.
+* `oncoPrint()`: now draw legends the same as `alter_fun`.
+* add a new function `attach_annotation()`.
+* legends for row annotations can be grouped with column annotation legends.
+* annotation name allows rotations.
 
 ======================
 

R/00_S4_generic_methods.R

@@ -1,31 +1,32 @@
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
 setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
 setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
 setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
 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_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
 setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
 setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
 setGeneric('draw', function(object, ...) standardGeneric('draw'))
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))

R/HeatmapAnnotation-class.R

@@ -63,7 +63,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",
 # -annotation_name_gp Graphic parameters for anntation names. Graphic paramters can be vectors.
 # -annotation_name_offset Offset to the annotation names, a `grid::unit` object. The value can be a vector.
 # -annotation_name_side Side of the annotation names.
-# -annotation_name_rot Rotation of the annotation names, it can only take values in ``c(00, 90, 180, 270)``. The value can be a vector.
+# -annotation_name_rot Rotation of the annotation names. The value can be a vector.
 # -annotation_name_align Whether to align the annotation names.
 # -annotation_height Height of each annotation if annotations are column annotations.
 # -annotation_width Width of each annotation if annotations are row annotations.
@@ -900,7 +900,7 @@ setMethod(f = "add_heatmap",
 # ha3 = HeatmapAnnotation(sth = cbind(1:10, 10:1))
 # ha = c(ha1, ha2, ha3, gap = unit(c(1, 4), "mm"))
 # ha
-c.HeatmapAnnotation = function(..., gap = unit(0, "mm")) {
+c.HeatmapAnnotation = function(..., gap = unit(1, "points")) {
 	anno_list = list(...)
 	if(length(anno_list) == 1) {
 		return(anno_list[[1]])
@@ -1410,3 +1410,90 @@ has_zoomed_anno_empty = function(ha) {
 	}
 	return(FALSE)
 }
+
+# == title
+# Attach heatmap annotations to the heatmap
+#
+# == param
+# -object A `Heatmap-class` object.
+# -ha A `HeatmapAnnotation-class` object.
+# -side Which side of the heatmap. Value should be in "top", "bottom", "left", "right".
+# -gap Space between the two heatmap annotations.
+#
+# == example
+# m = matrix(rnorm(100), 10)
+# ht = Heatmap(m)
+# ha = HeatmapAnnotation(foo = 1:10)
+# ht = attach_annotation(ht, ha)
+# ht
+# ha2 = HeatmapAnnotation(bar = letters[1:10])
+# ht = attach_annotation(ht, ha2)
+# ht
+setMethod(f = "attach_annotation",
+    signature = "Heatmap",
+    definition = function(object, ha, side = c("top", "bottom", "left", "right"), 
+    gap = unit(1, "points")) {
+
+    if(missing(side)) {
+    	side = ifelse(ha@which == "column", "top", "left")
+    } else {
+    	side = match.arg(side)[1]
+    }
+    ha_which = ha@which
+    if(ha_which == "column" && side %in% c("left", "right")) {
+    	stop_wrap("Column annotations can only be attached to the top/bottom side of the heatmap.")
+    } else if(ha_which == "row" && side %in% c("top", "bottom")) {
+    	stop_wrap("Row annotations can only be attached to the left/right side of the heatmap.")
+    }
+
+    if(side == "top") {
+    	if(is.null(object@top_annotation)) {
+    		object@top_annotation = ha
+    		h = height(ha) + ht_opt$COLUMN_ANNO_PADDING
+    		h = convertHeight(h, "mm")
+    		object@top_annotation_param = list(height = h)
+    	} else {
+    		object@top_annotation = c(object@top_annotation, ha, gap = gap)
+    		h = height(object@top_annotation) + height(ha) + gap
+    		h = convertHeight(h, "mm")
+    		object@top_annotation_param = list(height = h)
+    	}
+    } else if(side == "bottom") {
+    	if(is.null(object@bottom_annotation)) {
+    		object@bottom_annotation = ha
+    		h = height(ha) + ht_opt$COLUMN_ANNO_PADDING
+    		h = convertHeight(h, "mm")
+    		object@bottom_annotation_param = list(height = h)
+    	} else {
+    		object@bottom_annotation = c(object@bottom_annotation, ha, gap = gap)
+    		h = height(object@bottom_annotation) + height(ha) + gap
+    		h = convertHeight(h, "mm")
+    		object@bottom_annotation_param = list(height = h)
+    	}
+    } else if(side == "left") {
+    	if(is.null(object@left_annotation)) {
+    		object@left_annotation = ha
+    		w = width(ha) + ht_opt$ROW_ANNO_PADDING
+    		w = convertWidth(w, "mm")
+    		object@left_annotation_param = list(width = w)
+    	} else {
+    		object@left_annotation = c(object@left_annotation, ha, gap = gap)
+    		w = width(object@left_annotation) + width(ha) + gap
+    		w = convertWidth(w, "mm")
+    		object@left_annotation_param = list(width = w)
+    	}
+    } else if(side == "right") {
+    	if(is.null(object@right_annotation)) {
+    		object@right_annotation = ha
+    		w = width(ha) + ht_opt$ROW_ANNO_PADDING
+    		w = convertWidth(w, "mm")
+    		object@right_annotation_param = list(width = w)
+    	} else {
+    		object@right_annotation = c(object@right_annotation, ha, gap = gap)
+    		w = width(object@right_annotation) + width(ha) + gap
+    		w = convertWidth(w, "mm")
+    		object@right_annotation_param = list(height = w)
+    	}
+    }
+    object
+})

R/HeatmapList-class.R

@@ -218,6 +218,8 @@ setMethod(f = "add_heatmap",
 # -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".
+# -legend_grouping How the legends are grouped. Values should be "adjusted" or "original". If it is set as
+#             "original", all annotation legends are grouped together.
 # -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
@@ -320,6 +322,7 @@ setMethod(f = "draw",
     annotation_legend_list = list(),
     align_heatmap_legend = NULL,
     align_annotation_legend = NULL,
+    legend_grouping = c("adjusted", "original"),
 
     gap = unit(2, "mm"), 
     ht_gap = gap, 
@@ -513,6 +516,7 @@ setMethod(f = "draw",
         annotation_legend_list = annotation_legend_list,
         align_heatmap_legend = align_heatmap_legend,
         align_annotation_legend = align_annotation_legend,
+        legend_grouping = legend_grouping,
 
         ht_gap = ht_gap,