1. ComplexHeatmap
  2. Commit ad35494a5e7647cd922852e0a25e331ae33551c3
Browse code

R CMD check passed

Zuguang Gu authored on 20/09/2018 12:48:08
Showing225 changed files
.Rbuildignore
History View file @ad35494
... ... 
@@ -1,7 +1,9 @@
1 1 
 ^\..*
2 2 
 README.*
3 
-test/
3 
+tests/
4 4 
 check.bat
5 5 
 ^.*\.Rproj$
6 6 
 ^\.Rproj\.user$
7 7 
 .travis.yml
8 
+vignettes_old
9 
+
DESCRIPTION
History View file @ad35494
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: ComplexHeatmap
2 2 
 Type: Package
3 3 
 Title: Making Complex Heatmaps
4 
-Version: 1.19.1
4 
+Version: 1.99.0
5 5 
 Date: 2018-6-9
6 6 
 Author: Zuguang Gu
7 7 
 Maintainer: Zuguang Gu <z.gu@dkfz.de>
... ... 
@@ -10,7 +10,7 @@ Imports: circlize (>= 0.4.1), GetoptLong, colorspace,
10 10 
     RColorBrewer, GlobalOptions (>= 0.1.0)
11 11 
 Suggests: testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust,
12 12 
     dendsort, HilbertCurve, Cairo, png, jpeg, tiff, fastcluster,
13 
-    dendextend (>= 1.0.1)
13 
+    dendextend (>= 1.0.1), grImport, grImport2, rsvg
14 14 
 VignetteBuilder: knitr
15 15 
 Description: Complex heatmaps are efficient to visualize associations
16 16 
     between different sources of data sets and reveal potential structures.
NAMESPACE
History View file @ad35494
... ... 
@@ -1,100 +1,197 @@
1 
-export('+.AdditiveUnit')
2 
-export('grid.dendrogram')
3 
-export('grid.dendrogram2')
4 
-export(AdditiveUnit)
5 
-export(ColorMapping)
6 
-export(Heatmap)
7 
-export(HeatmapAnnotation)
8 
-export(HeatmapList)
9 
-export(Legend)
10 
-export(SingleAnnotation)
11 
-export(adjust_dend_by_leaf_width)
12 
-export(anno_barplot)
13 
-export(anno_boxplot)
14 
-export(anno_density)
15 
-export(anno_histogram)
16 
-export(anno_link)
17 
-export(anno_oncoprint_barplot)
18 
-export(anno_points)
19 
-export(anno_text)
20 
-export(columnAnnotation)
21 
-export(column_anno_barplot)
22 
-export(column_anno_boxplot)
23 
-export(column_anno_density)
24 
-export(column_anno_histogram)
25 
-export(column_anno_link)
26 
-export(column_anno_points)
27 
-export(column_anno_text)
28 
-export(decorate_annotation)
29 
-export(decorate_column_dend)
30 
-export(decorate_column_names)
31 
-export(decorate_column_title)
32 
-export(decorate_dend)
33 
-export(decorate_dimnames)
34 
-export(decorate_heatmap_body)
35 
-export(decorate_row_dend)
36 
-export(decorate_row_names)
37 
-export(decorate_row_title)
38 
-export(decorate_title)
39 
-export(densityHeatmap)
40 
-export(dist2)
41 
-export(enhanced_basicplot)
42 
-export(ht_global_opt)
43 
-export(is_abs_unit)
44 
-export(max_text_height)
45 
-export(max_text_width)
46 
-export(oncoPrint)
47 
-export(packLegend)
48 
-export(plotDataFrame)
49 
-export(rowAnnotation)
50 
-export(row_anno_barplot)
51 
-export(row_anno_boxplot)
52 
-export(row_anno_density)
53 
-export(row_anno_histogram)
54 
-export(row_anno_link)
55 
-export(row_anno_points)
56 
-export(row_anno_text)
57 
-export(selectArea)
58 
-export(unify_mat_list)
59 
-exportClasses(AdditiveUnit)
60 
-export(AdditiveUnit)
61 
-exportClasses(ColorMapping)
62 
-export(ColorMapping)
63 
-exportClasses(Heatmap)
64 
-export(Heatmap)
65 
-exportClasses(HeatmapAnnotation)
66 
-export(HeatmapAnnotation)
67 
-exportClasses(HeatmapList)
68 
-export(HeatmapList)
69 
-exportClasses(SingleAnnotation)
70 
-export(SingleAnnotation)
71 
-exportMethods(add_heatmap)
72 
-exportMethods(annotation_legend_size)
73 
-exportMethods(color_mapping_legend)
74 
-exportMethods(column_dend)
75 
-exportMethods(column_order)
76 
-exportMethods(component_height)
77 
-exportMethods(component_width)
78 
-exportMethods(draw)
79 
-exportMethods(draw_annotation)
80 
-exportMethods(draw_annotation_legend)
81 
-exportMethods(draw_dend)
82 
-exportMethods(draw_dimnames)
83 
-exportMethods(draw_heatmap_body)
84 
-exportMethods(draw_heatmap_legend)
85 
-exportMethods(draw_heatmap_list)
86 
-exportMethods(draw_title)
87 
-exportMethods(get_color_mapping_list)
88 
-exportMethods(get_color_mapping_param_list)
89 
-exportMethods(heatmap_legend_size)
90 
-exportMethods(make_column_cluster)
91 
-exportMethods(make_layout)
92 
-exportMethods(make_row_cluster)
93 
-exportMethods(map_to_colors)
94 
-exportMethods(prepare)
95 
-exportMethods(row_dend)
96 
-exportMethods(row_order)
97 
-exportMethods(set_component_height)
1 
+S3method("+", "AdditiveUnit")
2 
+export("+.AdditiveUnit")
3 
+S3method("[", "AnnotationFunction")
4 
+export("[.AnnotationFunction")
5 
+S3method("[", "Heatmap")
6 
+export("[.Heatmap")
7 
+S3method("[", "HeatmapAnnotation")
8 
+export("[.HeatmapAnnotation")
9 
+S3method("[", "SingleAnnotation")
10 
+export("[.SingleAnnotation")
11 
+S3method("c", "HeatmapAnnotation")
12 
+export("c.HeatmapAnnotation")
13 
+S3method("dim", "Heatmap")
14 
+export("dim.Heatmap")
15 
+S3method("grid.draw", "Legends")
16 
+export("grid.draw.Legends")
17 
+S3method("height", "AnnotationFunction")
18 
+export("height.AnnotationFunction")
19 
+S3method("height", "HeatmapAnnotation")
20 
+export("height.HeatmapAnnotation")
21 
+S3method("height", "Legends")
22 
+export("height.Legends")
23 
+S3method("height", "SingleAnnotation")
24 
+export("height.SingleAnnotation")
25 
+S3method("height<-", "AnnotationFunction")
26 
+export("height<-.AnnotationFunction")
27 
+S3method("height<-", "HeatmapAnnotation")
28 
+export("height<-.HeatmapAnnotation")
29 
+S3method("height<-", "SingleAnnotation")
30 
+export("height<-.SingleAnnotation")
31 
+S3method("length", "HeatmapAnnotation")
32 
+export("length.HeatmapAnnotation")
33 
+S3method("merge", "dendrogram")
34 
+export("merge.dendrogram")
35 
+S3method("names", "HeatmapAnnotation")
36 
+export("names.HeatmapAnnotation")
37 
+S3method("names<-", "HeatmapAnnotation")
38 
+export("names<-.HeatmapAnnotation")
39 
+S3method("ncol", "Heatmap")
40 
+export("ncol.Heatmap")
41 
+S3method("nobs", "AnnotationFunction")
42 
+export("nobs.AnnotationFunction")
43 
+S3method("nobs", "HeatmapAnnotation")
44 
+export("nobs.HeatmapAnnotation")
45 
+S3method("nobs", "SingleAnnotation")
46 
+export("nobs.SingleAnnotation")
47 
+S3method("nrow", "Heatmap")
48 
+export("nrow.Heatmap")
49 
+S3method("size", "AnnotationFunction")
50 
+export("size.AnnotationFunction")
51 
+S3method("size", "HeatmapAnnotation")
52 
+export("size.HeatmapAnnotation")
53 
+S3method("size", "SingleAnnotation")
54 
+export("size.SingleAnnotation")
55 
+S3method("size<-", "AnnotationFunction")
56 
+export("size<-.AnnotationFunction")
57 
+S3method("size<-", "HeatmapAnnotation")
58 
+export("size<-.HeatmapAnnotation")
59 
+S3method("size<-", "SingleAnnotation")
60 
+export("size<-.SingleAnnotation")
61 
+S3method("summary", "Heatmap")
62 
+export("summary.Heatmap")
63 
+S3method("width", "AnnotationFunction")
64 
+export("width.AnnotationFunction")
65 
+S3method("width", "HeatmapAnnotation")
66 
+export("width.HeatmapAnnotation")
67 
+S3method("width", "Legends")
68 
+export("width.Legends")
69 
+S3method("width", "SingleAnnotation")
70 
+export("width.SingleAnnotation")
71 
+S3method("width<-", "AnnotationFunction")
72 
+export("width<-.AnnotationFunction")
73 
+S3method("width<-", "HeatmapAnnotation")
74 
+export("width<-.HeatmapAnnotation")
75 
+S3method("width<-", "SingleAnnotation")
76 
+export("width<-.SingleAnnotation")
77 
+export("%v%")
78 
+export("AdditiveUnit")
79 
+export("AnnotationFunction")
80 
+export("ColorMapping")
81 
+export("Heatmap")
82 
+export("HeatmapAnnotation")
83 
+export("HeatmapList")
84 
+export("Legend")
85 
+export("Legends")
86 
+export("SingleAnnotation")
87 
+export("adjust_dend_by_x")
88 
+export("anno_barplot")
89 
+export("anno_boxplot")
90 
+export("anno_density")
91 
+export("anno_empty")
92 
+export("anno_histogram")
93 
+export("anno_horizon")
94 
+export("anno_image")
95 
+export("anno_joyplot")
96 
+export("anno_lines")
97 
+export("anno_link")
98 
+export("anno_mark")
99 
+export("anno_oncoprint_barplot")
100 
+export("anno_points")
101 
+export("anno_simple")
102 
+export("anno_text")
103 
+export("cluster_within_group")
104 
+export("columnAnnotation")
105 
+export("decorate_annotation")
106 
+export("decorate_column_dend")
107 
+export("decorate_column_names")
108 
+export("decorate_column_title")
109 
+export("decorate_dend")
110 
+export("decorate_dimnames")
111 
+export("decorate_heatmap_body")
112 
+export("decorate_row_dend")
113 
+export("decorate_row_names")
114 
+export("decorate_row_title")
115 
+export("decorate_title")
116 
+export("default_axis_param")
117 
+export("dend_heights")
118 
+export("dend_xy")
119 
+export("dendrogramGrob")
120 
+export("densityHeatmap")
121 
+export("dist2")
122 
+export("grid.dendrogram")
123 
+export("height")
124 
+export("height<-")
125 
+export("ht_global_opt")
126 
+export("ht_opt")
127 
+export("is_abs_unit")
128 
+export("max_text_height")
129 
+export("max_text_width")
130 
+export("oncoPrint")
131 
+export("packLegend")
132 
+export("rowAnnotation")
133 
+export("row_anno_barplot")
134 
+export("row_anno_boxplot")
135 
+export("row_anno_density")
136 
+export("row_anno_histogram")
137 
+export("row_anno_link")
138 
+export("row_anno_points")
139 
+export("row_anno_text")
140 
+export("size")
141 
+export("size<-")
142 
+export("subset_gp")
143 
+export("subset_matrix_by_row")
144 
+export("subset_vector")
145 
+export("unify_mat_list")
146 
+export("width")
147 
+export("width<-")
148 
+exportClasses("AdditiveUnit")
149 
+export("AdditiveUnit")
150 
+exportClasses("AnnotationFunction")
151 
+export("AnnotationFunction")
152 
+exportClasses("ColorMapping")
153 
+export("ColorMapping")
154 
+exportClasses("Heatmap")
155 
+export("Heatmap")
156 
+exportClasses("HeatmapAnnotation")
157 
+export("HeatmapAnnotation")
158 
+exportClasses("HeatmapList")
159 
+export("HeatmapList")
160 
+exportClasses("Legends")
161 
+export("Legends")
162 
+exportClasses("SingleAnnotation")
163 
+export("SingleAnnotation")
164 
+exportMethods("add_heatmap")
165 
+exportMethods("adjust_heatmap_list")
166 
+exportMethods("annotation_legend_size")
167 
+exportMethods("color_mapping_legend")
168 
+exportMethods("column_dend")
169 
+exportMethods("column_order")
170 
+exportMethods("component_height")
171 
+exportMethods("component_width")
172 
+exportMethods("copy_all")
173 
+exportMethods("draw")
174 
+exportMethods("draw_annotation")
175 
+exportMethods("draw_annotation_legend")
176 
+exportMethods("draw_dend")
177 
+exportMethods("draw_dimnames")
178 
+exportMethods("draw_heatmap_body")
179 
+exportMethods("draw_heatmap_legend")
180 
+exportMethods("draw_heatmap_list")
181 
+exportMethods("draw_title")
182 
+exportMethods("get_color_mapping_list")
183 
+exportMethods("get_legend_param_list")
184 
+exportMethods("heatmap_legend_size")
185 
+exportMethods("make_column_cluster")
186 
+exportMethods("make_layout")
187 
+exportMethods("make_row_cluster")
188 
+exportMethods("map_to_colors")
189 
+exportMethods("prepare")
190 
+exportMethods("resize")
191 
+exportMethods("row_dend")
192 
+exportMethods("row_order")
193 
+exportMethods("set_component_height")
194 
+exportMethods("set_component_width")
98 195
99 196 
 import(grDevices)
100 197 
 import(graphics)
... ... 
@@ -106,6 +203,7 @@ importFrom("GetoptLong", qq.options)
106 203 
 importFrom("GetoptLong", qqcat)
107 204 
 importFrom("GlobalOptions", setGlobalOptions)
108 205 
 importFrom("RColorBrewer", brewer.pal)
206 
+importFrom("circlize", add_transparency)
109 207 
 importFrom("circlize", colorRamp2)
110 208 
 importFrom("circlize", rand_color)
111 209 
 importFrom("circlize", smartAlign)
... ... 
@@ -113,4 +211,5 @@ importFrom("colorspace", diverge_hcl)
113 211 
 importFrom("colorspace", rainbow_hcl)
114 212 
 importFrom("utils", "getFromNamespace")
115 213 
 importFrom("utils", "packageDescription")
214 
+importFrom("utils", "str")
116 215
R/00_S4_generic_methods.R
History View file @ad35494
... ... 
@@ -1,66 +1,31 @@
1 
-
2 
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
3 
-
4 1 
 setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
5 
-
6 2 
 setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
7 
-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
8 
-
9 3 
 setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
10 
-
11 
-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
12 
-
13 
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
14 
-
15 4 
 setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
16 
-
17 5 
 setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
18 
-
19 
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
20 
-
21 6 
 setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
22 
-
7 
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
8 
+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
9 
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
10 
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
11 
+setGeneric('resize', function(object, ...) standardGeneric('resize'))
12 
+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
13 
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
14 
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
15 
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
16 
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
17 
+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
18 
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
19 
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
23 20 
 setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
24 
-
25 
-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
26 
-
27 21 
 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
28 
-
29 
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
30 
-
22 
+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
31 23 
 setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
32 
-
33 
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
34 
-
35 24 
 setGeneric('draw', function(object, ...) standardGeneric('draw'))
36 
-
37 
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
38 
-
39 25 
 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
40 
-
41 
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
42 
-
26 
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
43 27 
 setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
44 
-
45 
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
46 
-
47 28 
 setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
48 
-
49 
-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
50 
-
51 29 
 setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
52 
-
53 
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
54 
-
55 
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
56 
-
57 
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
58 
-setGeneric('resize', function(object, ...) standardGeneric('resize'))
59 30 
 setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
60 
-setGeneric('width', function(object, ...) standardGeneric('width'))
61 
-setGeneric('height', function(object, ...) standardGeneric('height'))
62 
-setGeneric('size', function(object, ...) standardGeneric('size'))
63 
-setGeneric('width<-', function(object, value, ...) standardGeneric('width<-'))
64 
-setGeneric('height<-', function(object, value, ...) standardGeneric('height<-'))
65 
-setGeneric('size<-', function(object, value, ...) standardGeneric('size<-'))
66 
-
31 
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
R/00_size.R
History View file @ad35494
67 32 
new file mode 100644
... ... 
@@ -0,0 +1,404 @@
1 
+
2 
+# == title
3 
+# Generic method for width
4 
+#
5 
+# == param
6 
+# -x x
7 
+# -... other arguments
8 
+#
9 
+width = function (x, ...) {
10 
+	UseMethod("width", x)
11 
+}
12 
+
13 
+# == title
14 
+# Generic method for height
15 
+#
16 
+# == param
17 
+# -x x
18 
+# -... other arguments
19 
+#
20 
+height = function (x, ...) {
21 
+	UseMethod("height", x)
22 
+}
23 
+
24 
+# == title
25 
+# Generic method for size
26 
+#
27 
+# == param
28 
+# -x x
29 
+# -... other arguments
30 
+#
31 
+size = function (x, ...) {
32 
+	UseMethod("size", x)
33 
+}
34 
+
35 
+# == title
36 
+# Generic assignment method for width
37 
+#
38 
+# == param
39 
+# -x x
40 
+# -value value
41 
+# -... other arguments
42 
+#
43 
+"width<-" = function (x, ..., value) {
44 
+	UseMethod("width<-", x)
45 
+}
46 
+
47 
+# == title
48 
+# Generic assignment method for height
49 
+#
50 
+# == param
51 
+# -x x
52 
+# -value value
53 
+# -... other arguments
54 
+#
55 
+"height<-" = function (x, ..., value) {
56 
+	UseMethod("height<-", x)
57 
+}
58 
+
59 
+# == title
60 
+# Generic assignment method for size
61 
+#
62 
+# == param
63 
+# -x x
64 
+# -value value
65 
+# -... other arguments
66 
+#
67 
+"size<-" = function (x, ..., value) {
68 
+	UseMethod("size<-", x)
69 
+}
70 
+
71 
+# == title
72 
+# Width of the AnnotationFunction x
73 
+#
74 
+# == param
75 
+# -x The `AnnotationFunction-class` x.
76 
+# -... other arguments
77 
+#
78 
+# == example
79 
+# anno = anno_points(1:10)
80 
+# width(anno)
81 
+# anno = anno_points(1:10, which = "row")
82 
+# width(anno)
83 
+width.AnnotationFunction = function(x, ...) {
84 
+	x@width
85 
+}
86 
+
87 
+# == title
88 
+# Assign the Width to the AnnotationFunction x
89 
+#
90 
+# == param
91 
+# -x The `AnnotationFunction-class` x.
92 
+# -value A `grid::unit` x.
93 
+# -... other arguments
94 
+#
95 
+"width<-.AnnotationFunction" = function(x, ..., value) {
96 
+	x@width = value
97 
+	x
98 
+}
99 
+
100 
+# == title
101 
+# Height of the AnnotationFunction x
102 
+#
103 
+# == param
104 
+# -x The `AnnotationFunction-class` x.
105 
+# -... other arguments
106 
+#
107 
+# == example
108 
+# anno = anno_points(1:10)
109 
+# height(anno)
110 
+# anno = anno_points(1:10, which = "row")
111 
+# height(anno)
112 
+height.AnnotationFunction = function(x, ...) {
113 
+	x@height
114 
+}
115 
+
116 
+# == title
117 
+# Assign the Height to the AnnotationFunction x
118 
+#
119 
+# == param
120 
+# -x The `AnnotationFunction-class` x.
121 
+# -value A `grid::unit` x.
122 
+# -... other arguments
123 
+#
124 
+"height<-.AnnotationFunction" = function(x, ..., value) {
125 
+	x@height = value
126 
+	x
127 
+}
128 
+
129 
+# == title
130 
+# Size of the AnnotationFunction x
131 
+#
132 
+# == param
133 
+# -x The `AnnotationFunction-class` x.
134 
+# -... other arguments
135 
+#
136 
+# == detail
137 
+# It returns the width if it is a row annotation and the height if it is a column annotation.
138 
+#
139 
+# == example
140 
+# anno = anno_points(1:10)
141 
+# size(anno)
142 
+# anno = anno_points(1:10, which = "row")
143 
+# size(anno)
144 
+size.AnnotationFunction = function(x, ...) {
145 
+	if(x@which == "row") {
146 
+		x@width
147 
+	} else {
148 
+		x@height
149 
+	}
150 
+}
151 
+
152 
+# == title
153 
+# Assign the Size to the AnnotationFunction x
154 
+#
155 
+# == param
156 
+# -x The `AnnotationFunction-class` x.
157 
+# -value A `grid::unit` x.
158 
+# -... other arguments
159 
+#
160 
+# == detail
161 
+# It assigns the width if it is a row annotation and the height if it is a column annotation.
162 
+#
163 
+# == example
164 
+# anno = anno_points(1:10)
165 
+# size(anno) = unit(4, "cm")
166 
+# size(anno)
167 
+"size<-.AnnotationFunction" = function(x, ..., value) {
168 
+	if(x@which == "row") {
169 
+		x@width = value
170 
+	} else {
171 
+		x@height = value
172 
+	}
173 
+	x
174 
+}
175 
+
176 
+
177 
+
178 
+# == title
179 
+# Width of the SingleAnnotation x
180 
+#
181 
+# == param
182 
+# -x The `SingleAnnotation-class` x.
183 
+# -... other arguments
184 
+#
185 
+width.SingleAnnotation = function(x, ...) {
186 
+    x@width
187 
+}
188 
+
189 
+# == title
190 
+# Assign the Width to the SingleAnnotation x
191 
+#
192 
+# == param
193 
+# -x The `SingleAnnotation-class` x.
194 
+# -value A `grid::unit` x.
195 
+# -... other arguments
196 
+#
197 
+"width<-.SingleAnnotation" = function(x, ..., value) {
198 
+    x@width = value
199 
+    if(inherits(x@fun, "AnnotationFunction")) {
200 
+        width(x@fun) = value
201 
+    }
202 
+    x
203 
+}
204 
+
205 
+# == title
206 
+# Height of the SingleAnnotation x
207 
+#
208 
+# == param
209 
+# -x The `SingleAnnotation-class` x.
210 
+# -... other arguments
211 
+#
212 
+height.SingleAnnotation = function(x, ...) {
213 
+    x@height
214 
+}
215 
+
216 
+# == title
217 
+# Assign the Height to the SingleAnnotation x
218 
+#
219 
+# == param
220 
+# -x The `SingleAnnotation-class` x.
221 
+# -value A `grid::unit` x.
222 
+# -... other arguments
223 
+#
224 
+"height<-.SingleAnnotation" = function(x, ..., value) {
225 
+    x@height = value
226 
+    if(inherits(x@fun, "AnnotationFunction")) {
227 
+        height(x@fun) = value
228 
+    }
229 
+    x
230 
+}
231 
+
232 
+# == title
233 
+# Size of the SingleAnnotation x
234 
+#
235 
+# == param
236 
+# -x The `SingleAnnotation-class` x.
237 
+# -... other arguments
238 
+#
239 
+# == detail
240 
+# It returns the width if it is a row annotation and the height if it is a column annotation.
241 
+#
242 
+size.SingleAnnotation = function(x, ...) {
243 
+    if(x@which == "row") {
244 
+        x@width
245 
+    } else {
246 
+        x@height
247 
+    }
248 
+}
249 
+
250 
+# == title
251 
+# Assign the Size of the SingleAnnotation x
252 
+#
253 
+# == param
254 
+# -x The `SingleAnnotation-class` x.
255 
+# -value A `grid::unit` x.
256 
+# -... other arguments
257 
+#
258 
+# == detail
259 
+# It assigns the width if it is a row annotation and the height if it is a column annotation.
260 
+#
261 
+"size<-.SingleAnnotation" = function(x, ..., value) {
262 
+    if(x@which == "row") {
263 
+        width(x) = value
264 
+    } else {
265 
+        height(x) = value
266 
+    }
267 
+    x
268 
+}
269 
+
270 
+
271 
+
272 
+# == title
273 
+# Width of the HeatmapAnnotation x
274 
+#
275 
+# == param
276 
+# -x The `HeatmapAnnotation-class` x.
277 
+# -... other arguments
278 
+#
279 
+width.HeatmapAnnotation = function(x, ...) {
280 
+    x@width
281 
+}
282 
+
283 
+# == title
284 
+# Assign the Width to the HeatmapAnnotation x
285 
+#
286 
+# == param
287 
+# -x The `HeatmapAnnotation-class` x.
288 
+# -value A `grid::unit` x.
289 
+# -... other arguments
290 
+#
291 
+"width<-.HeatmapAnnotation" = function(x, ..., value) {
292 
+
293 
+    if(x@which == "column") {
294 
+    	x@width = value
295 
+    	for(i in seq_along(x@anno_list)) {
296 
+    		width(x@anno_list[[i]]) = value
297 
+    	}
298 
+    } else {
299 
+    	x = resize(x, width = value)
300 
+    }
301 
+    x
302 
+}
303 
+
304 
+
305 
+# == title
306 
+# Height of the HeatmapAnnotation x
307 
+#
308 
+# == param
309 
+# -x The `HeatmapAnnotation-class` x.
310 
+# -... other arguments
311 
+#
312 
+height.HeatmapAnnotation = function(x, ...) {
313 
+    x@height
314 
+}
315 
+
316 
+# == title
317 
+# Assign the Height to the HeatmapAnnotation x
318 
+#
319 
+# == param
320 
+# -x The `HeatmapAnnotation-class` x.
321 
+# -value A `grid::unit` x.
322 
+# -... other arguments
323 
+#
324 
+"height<-.HeatmapAnnotation" = function(x, ..., value) {
325 
+
326 
+    if(x@which == "row") {
327 
+    	x@height = value
328 
+    	for(i in seq_along(x@anno_list)) {
329 
+    		height(x@anno_list[[i]]) = height
330 
+    	}
331 
+    } else {
332 
+    	x = resize(x, height = value)
333 
+    }
334 
+    x
335 
+}
336 
+
337 
+# == title
338 
+# Size of the HeatmapAnnotation x
339 
+#
340 
+# == param
341 
+# -x The `HeatmapAnnotation-class` x.
342 
+# -... other arguments
343 
+#
344 
+# == detail
345 
+# It returns the width if it is a row annotation and the height if it is a column annotation.
346 
+#
347 
+size.HeatmapAnnotation = function(x, ...) {
348 
+    if(x@which == "row") {
349 
+        x@width
350 
+    } else {
351 
+        x@height
352 
+    }
353 
+}
354 
+
355 
+# == title
356 
+# Assign the Size to the HeatmapAnnotation x
357 
+#
358 
+# == param
359 
+# -x The `HeatmapAnnotation-class` x.
360 
+# -value A `grid::unit` x.
361 
+# -... other arguments
362 
+#
363 
+# == detail
364 
+# It assigns the width if it is a row annotation and the height if it is a column annotation.
365 
+#
366 
+"size<-.HeatmapAnnotation" = function(x, ..., value) {
367 
+    if(x@which == "row") {
368 
+        width(x) = value
369 
+    } else {
370 
+        height(x) = value
371 
+    }
372 
+    x
373 
+}
374 
+
375 
+
376 
+
377 
+# == title
378 
+# Width of the Legends
379 
+#
380 
+# == param
381 
+# -x The `grid::grob` x returned by `Legend` or `packLegend`.
382 
+# -... other arguments
383 
+#
384 
+# == value
385 
+# The returned unit x is in ``mm``.
386 
+#
387 
+width.Legends = function(x, ...) {
388 
+	attr(x@grob, "width")
389 
+}
390 
+
391 
+# == title
392 
+# Height of the Legends
393 
+#
394 
+# == param
395 
+# -x The `grid::grob` x returned by `Legend` or `packLegend`.
396 
+# -... other arguments
397 
+#
398 
+# == value
399 
+# The returned unit x is in ``mm``.
400 
+#
401 
+height.Legends = function(x, ...) {
402 
+	attr(x@grob, "height")
403 
+}
404 
+
R/AdditiveUnit-class.R
History View file @ad35494
... ... 
@@ -45,7 +45,7 @@ AdditiveUnit = function(...) {
45 45 
 # A `HeatmapList-class` object.
46 46 
 #
47 47 
 # == seealso
48 
-# `%v%` operator is used for vertical heatmap list.
48 
+# `\%v\%` operator is used for vertical heatmap list.
49 49 
 #
50 50 
 # == author
51 51 
 # Zuguang Gu <z.gu@dkfz.de>
R/AnnotationFunction-class.R
History View file @ad35494
... ... 
@@ -1,10 +1,17 @@
1 1
2 2 
 # == title
3 
-# AnnotationFunction class
3 
+# The AnnotationFunction class
4 4 
 #
5 5 
 # == details
6 
-# THe AnnotationFunction class is a wrapper of user-defined annotation functions.
7 
-# See `AnnotationFunction` constructor for details
6 
+# The heatmap annotation is basically graphics aligned to the columns or heatmap if it is column annotation
7 
+# or heatmap rows if it is row annotation, while the type of the graphics can be arbitory, e.g.
8 
+# it can be heatmap-like or points. Here the AnnotationFunction class is designed for creating
9 
+# complex and flexible annotation graphics. As the main part, it uses a use-defined function
10 
+# to define the graphics. It also keeps information of the size of the plotting regions of the annotation.
11 
+# And most importantly, it allows subsetting of the annotation to draw a subset of the graphics, which
12 
+# is the base for the splitting of the annotations.
13 
+#
14 
+# See `AnnotationFunction` constructor for details.
8 15 
 #
9 16 
 AnnotationFunction = setClass("AnnotationFunction",
10 17 
 	slots = list(
... ... 
@@ -69,16 +76,17 @@ anno_width_and_height = function(which, width = NULL, height = NULL,
69 76
70 77
71 78 
 # == title
72 
-# Constructor of AnnotationFunction class
79 
+# Constructor of AnnotationFunction Class
73 80 
 #
74 81 
 # == param
75 
-# -fun A function which defines how to draw annotation. See **Details** section.
76 
-# -fun_name The name of the function. It is only used for `show,AnnotationFunction-method`.
82 
+# -fun A function which defines how to draw this annotation. See **Details** section.
83 
+# -fun_name The name of the function. It is only used for printing the object.
77 84 
 # -which Whether it is drawn as a column annotation or a row annotation?
78 
-# -var_imported The name of the object or the objects themselves that the annotation function depends on. See **Details** section.
79 
-# -n Number of observations in the annotation. It is not mandatory, but it is better to provide this information.
85 
+# -var_import The names of the variables or the variable themselves that the annotation function depends on. See **Details** section.
86 
+# -n Number of observations in the annotation. It is not mandatory, but it is better to provide this information
87 
+#   so that the higher order `HeatmapAnnotation` knows it and it can perform check on the consistency of annotations and heatmaps.
80 88 
 # -data_scale The data scale on the data axis (y-axis for column annotation and x-axis for row annotation). It is only used
81 
-#             when `decoration_annotation` is used with "native" unit coordinates.
89 
+#             when `decorate_annotation` is used with "native" unit coordinates.
82 90 
 # -subset_rule The rule of subsetting variables in ``var_import``. It should be set when users want the final object to
83 91 
 #              be subsetable. See **Details** section.
84 92 
 # -subsetable Whether the object is subsetable?
... ... 
@@ -88,12 +96,83 @@ anno_width_and_height = function(which, width = NULL, height = NULL,
88 96 
 #        the width must be an absolute unit.
89 97 
 #
90 98 
 # == details
91 
-# The AnnotationFunction class is a wrapper of the function which draws heatmap annotation.
99 
+# A normal R function defines how to draw the annotation graphics. As expected, the main part of the AnnotationFunction
100 
+# class is this function. The function defines how to draw at specific positions which correspond to rows or columns
101 
+# in the heatmap. The function should have three arguments: ``index``, ``k`` and ``n`` (the names of the arguments can
102 
+# be arbitory) where ``k`` and ``n`` are optional. ``index`` corresponds to the indices of rows or columns of the heatmap.
103 
+# The value of ``index`` is not necessarily to be the whole row indices or column indices. It can also be a subset of
104 
+# the indices if the annotation is split into slices according to the split of the heatmap. The value in ``index`` is
105 
+# always sorted according to the reordering of heatmap rows or columns (e.g. by clustering). So, ``index`` actually contains
106 
+# a list of row or column indices for the current slice after row or column reordering. This type of design makes sure
107 
+# the annotation graphics are drawn at the correct positions and can be correctly corresponded to the heatmap rows or columns.
108 
+#
109 
+# As mentioned, annotation can be split into slices. ``k`` corresponds to the current slice and ``n`` corresponds to
110 
+# the total number of slices. The information of ``k`` and ``n`` sometimes can be useful, for example, we want to add axis
111 
+# in the annotation, and if it is a column annotation and axis is drawn on the very right of the annotation area, the axis
112 
+# is only drawn when ``k == n``.
113 
+#
114 
+# Since the function only allows ``index``, ``k`` and ``n``, the function sometimes uses several external variables which can
115 
+# not be defined inside the function, e.g. the data points for the annotation. These variables should be imported
116 
+# into the AnnotationFunction class so that the function can correctly find these variables.
117 
+#
118 
+# One important feature for AnnotationFunction class is it can be subsetable. To allow subsetting of the object,
119 
+# users need to define the rule for the imported variables if there is any. The rules are simple function which
120 
+# accpets the variable and indices, and returns the subset of the variable. The subset rule functions implemented
121 
+# in this package are `subset_gp`, `subset_matrix_by_row` and `subset_vector`. These three functions are enough for
122 
+# most of the cases.
123 
+#
124 
+# In following, we defined three AnnotationFunction objects:
125 
+#
126 
+# 1. It needs external variable and support subsetting
127 
+#
128 
+#	x = 1:10
129 
+#	anno1 = AnnotationFunction(
130 
+#		fun = function(index) {
131 
+#			n = length(index)
132 
+#			pushViewport(viewport())
133 
+#			grid.points(1:n, x[index])
134 
+#			popViewport()
135 
+#		},
136 
+#		var_imported = list(x = x),
137 
+#		n = 10,
138 
+#		subset_rule = list(x = subset_vector),
139 
+#		subsetable = TRUE
140 
+#	)
141 
+#
142 
+# 2. The data variable is defined inside the function and no need to import other variables.
143 
+#
144 
+#	anno2 = AnnotationFunction(
145 
+#		fun = function(index) {
146 
+#			x = 1:10
147 
+#			n = length(index)
148 
+#			pushViewport(viewport())
149 
+#			grid.points(1:n, x[index])
150 
+#			popViewport()
151 
+#		},
152 
+#		n = 10,
153 
+#		subsetable = TRUE
154 
+#	)
155 
+#
156 
+# 3. The most compact way to only specify the function to the constructor.
157 
+#
158 
+#	anno3 = AnnotationFunction(
159 
+#		fun = function(index) {
160 
+#			x = 1:10
161 
+#			n = length(index)
162 
+#			pushViewport(viewport())
163 
+#			grid.points(1:n, x[index])
164 
+#			popViewport()
165 
+#		}
166 
+#	)
92 167 
 #
93 
-# If the annotation function is subsetable, the annotation graphics can be split by rows or by columns
94 
-# according to the split of the heatmap.
168 
+# Finally, you need to push a viewport for graphics and finally pop the viewport.
169 
+#
170 
+# In the package, quite a lot annotation function are constructed by `AnnotationFunction` constructor:
171 
+# `anno_empty`, `anno_image`, `anno_points`, `anno_lines`, `anno_barplot`, `anno_boxplot`, `anno_histogram`,
172 
+# `anno_density`, `anno_joyplot`, `anno_horizon`, `anno_text` and `anno_mark`. Thess built-in annotation functions
173 
+# are all subsettable.
95 174 
 AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),
96 
-	var_imported = list(), n = 0, data_scale = c(0, 1), subset_rule = list(),
175 
+	var_import = list(), n = 0, data_scale = c(0, 1), subset_rule = list(),
97 176 
 	subsetable = FALSE, width = NULL, height = NULL) {
98 177
99 178 
 	which = match.arg(which)[1]
... ... 
@@ -114,25 +193,32 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),
114 193 
 	anno@n = n
115 194 
 	anno@data_scale = data_scale
116 195
117 
-	anno@var_env = new.env()
118 
-	if(is.character(var_imported)) {
119 
-		for(nm in var_imported) {
120 
-			anno@var_env[[nm]] = get(nm, envir = parent.frame())
121 
-		}
122 
-	} else if(inherits(var_imported, "list")) {
123 
-		if(is.null(names(var_imported))) {
124 
-			var_imported_nm = sapply(as.list(substitute(var_imported))[-1], as.character)
125 
-			names(var_imported) = var_imported_nm
126 
-		}
196 
+	if(length(var_import)) {
197 
+		anno@var_env = new.env()
198 
+		if(is.character(var_import)) {
199 
+			for(nm in var_import) {
200 
+				anno@var_env[[nm]] = get(nm, envir = parent.frame())
201 
+			}
202 
+		} else if(inherits(var_import, "list")) {
203 
+			if(is.null(names(var_import))) {
204 
+				var_imported_nm = sapply(as.list(substitute(var_import))[-1], as.character)
205 
+				names(var_import) = var_imported_nm
206 
+			}
127 207
128 
-		for(nm in names(var_imported)) {
129 
-			anno@var_env[[nm]] = var_imported[[nm]]
208 
+			for(nm in names(var_import)) {
209 
+				anno@var_env[[nm]] = var_import[[nm]]
210 
+			}
211 
+		} else {
212 
+			stop_wrap("`var_import` needs to be a character vector which contains variable names or a list of variables")
130 213 
 		}
214 
+		environment(fun) = anno@var_env
131 215 
 	} else {
132 
-		stop_wrap("`var_import` needs to be a character vector which contains variable names or a list of variables")
216 
+		anno@var_env = environment(fun)
217 
+	}
218 
+
219 
+	if(length(as.list(formals(fun))) == 1) {
220 
+		formals(fun) = alist(index = , k = 1, n = 1)
133 221 
 	}
134 
-
135 
-	environment(fun) = anno@var_env
136 222 
 	anno@fun = fun
137 223
138 224 
 	if(is.null(subset_rule)) {
... ... 
@@ -173,7 +259,8 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),
173 259 
 # -i A vector of indices.
174 260 
 #
175 261 
 # == details
176 
-# One good thing for designing the `AnnotationFunction-class` can be subsetted.
262 
+# One good thing for designing the `AnnotationFunction-class` object is it can be subsetted,
263 
+# and this is the base for the splitting of the annotations.
177 264 
 #
178 265 
 # == example
179 266 
 # anno = anno_simple(1:10)
... ... 
@@ -204,11 +291,13 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),
204 291 
 }
205 292
206 293 
 # == title
207 
-# Draw the AnnotationFunction object
294 
+# Draw the AnnotationFunction Object
208 295 
 #
209 296 
 # == param
210 297 
 # -object The `AnnotationFunction-class` object.
211 298 
 # -index Index of observations.
299 
+# -k Current index of slice.
300 
+# -n Total number of slices.
212 301 
 # -test Is it in test mode? The value can be logical or a text which is plotted as the title of plot.
213 302 
 #
214 303 
 # == detail
... ... 
@@ -219,7 +308,7 @@ AnnotationFunction = function(fun, fun_name = "", which = c("column", "row"),
219 308 
 #
220 309 
 setMethod(f = "draw",
221 310 
 	signature = "AnnotationFunction",
222 
-	definition = function(object, index, test = FALSE) {
311 
+	definition = function(object, index, k = 1, n = 1, test = FALSE) {
223 312
224 313 
 	if(is.character(test)) {
225 314 
 		test2 = TRUE
... ... 
@@ -242,7 +331,7 @@ setMethod(f = "draw",
242 331 
     # names should be passed to the data viewport
243 332 
 	pushViewport(viewport(width = anno_width, height = anno_height))
244 333 
 	vp_name1 = current.viewport()$name
245 
-	object@fun(index)
334 
+	object@fun(index, k, n)
246 335 
 	if(test2) {
247 336 
 		grid.text(test, y = unit(1, "npc") + unit(2, "mm"), just = "bottom")
248 337
... ... 
@@ -283,6 +372,8 @@ setMethod(f = "draw",
283 372 
 # In `AnnotationFunction-class`, there is an environment which stores some external variables
284 373 
 # for the annotation function. This `copy_all,AnnotationFunction-method` hard copy all the variables
285 374 
 # in that environment to a new environment.
375 
+#
376 
+# The environment is at ``object@var_env``.
286 377 
 setMethod(f = "copy_all",
287 378 
 	signature = "AnnotationFunction",
288 379 
 	definition = function(object) {
... ... 
@@ -333,112 +424,22 @@ setMethod(f = "show",
333 424
334 425 
 })
335 426
336 
-# == title
337 
-# Width of the AnnotationFunction object
338 
-#
339 
-# == param
340 
-# -object The `AnnotationFunction-class` object.
341 
-#
342 
-setMethod(f = "width",
343 
-	signature = "AnnotationFunction",
344 
-	definition = function(object) {
345 
-	object@width
346 
-})
347 
-
348 
-# == title
349 
-# Assign the Width of the AnnotationFunction object
350 
-#
351 
-# == param
352 
-# -object The `AnnotationFunction-class` object.
353 
-# -value A `grid::unit` object.
354 
-# -... Other arguments
355 
-#
356 
-setReplaceMethod(f = "width",
357 
-	signature = "AnnotationFunction",
358 
-	definition = function(object, value, ...) {
359 
-	object@width = value
360 
-	object
361 
-})
362 
-
363 
-# == title
364 
-# Height of the AnnotationFunction object
365 
-#
366 
-# == param
367 
-# -object The `AnnotationFunction-class` object.
368 
-#
369 
-setMethod(f = "height",
370 
-	signature = "AnnotationFunction",
371 
-	definition = function(object) {
372 
-	object@height
373 
-})
374 
-
375 
-# == title
376 
-# Assign the Height of the AnnotationFunction object
377 
-#
378 
-# == param
379 
-# -object The `AnnotationFunction-class` object.
380 
-# -value A `grid::unit` object.
381 
-# -... Other arguments
382 
-#
383 
-setReplaceMethod(f = "height",
384 
-	signature = "AnnotationFunction",
385 
-	definition = function(object, value, ...) {
386 
-	object@height = value
387 
-	object
388 
-})
389 
-
390 
-# == title
391 
-# Size of the AnnotationFunction object
392 
-#
393 
-# == param
394 
-# -object The `AnnotationFunction-class` object.
395 
-#
396 
-# == detail
397 
-# It returns the width if it is a row annotation and the height if it is a column annotation.
398 
-#
399 
-setMethod(f = "size",
400 
-	signature = "AnnotationFunction",
401 
-	definition = function(object) {
402 
-	if(object@which == "row") {
403 
-		object@width
404 
-	} else {
405 
-		object@height
406 
-	}
407 
-})
408 
-
409 
-# == title
410 
-# Assign the Size of the AnnotationFunction object
411 
-#
412 
-# == param
413 
-# -object The `AnnotationFunction-class` object.
414 
-# -value A `grid::unit` object.
415 
-# -... Other arguments
416 
-#
417 
-# == detail
418 
-# It assigns the width if it is a row annotation and the height if it is a column annotation.
419 
-#
420 
-setReplaceMethod(f = "size",
421 
-	signature = "AnnotationFunction",
422 
-	definition = function(object, value, ...) {
423 
-	if(object@which == "row") {
424 
-		object@width = value
425 
-	} else {
426 
-		object@height = value
427 
-	}
428 
-	object
429 
-})
430 
-
431 427 
 # == title
432 428 
 # Number of Observations
433 429 
 #
434 430 
 # == param
435 
-# -x The `AnnotationFunction-class` object.
431 
+# -object The `AnnotationFunction-class` object.
432 
+# -... other arguments
436 433 
 #
437 434 
 # == details
438 
-# It returns the ``n`` slot in the object.
439 
-nobs.AnnotationFunction = function(x) {
440 
-	if(x@n > 0) {
441 
-		x@n
435 
+# It returns the ``n`` slot in the object. If there does not exist, it returns ``NA``.
436 
+#
437 
+# == example
438 
+# anno = anno_points(1:10)
439 
+# nobs(anno)
440 
+nobs.AnnotationFunction = function(object, ...) {
441 
+	if(object@n > 0) {
442 
+		object@n
442 443 
 	} else {
443 444 
 		NA
444 445 
 	}
R/AnnotationFunction-function.R
History View file @ad35494
... ... 
@@ -66,7 +66,22 @@ anno_empty = function(which = c("column", "row"), border = TRUE, width = NULL, h
66 66 
 	return(anno)
67 67 
 }
68 68
69 
+# == title
70 
+# Subset the Matrix by Rows
71 
+#
72 
+# == param
73 
+# -x A matrix
74 
+# -i The row indices.
75 
+#
69 76 
 subset_matrix_by_row = function(x, i) x[i, , drop = FALSE]
77 
+
78 
+# == title
79 
+# Subset the vector
80 
+#
81 
+# == param
82 
+# -x A vector
83 
+# -i The indices
84 
+#
70 85 
 subset_vector = function(x, i) x[i]
71 86
72 87 
 # == title
... ... 
@@ -81,7 +96,7 @@ subset_vector = function(x, i) x[i]
81 96 
 #      vector of colors. Normally it is generated by `circlize::colorRamp2`. If ``x`` is discrete
82 97 
 #      (numeric or character) and needs a discrete color mapping, ``col`` should be a vector of
83 98 
 #      colors with levels in ``x`` as vector names. If ``col`` is not specified, the color mapping
84 
-#      is randomly generated by `default_col`.
99 
+#      is randomly generated by ``ComplexHeatmap:::default_col``.
85 100 
 # -na_col Color for NA value.
86 101 
 # -which Whether it is a column annotation or a row annotation?
87 102 
 # -border Wether draw borders of the annotation region?
... ... 
@@ -115,7 +130,7 @@ subset_vector = function(x, i) x[i]
115 130 
 # anno = anno_simple(1:10, pch = c(1:4, NA, 6:8, NA, 10))
116 131 
 # draw(anno, test = "pch has NA values")
117 132 
 #
118 
-# anno = anno_simple(1:10, pch = c(rep("A", 5, rep(NA, 5))))
133 
+# anno = anno_simple(1:10, pch = c(rep("A", 5), rep(NA, 5)))
119 134 
 # draw(anno, test = "pch has NA values")
120 135 
 #
121 136 
 # pch = matrix(1:20, nc = 2)
... ... 
@@ -289,7 +304,7 @@ anno_simple = function(x, col, na_col = "grey",
289 304 
 # == details
290 305 
 # This function supports image formats in ``png``, ``svg``, ``pdf``, ``eps``, ``jpeg/jpg``, ``tiff``.
291 306 
 # ``png``, ``jpeg/jpg`` and ``tiff`` images are imported by `png::readPNG`, `jpeg::readJPEG` and
292 
-# `tiff::readTIFF`, and drawn by `grid.grid.raster`. ``svg`` images are firstly reformatted by `rsvg::rsvg_svg`
307 
+# `tiff::readTIFF`, and drawn by `grid::grid.raster`. ``svg`` images are firstly reformatted by `rsvg::rsvg_svg`
293 308 
 # and then imported by `grImport2::readPicture` and drawn by `grImport2::grid.picture`. ``pdf`` and ``eps``
294 309 
 # images are imported by `grImport::PostScriptTrace` and `grImport::readPicture`, later drawn by `grImport::grid.picture`.
295 310 
 #
... ... 
@@ -401,7 +416,7 @@ anno_image = function(image, which = c("column", "row"), border = TRUE,
401 416 
 		n = length(index)
402 417
403 418 
 		pushViewport(viewport())
404 
-		asp = convertHeight(unit(1, "npc") - space*2, "mm", valueOnly = TRUE)/convertWidth(unit(1/n, "npc") - space*2, "mm", value = TRUE)
419 
+		asp = convertHeight(unit(1, "npc") - space*2, "mm", valueOnly = TRUE)/convertWidth(unit(1/n, "npc") - space*2, "mm", valueOnly = TRUE)
405 420 
 		grid.rect(x = (1:n - 0.5)/n, width = 1/n, gp = subset_gp(gp, index))
406 421 
 		for(i in seq_len(n)) {
407 422 
 			if(identical(image_list[[i]], NA)) next
... ... 
@@ -430,7 +445,7 @@ anno_image = function(image, which = c("column", "row"), border = TRUE,
430 445 
 		n = length(index)
431 446
432 447 
 		pushViewport(viewport())
433 
-		asp = convertHeight(unit(1/n, "npc") - space*2, "mm", valueOnly = TRUE)/convertWidth(unit(1, "npc") - space*2, "mm", value = TRUE)
448 
+		asp = convertHeight(unit(1/n, "npc") - space*2, "mm", valueOnly = TRUE)/convertWidth(unit(1, "npc") - space*2, "mm", valueOnly = TRUE)
434 449 
 		grid.rect(y = (n - 1:n + 0.5)/n, height = 1/n, gp = subset_gp(gp, index))
435 450 
 		for(i in seq_len(n)) {
436 451 
 			if(identical(image_list[[i]], NA)) next
... ... 
@@ -621,7 +636,7 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()
621 636 
 	axis_param = validate_axis_param(axis_param, which)
622 637 
 	axis_grob = if(axis) construct_axis_grob(axis_param, which, data_scale) else NULL
623 638
624 
-	row_fun = function(index) {
639 
+	row_fun = function(index, k = 1, N = 1) {
625 640 
 		n = length(index)
626 641
627 642 
 		pushViewport(viewport(xscale = data_scale, yscale = c(0.5, n+0.5)))
... ... 
@@ -634,12 +649,17 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()
634 649 
 			grid.points(value[index], n - seq_along(index) + 1, gp = gp, default.units = "native",
635 650 
 				pch = pch[index], size = size[index])
636 651 
 		}
652 
+		if(axis_param$side == "top") {
653 
+			if(k > 1) axis = FALSE
654 
+		} else if(axis_param$side == "bottom") {
655 
+			if(k < N) axis = FALSE
656 
+		}
637 657 
 		if(axis) grid.draw(axis_grob)
638 658 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
639 659 
 		popViewport()
640 660 
 	}
641 661
642 
-	column_fun = function(index) {
662 
+	column_fun = function(index, k = 1, N = 1) {
643 663 
 		n = length(index)
644 664
645 665 
 		pushViewport(viewport(yscale = data_scale, xscale = c(0.5, n+0.5)))
... ... 
@@ -650,6 +670,11 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()
650 670 
 		} else {
651 671 
 			grid.points(seq_along(index), value[index], gp = gp, default.units = "native", pch = pch[index], size = size[index])
652 672 
 		}
673 
+		if(axis_param$side == "left") {
674 
+			if(k > 1) axis = FALSE
675 
+		} else if(axis_param$side == "right") {
676 
+			if(k < N) axis = FALSE
677 
+		}
653 678 
 		if(axis) grid.draw(axis_grob)
654 679 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
655 680 
 		popViewport()
... ... 
@@ -717,7 +742,7 @@ update_anno_extend = function(anno, axis_grob, axis_param) {
717 742 
 # -add_points Whether to add points on the lines?
718 743 
 # -pch Point type. The length setting is the same as ``gp``.
719 744 
 # -size Point size, the value should be a `grid::unit` object. The length setting is the same as ``gp``.
720 
-# -pt_size Graphic parameters for points. The length setting is the same as ``gp``.
745 
+# -pt_gp Graphic parameters for points. The length setting is the same as ``gp``.
721 746 
 # -ylim Data ranges. By default it is ``range(x)``.
722 747 
 # -extend The extension to both side of ``ylim``. The value is a percent value corresponding to ``ylim[2] - ylim[1]``.
723 748 
 # -axis Whether to add axis?
... ... 
@@ -791,7 +816,7 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),
791 816 
 	axis_param = validate_axis_param(axis_param, which)
792 817 
 	axis_grob = if(axis) construct_axis_grob(axis_param, which, data_scale) else NULL
793 818
794 
-	row_fun = function(index) {
819 
+	row_fun = function(index, k = 1, N = 1) {
795 820 
 		n = length(index)
796 821
797 822 
 		pushViewport(viewport(xscale = data_scale, yscale = c(0.5, n+0.5)))
... ... 
@@ -812,12 +837,17 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),
812 837 
 					pch = pch[index], size = size[index])
813 838 
 			}
814 839 
 		}
840 
+		if(axis_param$side == "top") {
841 
+			if(k > 1) axis = FALSE
842 
+		} else if(axis_param$side == "bottom") {
843 
+			if(k < N) axis = FALSE
844 
+		}
815 845 
 		if(axis) grid.draw(axis_grob)
816 846 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
817 847 
 		popViewport()
818 848 
 	}
819 849
820 
-	column_fun = function(index) {
850 
+	column_fun = function(index, k = 1, N = 1) {
821 851 
 		n = length(index)
822 852
823 853 
 		pushViewport(viewport(yscale = data_scale, xscale = c(0.5, n+0.5)))
... ... 
@@ -837,6 +867,11 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),
837 867 
 					pch = pch[index], size = size[index])
838 868 
 			}
839 869 
 		}
870 
+		if(axis_param$side == "left") {
871 
+			if(k > 1) axis = FALSE
872 
+		} else if(axis_param$side == "right") {
873 
+			if(k < N) axis = FALSE
874 
+		}
840 875 
 		if(axis) grid.draw(axis_grob)
841 876 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
842 877 
 		popViewport()
... ... 
@@ -967,7 +1002,7 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
967 1002 
 	axis_param = validate_axis_param(axis_param, which)
968 1003 
 	axis_grob = if(axis) construct_axis_grob(axis_param, which, data_scale) else NULL
969 1004
970 
-	row_fun = function(index) {
1005 
+	row_fun = function(index, k = 1, N = 1) {
971 1006 
 		n = length(index)
972 1007
973 1008 
 		pushViewport(viewport(xscale = data_scale, yscale = c(0.5, n+0.5)))
... ... 
@@ -982,11 +1017,16 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
982 1017 
 				grid.rect(x = x_coor, y = n - seq_along(index) + 1, width = abs(width), height = 1*bar_width, default.units = "native", gp = subset_gp(gp, i))
983 1018 
 			}
984 1019 
 		}
1020 
+		if(axis_param$side == "top") {
1021 
+			if(k > 1) axis = FALSE
1022 
+		} else if(axis_param$side == "bottom") {
1023 
+			if(k < N) axis = FALSE
1024 
+		}
985 1025 
 		if(axis) grid.draw(axis_grob)
986 1026 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
987 1027 
 		popViewport()
988 1028 
 	}
989 
-	column_fun = function(index) {
1029 
+	column_fun = function(index, k = 1, N = 1) {
990 1030 
 		n = length(index)
991 1031
992 1032 
 		pushViewport(viewport(yscale = data_scale, xscale = c(0.5, n+0.5)))
... ... 
@@ -1001,6 +1041,11 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
1001 1041 
 				grid.rect(y = y_coor, x = seq_along(index), height = abs(height), width = 1*bar_width, default.units = "native", gp = subset_gp(gp, i))
1002 1042 
 			}
1003 1043 
 		}
1044 
+		if(axis_param$side == "left") {
1045 
+			if(k > 1) axis = FALSE
1046 
+		} else if(axis_param$side == "right") {
1047 
+			if(k < N) axis = FALSE
1048 
+		}
1004 1049 
 		if(axis) grid.draw(axis_grob)
1005 1050 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
1006 1051 
 		popViewport()
... ... 
@@ -1110,7 +1155,7 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
1110 1155 
 	axis_param = validate_axis_param(axis_param, which)
1111 1156 
 	axis_grob = if(axis) construct_axis_grob(axis_param, which, data_scale) else NULL
1112 1157
1113 
-	row_fun = function(index) {
1158 
+	row_fun = function(index, k = 1, N = 1) {
1114 1159
1115 1160 
 		n_all = length(value)
1116 1161 
 		value = value[index]
... ... 
@@ -1149,11 +1194,16 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
1149 1194 
 					default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i])
1150 1195 
 			}
1151 1196 
 		}
1197 
+		if(axis_param$side == "top") {
1198 
+			if(k > 1) axis = FALSE
1199 
+		} else if(axis_param$side == "bottom") {
1200 
+			if(k < N) axis = FALSE
1201 
+		}
1152 1202 
 		if(axis) grid.draw(axis_grob)
1153 1203 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
1154 1204 
 		popViewport()
1155 1205 
 	}
1156 
-	column_fun = function(index) {
1206 
+	column_fun = function(index, k = 1, N = 1) {
1157 1207 
 		value = value[index]
1158 1208 
 		boxplot_stats = boxplot(value, plot = FALSE)$stats
1159 1209
... ... 
@@ -1189,6 +1239,11 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
1189 1239 
 					default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i])
1190 1240 
 			}
1191 1241 
 		}
1242 
+		if(axis_param$side == "left") {
1243 
+			if(k > 1) axis = FALSE
1244 
+		} else if(axis_param$side == "right") {
1245 
+			if(k < N) axis = FALSE
1246 
+		}
1192 1247 
 		if(axis) grid.draw(axis_grob)
1193 1248 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
1194 1249 
 		popViewport()
... ... 
@@ -1288,7 +1343,7 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
1288 1343 
 	axis_param = validate_axis_param(axis_param, which)
1289 1344 
 	axis_grob = if(axis) construct_axis_grob(axis_param, which, xscale) else NULL
1290 1345
1291 
-	row_fun = function(index) {
1346 
+	row_fun = function(index, k = 1, N = 1) {
1292 1347
1293 1348 
 		n_all = length(value)
1294 1349 
 		value = value[index]
... ... 
@@ -1305,11 +1360,16 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
1305 1360 
 			popViewport()
1306 1361 
 		}
1307 1362 
 		pushViewport(viewport(xscale = xscale))
1363 
+		if(axis_param$side == "top") {
1364 
+			if(k > 1) axis = FALSE
1365 
+		} else if(axis_param$side == "bottom") {
1366 
+			if(k < N) axis = FALSE
1367 
+		}
1308 1368 
 		if(axis) grid.draw(axis_grob)
1309 1369 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
1310 1370 
 		popViewport()
1311 1371 
 	}
1312 
-	column_fun = function(index) {
1372 
+	column_fun = function(index, k = 1, N = 1) {
1313 1373
1314 1374 
 		n_all = length(value)
1315 1375 
 		value = value[index]
... ... 
@@ -1332,6 +1392,11 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
1332 1392 
 			popViewport()
1333 1393 
 		}
1334 1394 
 		pushViewport(viewport(yscale = yscale))
1395 
+		if(axis_param$side == "left") {
1396 
+			if(k > 1) axis = FALSE
1397 
+		} else if(axis_param$side == "right") {
1398 
+			if(k < N) axis = FALSE
1399 
+		}
1335 1400 
 		if(axis) grid.draw(axis_grob)
1336 1401 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
1337 1402 
 		popViewport()
... ... 
@@ -1390,13 +1455,14 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,
1390 1455 
 # An annotation function which can be used in `HeatmapAnnotation`.
1391 1456 
 #
1392 1457 
 # == example
1393 
-# anno = anno_density(t(m), which = "row")
1458 
+# m = matrix(rnorm(100), 10)
1459 
+# anno = anno_density(m, which = "row")
1394 1460 
 # draw(anno, test = "normal density")
1395 
-# anno = anno_density(t(m), which = "row", type = "violin")
1461 
+# anno = anno_density(m, which = "row", type = "violin")
1396 1462 
 # draw(anno, test = "violin")
1397 
-# anno = anno_density(t(m), which = "row", type = "heatmap")
1463 
+# anno = anno_density(m, which = "row", type = "heatmap")
1398 1464 
 # draw(anno, test = "heatmap")
1399 
-# anno = anno_density(t(m), which = "row", type = "heatmap",
1465 
+# anno = anno_density(m, which = "row", type = "heatmap",
1400 1466 
 #     heatmap_colors = c("white", "orange"))
1401 1467 
 # draw(anno, test = "heatmap, colors")
1402 1468 
 anno_density = function(x, which = c("column", "row"),
... ... 
@@ -1457,7 +1523,7 @@ anno_density = function(x, which = c("column", "row"),
1457 1523 
 	axis_param = validate_axis_param(axis_param, which)
1458 1524 
 	axis_grob = if(axis) construct_axis_grob(axis_param, which, xscale) else NULL
1459 1525
1460 
-	row_fun = function(index) {
1526 
+	row_fun = function(index, k = 1, N = 1) {
1461 1527
1462 1528 
 		n = length(index)
1463 1529 
 		value = value[index]
... ... 
@@ -1502,11 +1568,16 @@ anno_density = function(x, which = c("column", "row"),
1502 1568 
 			popViewport()
1503 1569 
 		}
1504 1570 
 		pushViewport(viewport(xscale = xscale))
1571 
+		if(axis_param$side == "top") {
1572 
+			if(k > 1) axis = FALSE
1573 
+		} else if(axis_param$side == "bottom") {
1574 
+			if(k < N) axis = FALSE
1575 
+		}
1505 1576 
 		if(axis) grid.draw(axis_grob)
1506 1577 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
1507 1578 
 		popViewport()
1508 1579 
 	}
1509 
-	column_fun = function(index) {
1580 
+	column_fun = function(index, k = 1, N = 1) {
1510 1581
1511 1582 
 		n_all = length(value)
1512 1583 
 		value = value[index]
... ... 
@@ -1573,6 +1644,11 @@ anno_density = function(x, which = c("column", "row"),
1573 1644 
 			popViewport()
1574 1645 
 		}
1575 1646 
 		pushViewport(viewport(yscale = yscale))
1647 
+		if(axis_param$side == "left") {
1648 
+			if(k > 1) axis = FALSE
1649 
+		} else if(axis_param$side == "right") {
1650 
+			if(k < N) axis = FALSE
1651 
+		}
1576 1652 
 		if(axis) grid.draw(axis_grob)
1577 1653 
 		if(border) grid.rect(gp = gpar(fill = "transparent"))
1578 1654 
 		popViewport()
... ... 
@@ -1593,7 +1669,7 @@ anno_density = function(x, which = c("column", "row"),
1593 1669 
 		n = n,
1594 1670 
 		data_scale = xscale,
1595 1671 
 		var_import = list(value, gp, border, type, axis, axis_param, axis_grob, xscale, yscale, density_x,
1596 
-			density_y, min_density_x, max_density_x, joyplot_scale)
1672 
+			density_y, min_density_x, max_density_x, joyplot_scale, heatmap_colors)
1597 1673 
 	)
1598 1674
1599 1675 
 	if(type == "heatmap") {
... ... 
@@ -1652,11 +1728,11 @@ anno_text = function(x, which = c("column", "row"), gp = gpar(),
1652 1728 
 	rot = guess_rot(), just = guess_just(),
1653 1729 
 	offset = guess_location(), location = guess_location(),
1654 1730 
 	width = NULL, height = NULL) {
1655 
-
1656 
-	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
1657 
-		which = get("which", envir = parent.frame())
1658 
-	} else {
1731 
+
1732 
+	if(is.null(.ENV$current_annotation_which)) {
1659 1733 
 		which = match.arg(which)[1]
1734 
+	} else {
1735 
+		which = .ENV$current_annotation_which
1660 1736 
 	}
1661 1737
1662 1738 
 	n = length(x)
... ... 
@@ -1807,7 +1883,7 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000
1807 1883 
 	if(is.matrix(x) || is.data.frame(x)) {
1808 1884 
 		value = vector("list", ncol(x))
1809 1885 
 		for(i in seq_len(ncol(x))) {
1810 
-			value[[i]] = cbind(seq_len(nrow(x), x[, i]))
1886 
+			value[[i]] = cbind(seq_len(nrow(x)), x[, i])
1811 1887 
 		}
1812 1888 
 	} else if(inherits(x, "list")){
1813 1889 
 		if(all(sapply(x, is.atomic))) {
... ... 
@@ -1842,7 +1918,7 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000
1842 1918 
 	axis_param = validate_axis_param(axis_param, which)
1843 1919 
 	axis_grob = if(axis) construct_axis_grob(axis_param, which, xscale) else NULL
1844 1920
1845 
-	row_fun = function(index) {
1921 
+	row_fun = function(index, k = 1, N = 1) {
1846 1922
1847 1923 
 		n_all = length(value)
1848 1924 
 		value = value[index]
... ... 
@@ -1867,10 +1943,15 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000
1867 1943 
 			popViewport()
1868 1944 
 		}
1869 1945 
 		pushViewport(viewport(xscale = xscale))
1946 
+		if(axis_param$side == "top") {
1947 
+			if(k > 1) axis = FALSE
1948 
+		} else if(axis_param$side == "bottom") {
1949 
+			if(k < N) axis = FALSE
1950 
+		}
1870 1951 
 		if(axis) grid.draw(axis_grob)
1871 1952 
 		popViewport()
1872 1953 
 	}
1873 
-	column_fun = function(index) {
1954 
+	column_fun = function(index, k = 1, N = 1) {
1874 1955
1875 1956 
 		n_all = length(value)
1876 1957 
 		value = value[index]
... ... 
@@ -1900,6 +1981,11 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000
1900 1981 
 			popViewport()
1901 1982 
 		}
1902 1983 
 		pushViewport(viewport(yscale = yscale))
1984 
+		if(axis_param$side == "left") {
1985 
+			if(k > 1) axis = FALSE
1986 
+		} else if(axis_param$side == "right") {
1987 
+			if(k < N) axis = FALSE
1988 
+		}
1903 1989 
 		if(axis) grid.draw(axis_grob)
1904 1990 
 		popViewport()
1905 1991 
 	}
... ... 
@@ -1938,7 +2024,7 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000
1938 2024 
 # -x A matrix or a list. If ``x`` is a matrix or a data frame, columns correspond to observations.
1939 2025 
 # -which Whether it is a column annotation or a row annotation?
1940 2026 
 # -gp Graphic parameters for the boxes. The length of the graphic parameters should be one or the number of observations.
1941 
-#     There are two unstandard parameters specificly for horizon chart: ``pos_fill`` and ``neg_fill` controls the filled
2027 
+#     There are two unstandard parameters specificly for horizon chart: ``pos_fill`` and ``neg_fill`` controls the filled
1942 2028 
 #     color for positive values and negative values.
1943 2029 
 # -n_slice Number of slices on y-axis.
1944 2030 
 # -slice_size Height of the slice. If the value is not ``NULL``, ``n_slice`` will be recalculated.
... ... 
@@ -1956,7 +2042,7 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000
1956 2042 
 # == value
1957 2043 
 # An annotation function which can be used in `HeatmapAnnotation`.
1958 2044 
 #
1959 
-# == detail
2045 
+# == example
1960 2046 
 # lt = lapply(1:20, function(x) cumprod(1 + runif(1000, -x/100, x/100)) - 1)
1961 2047 
 # anno = anno_horizon(lt, which = "row")
1962 2048 
 # draw(anno, test = "horizon chart")
... ... 
@@ -1990,7 +2076,7 @@ anno_horizon = function(x, which = c("column", "row"),
1990 2076 
 	if(is.matrix(x) || is.data.frame(x)) {
1991 2077 
 		value = vector("list", ncol(x))
1992 2078 
 		for(i in seq_len(ncol(x))) {
1993 
-			value[[i]] = cbind(seq_len(nrow(x), x[, i]))
2079 
+			value[[i]] = cbind(seq_len(nrow(x)), x[, i])
1994 2080 
 		}
1995 2081 
 	} else if(inherits(x, "list")){
1996 2082 
 		if(all(sapply(x, is.atomic))) {
... ... 
@@ -2041,7 +2127,7 @@ anno_horizon = function(x, which = c("column", "row"),
2041 2127 
 	axis_param = validate_axis_param(axis_param, which)
2042 2128 
 	axis_grob = if(axis) construct_axis_grob(axis_param, which, xscale) else NULL
2043 2129
2044 
-	row_fun = function(index) {
2130 
+	row_fun = function(index, k = 1, N = 1) {
2045 2131
2046 2132 
 		n_all = length(value)
2047 2133 
 		value = value[index]
... ... 
@@ -2066,6 +2152,11 @@ anno_horizon = function(x, which = c("column", "row"),
2066 2152 
 			popViewport()
2067 2153 
 		}
2068 2154 
 		pushViewport(viewport(xscale = xscale))
2155 
+		if(axis_param$side == "top") {
2156 
+			if(k > 1) axis = FALSE
2157 
+		} else if(axis_param$side == "bottom") {
2158 
+			if(k < N) axis = FALSE
2159 
+		}
2069 2160 
 		if(axis) grid.draw(axis_grob)
2070 2161 
 		popViewport()
2071 2162 
 	}
... ... 
@@ -2215,6 +2306,9 @@ row_anno_points = function(...) {
2215 2306 
 # See help page of `anno_barplot`
2216 2307 
 #
2217 2308 
 row_anno_barplot = function(...) {
2309 
+	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
2310 
+		message("From this version of ComplexHeatmap, you can directly use `anno_barplot()` for row annotation if you call it in `rowAnnotation()`.")
2311 
+	}
2218 2312 
 	anno_barplot(..., which = "row")
2219 2313 
 }
2220 2314
... ... 
@@ -2234,6 +2328,9 @@ row_anno_barplot = function(...) {
2234 2328 
 # See help page of `anno_boxplot`
2235 2329 
 #
2236 2330 
 row_anno_boxplot = function(...) {
2331 
+	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
2332 
+		message("From this version of ComplexHeatmap, you can directly use `anno_boxplot()` for row annotation if you call it in `rowAnnotation()`.")
2333 
+	}
2237 2334 
 	anno_boxplot(..., which = "row")
2238 2335 
 }
2239 2336
... ... 
@@ -2252,6 +2349,9 @@ row_anno_boxplot = function(...) {
2252 2349 
 # See help page of `anno_histogram`
2253 2350 
 #
2254 2351 
 row_anno_histogram = function(...) {
2352 
+	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
2353 
+		message("From this version of ComplexHeatmap, you can directly use `anno_histogram()` for row annotation if you call it in `rowAnnotation()`.")
2354 
+	}
2255 2355 
 	anno_histogram(..., which = "row")
2256 2356 
 }
2257 2357
... ... 
@@ -2270,6 +2370,9 @@ row_anno_histogram = function(...) {
2270 2370 
 # See help page of `anno_density`
2271 2371 
 #
2272 2372 
 row_anno_density = function(...) {
2373 
+	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
2374 
+		message("From this version of ComplexHeatmap, you can directly use `anno_density()` for row annotation if you call it in `rowAnnotation()`.")
2375 
+	}
2273 2376 
 	anno_density(..., which = "row")
2274 2377 
 }
2275 2378
... ... 
@@ -2288,6 +2391,9 @@ row_anno_density = function(...) {
2288 2391 
 # See help page of `anno_text`
2289 2392 
 #
2290 2393 
 row_anno_text = function(...) {
2394 
+	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
2395 
+		message("From this version of ComplexHeatmap, you can directly use `anno_text()` for row annotation if you call it in `rowAnnotation()`.")
2396 
+	}
2291 2397 
 	anno_text(..., which = "row")
2292 2398 
 }
2293 2399
... ... 
@@ -2323,7 +2429,7 @@ row_anno_text = function(...) {
2323 2429 
 #
2324 2430 
 # m = matrix(1:1000, byrow = TRUE, nr = 100)
2325 2431 
 # anno = anno_mark(at = c(1:4, 20, 60, 97:100), labels = month.name[1:10], which = "row")
2326 
-# Heatmap(m, cluster_rows = F, cluster_columns = F) + rowAnnotation(mark = anno)
2432 
+# Heatmap(m, cluster_rows = FALSE, cluster_columns = FALSE) + rowAnnotation(mark = anno)
2327 2433 
 # Heatmap(m) + rowAnnotation(mark = anno)
2328 2434 
 anno_mark = function(at, labels, which = c("column", "row"),
2329 2435 
 	side = ifelse(which == "column", "top", "right"),
... ... 
@@ -2495,6 +2601,9 @@ anno_link = function(...) {
2495 2601 
 # See help page of `anno_link`
2496 2602 
 #
2497 2603 
 row_anno_link = function(...) {
2604 
+	if(exists(".__under_SingleAnnotation__", envir = parent.frame())) {
2605 
+		message("From this version of ComplexHeatmap, you can directly use `anno_mark()` for row annotation if you call it in `rowAnnotation()`.")
2606 
+	}
2498 2607 
 	anno_link(..., which = "row")
2499 2608 
 }
2500 2609
R/ColorMapping-class.R
History View file @ad35494
... ... 
@@ -7,7 +7,7 @@
7 7 
 # Class for Mapping Values to Colors
8 8 
 #
9 9 
 # == details
10 
-# The `ColorMapping-class` handles color mapping with both discrete values and continuous values.
10 
+# The `ColorMapping-class` handles color mapping for discrete values and continuous values.
11 11 
 # Discrete values are mapped by setting a vector of colors and continuous values are mapped by setting
12 12 
 # a color mapping function.
13 13 
 #
... ... 
@@ -16,7 +16,7 @@
16 16 
 #
17 17 
 # - `ColorMapping`: contructor methods.
18 18 
 # - `map_to_colors,ColorMapping-method`: mapping values to colors.
19 
-# - `color_mapping_legend,ColorMapping-method`: draw legend or get legend as a `grid::grob` object.
19 
+# - `color_mapping_legend,ColorMapping-method`: draw legend or get legend as an object.
20 20 
 #
21 21 
 # == author
22 22 
 # Zuguang Gu <z.gu@dkfz.de>
... ... 
@@ -42,7 +42,7 @@ ColorMapping = setClass("ColorMapping",
42 42 
 #         ``levels`` can be ignored.
43 43 
 # -col_fun Color mapping function that maps continuous values to colors.
44 44 
 # -breaks Breaks for the continuous color mapping. If ``col_fun`` is
45 
-#         generated by `circlize::colorRamp2`, ``breaks`` can be ignored.
45 
+#         generated by `circlize::colorRamp2`, ``breaks`` is automatically inferred from the color mapping function.
46 46 
 # -na_col Colors for ``NA`` values.
47 47 
 #
48 48 
 # == detail
... ... 
@@ -55,6 +55,12 @@ ColorMapping = setClass("ColorMapping",
55 55 
 # == author
56 56 
 # Zuguang Gu <z.gu@dkfz.de>
57 57 
 #
58 
+# == examples
59 
+# cm = ColorMapping(colors = c("A" = "red", "B" = "black"))
60 
+# cm
61 
+# require(circlize)
62 
+# col_fun = colorRamp2(c(0, 1), c("white", "red"))
63 
+# cm = ColorMapping(col_fun = col_fun)
58 64 
 ColorMapping = function(name, colors = NULL, levels = NULL,
59 65 
 	col_fun = NULL, breaks = NULL, na_col = "#FFFFFF") {
60 66
... ... 
@@ -168,12 +174,21 @@ setMethod(f = "show",
168 174 
 # == details
169 175 
 # It maps a vector of values to a vector of colors.
170 176 
 #
177 
+# This function provides a uniform way for discrete and continuous color mapping.
178 
+#
171 179 
 # == value
172 180 
 # A vector of colors.
173 181 
 #
174 182 
 # == author
175 183 
 # Zuguang Gu <z.gu@dkfz.de>
176 184 
 #
185 
+# == example
186 
+# cm = ColorMapping(colors = c("A" = "red", "B" = "black"))
187 
+# map_to_colors(cm, sample(c("A", "B"), 10, replace = TRUE))
188 
+# require(circlize)
189 
+# col_fun = colorRamp2(c(0, 1), c("white", "red"))
190 
+# cm = ColorMapping(col_fun = col_fun)
191 
+# map_to_colors(cm, runif(10))
177 192 
 setMethod(f = "map_to_colors",
178 193 
 	signature = "ColorMapping",
179 194 
 	definition = function(object, x) {
... ... 
@@ -211,56 +226,60 @@ setMethod(f = "map_to_colors",
211 226 
 #
212 227 
 # == param
213 228 
 # -object A `ColorMapping-class` object.
214 
-# -plot Whether to plot or just return legend object?
215 
-# -title Title of the legend, by default it is the name of the legend
216 
-# -title_gp Traphical parameters for legend title
217 
-# -title_position Position of the title
218 
-# -color_bar A string of "continous" or "discrete". If the mapping is continuous, whether show the legend as discrete color bar or continuous color bar
219 
-# -grid_height Height of each legend grid.
220 
-# -grid_width Width of each legend grid.
221 
-# -border Color for legend grid borders.
222 
-# -at Break values of the legend
223 
-# -labels Labels corresponding to break values
224 
-# -labels_gp Graphcial parameters for legend labels
225 
-# -nrow If there are too many legend grids, they can be put as an array, this controls number of rows
226 
-# -ncol If there are too many legend grids, they can be put as an array, this controls number of columns
227 
-# -by_row When there are multiple columns for legends, whether to arrange them by rows.
228 
-# -legend_height Height of the legend, only works when ``color_bar`` is ``continuous`` and ``direction`` is ``vertical``
229 
-# -legend_width Width of the legend, only works when ``color_bar`` is ``continuous`` and ``direction`` is ``horizontal``
230 
-# -legend_direction When ``color_bar`` is ``continuous``, should the legend be vertical or horizontal? When ``color_bar`` is ``discrete``, should the items in the legend proceed vertically or horizontally?
231 
-# -param will be parsed if the parameters are specified as a list
232 
-# -... pass to `grid::viewport`.
229 
+# -plot Whether to plot or just return the legend object?
230 
+# -... Pass to `draw,Legends-method`.
231 
+# -color_bar "continous" or "discrete". It controls whether to show the discrete legend for the continuous color mapping.
232 
+# -title Title of the legend, by default it is the name of the legend.
233 
+# -title_gp Graphical parameters for legend title.
234 
+# -title_position Position of the title. See `Legend` for all possible values.
235 
+# -grid_height Height of each legend grid. Pass to `Legend`.
236 
+# -grid_width Width of each legend grid. Pass to `Legend`.
237 
+# -border Color for legend grid borders. Pass to `Legend`.
238 
+# -at Break values of the legend. By default it is the levels in the `ColorMapping-class` object.
239 
+# -labels Labels corresponding to break values.
240 
+# -labels_gp Graphcial parameters for legend labels.
241 
+# -labels_rot Rotation of labels.
242 
+# -nrow Pass to `Legend`. It controls the layout of legend grids if they are arranged in multiple rows or columns.
243 
+# -ncol Pass to `Legend`. It controls the layout of legend grids if they are arranged in multiple rows or columns.
244 
+# -by_row Pass to `Legend`. It controls the order of legend grids if they are arranged in multiple rows or columns.
245 
+# -legend_height Height of the legend body. It only works when ``color_bar`` is ``continuous`` and ``direction`` is ``vertical``. Pass to `Legend`.
246 
+# -legend_width Width of the legend body. It only works when ``color_bar`` is ``continuous`` and ``direction`` is ``horizontal``. Pass to `Legend`.
247 
+# -legend_direction When ``color_bar`` is ``continuous``, whether the legend is vertical or horizontal? Pass to `Legend`.
248 
+# -param All the legend-related parameters can be specified as a single list.
233 249 
 #
234 250 
 # == details
235 
-# A viewport is created which contains a legend title, legend grids and corresponding labels.
236 
-#
237 
-# This function will be improved in the future to support more types of legends.
251 
+# The legend is constructed by `Legend`.
238 252 
 #
239 253 
 # == value
240 
-# A `grid::grob` object which contains the legend
254 
+# A `Legends-class` object.
241 255 
 #
242 256 
 # == author
243 257 
 # Zuguang Gu <z.gu@dkfz.de>
244 258 
 #
245 259 
 setMethod(f = "color_mapping_legend",
246 260 
 	signature = "ColorMapping",
247 
-	definition = function(object, ...,
248 
-	plot = TRUE,
261 
+	definition = function(object,
262 
+	plot = TRUE, ...,
263 
+
264 
+	color_bar = object@type,
265 
+
249 266 
 	title = object@name,
250 267 
 	title_gp = gpar(fontsize = 10, fontface = "bold"),
251 268 
 	title_position = "topleft",
252 
-	color_bar = object@type,
253 269 
 	grid_height = unit(4, "mm"),
254 270 
 	grid_width = unit(4, "mm"),
255 271 
 	border = NULL,
256 272 
 	at = object@levels,
257 273 
 	labels = at,
258 274 
 	labels_gp = gpar(fontsize = 10),
275 
+	labels_rot = 0,
259 276 
 	nrow = NULL,
260 277 
 	ncol = 1,
261 278 
 	by_row = FALSE,
262 
-	legend_height = NULL, legend_width = NULL,
279 
+	legend_height = NULL,
280 
+	legend_width = NULL,
263 281 
 	legend_direction = c("vertical", "horizontal"),
282 
+
264 283 
 	param = NULL) {
265 284
266 285 
 	e = environment()
... ... 
@@ -273,8 +292,6 @@ setMethod(f = "color_mapping_legend",
273 292 
 	title_gp = check_gp(title_gp)
274 293 
 	labels_gp = check_gp(labels_gp)
275 294
276 
-	# color_bar = match.arg(color_bar)
277 
-
278 295 
 	if(object@type == "discrete" && color_bar == "continuous") {
279 296 
 		stop("'color_bar' can only be set to 'discrete' only if the color mapping is discrete")
280 297 
 	}
... ... 
@@ -302,17 +319,14 @@ setMethod(f = "color_mapping_legend",
302 319 
 	} else {
303 320
304 321 
 		gf = Legend(at = at, labels = labels, col_fun = object@col_fun, title = title, title_gp = title_gp, grid_height = grid_height,
305 
-			grid_width = grid_width, border = border, labels_gp = labels_gp, direction = legend_direction,
322 
+			grid_width = grid_width, border = border, labels_gp = labels_gp, labels_rot = labels_rot, direction = legend_direction,
306 323 
 			legend_width = legend_width, legend_height = legend_height, title_position = title_position, by_row = by_row)
307 324
308 325 
 	}
309 326
310 327 
 	if(plot) {
311 
-		pushViewport(viewport(..., width = grobWidth(gf), height = grobHeight(gf), name = paste0("legend_", object@name)))
312 
-		grid.draw(gf)
313 
-		popViewport()
328 
+		draw(gf, ...)
314 329 
 	}
315 330
316 
-	#size = unit.c(vp_width, vp_height)
317 331 
 	return(invisible(gf))
318 332 
 })
R/Heatmap-class.R
History View file @ad35494
... ... 
@@ -125,11 +125,12 @@ Heatmap = setClass("Heatmap",
125 125 
 # -rect_gp graphic parameters for drawing rectangles (for heatmap body).
126 126 
 # -color_space the color space in which colors are interpolated. Only used if ``matrix`` is numeric and
127 127 
 #            ``col`` is a vector of colors. Pass to `circlize::colorRamp2`.
128 
-# -border
128 
+# -border border
129 129 
 # -cell_fun self-defined function to add graphics on each cell. Seven parameters will be passed into
130 130 
 #           this function: ``i``, ``j``, ``x``, ``y``, ``width``, ``height``, ``fill`` which are row index,
131 131 
 #           column index in ``matrix``, coordinate of the middle points in the heatmap body viewport,
132 132 
 #           the width and height of the cell and the filled color. ``x``, ``y``, ``width`` and ``height`` are all `grid::unit` objects.
133 
+# -layer_fun layer fun
133 134 
 # -row_title title on row.
134 135 
 # -row_title_side will the title be put on the left or right of the heatmap?
135 136 
 # -row_title_gp graphic parameters for drawing text.
... ... 
@@ -157,7 +158,6 @@ Heatmap = setClass("Heatmap",
157 158 
 #                object with edges rendered, this argument will be ignored.
158 159 
 # -row_dend_reorder apply reordering on rows. The value can be a logical value or a vector which contains weight
159 160 
 #               which is used to reorder rows
160 
-# -row_dend_gp
161 161 
 # -cluster_columns whether make cluster on columns. Same settings as ``cluster_rows``.
162 162 
 # -clustering_distance_columns same setting as ``clustering_distance_rows``.
163 163 
 # -clustering_method_columns method to make cluster, pass to `stats::hclust`.
... ... 
@@ -167,43 +167,42 @@ Heatmap = setClass("Heatmap",
167 167 
 # -column_dend_gp graphic parameters for drawling lines. Same settings as ``row_dend_gp``.
168 168 
 # -column_dend_reorder apply reordering on columns. The value can be a logical value or a vector which contains weight
169 169 
 #               which is used to reorder columns
170 
-# -column_dend_gp
171 170 
 # -row_order order of rows. It makes it easy to adjust row order for a list of heatmaps if this heatmap
172 171 
 #      is selected as the main heatmap. Manually setting row order should turn off clustering
173 172 
 # -column_order order of column. It makes it easy to adjust column order for both matrix and column annotations.
174 
-# -row_labels
173