Browse code

vignette check passed

Zuguang Gu authored on 20/09/2018 22:09:48
Showing135 changed files

... ...
@@ -28,6 +28,14 @@ S3method("height<-", "HeatmapAnnotation")
28 28
 export("height<-.HeatmapAnnotation")
29 29
 S3method("height<-", "SingleAnnotation")
30 30
 export("height<-.SingleAnnotation")
31
+S3method("heightDetails", "annotation_axis")
32
+export("heightDetails.annotation_axis")
33
+S3method("heightDetails", "legend")
34
+export("heightDetails.legend")
35
+S3method("heightDetails", "legend_body")
36
+export("heightDetails.legend_body")
37
+S3method("heightDetails", "packed_legends")
38
+export("heightDetails.packed_legends")
31 39
 S3method("length", "HeatmapAnnotation")
32 40
 export("length.HeatmapAnnotation")
33 41
 S3method("merge", "dendrogram")
... ...
@@ -74,6 +82,14 @@ S3method("width<-", "HeatmapAnnotation")
74 82
 export("width<-.HeatmapAnnotation")
75 83
 S3method("width<-", "SingleAnnotation")
76 84
 export("width<-.SingleAnnotation")
85
+S3method("widthDetails", "annotation_axis")
86
+export("widthDetails.annotation_axis")
87
+S3method("widthDetails", "legend")
88
+export("widthDetails.legend")
89
+S3method("widthDetails", "legend_body")
90
+export("widthDetails.legend_body")
91
+S3method("widthDetails", "packed_legends")
92
+export("widthDetails.packed_legends")
77 93
 export("%v%")
78 94
 export("AdditiveUnit")
79 95
 export("AnnotationFunction")
... ...
@@ -373,7 +373,6 @@ size.HeatmapAnnotation = function(x, ...) {
373 373
 }
374 374
 
375 375
 
376
-
377 376
 # == title
378 377
 # Width of the Legends
379 378
 #
... ...
@@ -385,9 +384,11 @@ size.HeatmapAnnotation = function(x, ...) {
385 384
 # The returned unit x is in ``mm``.
386 385
 #
387 386
 width.Legends = function(x, ...) {
388
-	attr(x@grob, "width")
387
+	s = attr(x@grob, "width")
388
+	s
389 389
 }
390 390
 
391
+
391 392
 # == title
392 393
 # Height of the Legends
393 394
 #
... ...
@@ -399,6 +400,7 @@ width.Legends = function(x, ...) {
399 400
 # The returned unit x is in ``mm``.
400 401
 #
401 402
 height.Legends = function(x, ...) {
402
-	attr(x@grob, "height")
403
+	s = attr(x@grob, "height")
404
+	s
403 405
 }
404 406
 
... ...
@@ -2607,3 +2607,24 @@ row_anno_link = function(...) {
2607 2607
 	anno_link(..., which = "row")
2608 2608
 }
2609 2609
 
2610
+anno_summarize = function(which = c("column", "row"),
2611
+	width = NULL, height = NULL, border = FALSE, ...) {
2612
+
2613
+	if(is.null(.ENV$current_annotation_which)) {
2614
+		which = match.arg(which)[1]
2615
+	} else {
2616
+		which = .ENV$current_annotation_which
2617
+	}
2618
+
2619
+	if(which == "column") {
2620
+		stop("`anno_summarize()` is only allowed as a column annotation.")
2621
+	}
2622
+
2623
+	anno_size = anno_width_and_height(which, width, height, unit(2, "cm"))
2624
+
2625
+	# get variables fron oncoPrint() function
2626
+	pf = parent.frame()
2627
+	# find where the heatmap object is.
2628
+	
2629
+}
2630
+
... ...
@@ -123,7 +123,7 @@ HeatmapAnnotation = function(...,
123 123
 	sc = sys.calls()
124 124
 	for(i in seq_along(sc)) {
125 125
 		scl = as.list(sc[[i]])
126
-		if(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation")) {
126
+		if(any(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation"))) {
127 127
 			arg_list = scl[-1]
128 128
 			break
129 129
 		}
... ...
@@ -309,7 +309,7 @@ HeatmapAnnotation = function(...,
309 309
 	if(!missing(col)) {
310 310
 		unused_col_name = setdiff(names(col), col_name_defined)
311 311
 		if(length(unused_col_name)) {
312
-			warning(paste0("Following are defined in `col` while have no corresponding annotations:\n", paste(unused_col_name, collapse = ", ")))
312
+			# warning(paste0("Following are defined in `col` while have no corresponding annotations:\n", paste(unused_col_name, collapse = ", ")))
313 313
 		}
314 314
 	}
315 315
 
... ...
@@ -120,10 +120,23 @@ annotation_axis_grob = function(at = NULL, labels = at, labels_rot = 0, gp = gpa
120 120
 	return(gb)
121 121
 }
122 122
 
123
+
124
+# == title
125
+# Grob width for annotation_axis
126
+#
127
+# == param
128
+# -x legend body
129
+#
123 130
 widthDetails.annotation_axis = function(x) {
124 131
 	attr(x, "width")
125 132
 }
126 133
 
134
+# == title
135
+# Grob width for annotation_axis
136
+#
137
+# == param
138
+# -x legend body
139
+#
127 140
 heightDetails.annotation_axis = function(x) {
128 141
 	attr(x, "height")
129 142
 }
... ...
@@ -4,7 +4,6 @@
4 4
 #
5 5
 # == details
6 6
 # This is a very simple class for legends that it only has one slot which is the real `grid::grob` of the legends.
7
-# The design of the ``Legends`` class is to support more helper functions such as `width.Legends` to get 
8 7
 # more information of the legends grob.
9 8
 # 
10 9
 # == example
... ...
@@ -218,7 +217,7 @@ Legend = function(at, labels = at, col_fun, nrow = NULL, ncol = 1, by_row = FALS
218 217
 			textGrob(title, x = title_x, y = unit(1, "npc"), just = title_just, gp = title_gp),
219 218
 			edit_vp_in_legend_grob(legend_body, x = unit(0, "npc"), y = unit(0, "npc"), valid.just = c(0, 0)),
220 219
 			vp = viewport(width = total_width, height = total_height),
221
-			cl = "Legend"
220
+			cl = "legend"
222 221
 		)
223 222
 		attr(gf, "width") = total_width
224 223
 		attr(gf, "height") = total_height
... ...
@@ -273,7 +272,7 @@ Legend = function(at, labels = at, col_fun, nrow = NULL, ncol = 1, by_row = FALS
273 272
 			edit_vp_in_legend_grob(legend_body, x = unit(1, "npc"), y = unit(1, "npc"), 
274 273
 				valid.just = c(1, 1)),
275 274
 			vp = viewport(width = total_width, height = total_height),
276
-			cl = "Legend"
275
+			cl = "legend"
277 276
 		)
278 277
 		attr(gf, "width") = total_width
279 278
 		attr(gf, "height") = total_height
... ...
@@ -761,6 +760,10 @@ packLegend = function(..., gap = unit(2, "mm"), direction = c("vertical", "horiz
761 760
 	} else {
762 761
 		legend_list = list(...)
763 762
 	}
763
+	if(length(legend_list) == 1) {
764
+		return(legend_list[[1]])
765
+	}
766
+
764 767
 	legend_list = lapply(legend_list, function(x) {
765 768
 		lgd = x@grob
766 769
 		lgd$name = legend_grob_name()
... ...
@@ -809,7 +812,6 @@ packLegend = function(..., gap = unit(2, "mm"), direction = c("vertical", "horiz
809 812
 
810 813
     	## pack_width is the width for each column
811 814
     	## pack_height is the total height of the packed legends
812
-
813 815
     	gl = list()
814 816
     	for(i in 1:nc) {
815 817
     		ind = ind_list[[i]]
... ...
@@ -1036,22 +1038,67 @@ grid.draw.Legends = function(x, recording = TRUE) {
1036 1038
 	grid.draw(x@grob, recording =  recording)
1037 1039
 }
1038 1040
 
1041
+# == title
1042
+# Grob width for legend_body
1043
+#
1044
+# == param
1045
+# -x legend body
1046
+#
1039 1047
 widthDetails.legend_body = function(x) {
1040 1048
 	attr(x, "width")
1041 1049
 }
1042 1050
 
1051
+# == title
1052
+# Grob height for legend_body
1053
+#
1054
+# == param
1055
+# -x legend body
1056
+#
1043 1057
 heightDetails.legend_body = function(x) {
1044 1058
 	attr(x, "height")
1045 1059
 }
1046 1060
 
1061
+# == title
1062
+# Grob width for packed_legends
1063
+#
1064
+# == param
1065
+# -x legend body
1066
+#
1067
+widthDetails.legend = function(x) {
1068
+	attr(x, "width")
1069
+}
1070
+
1071
+# == title
1072
+# Grob height for packed_legends
1073
+#
1074
+# == param
1075
+# -x legend body
1076
+#
1077
+heightDetails.legend = function(x) {
1078
+	attr(x, "height")
1079
+}
1080
+
1081
+# == title
1082
+# Grob width for packed_legends
1083
+#
1084
+# == param
1085
+# -x legend body
1086
+#
1047 1087
 widthDetails.packed_legends = function(x) {
1048 1088
 	attr(x, "width")
1049 1089
 }
1050 1090
 
1091
+# == title
1092
+# Grob height for packed_legends
1093
+#
1094
+# == param
1095
+# -x legend body
1096
+#
1051 1097
 heightDetails.packed_legends = function(x) {
1052 1098
 	attr(x, "height")
1053 1099
 }
1054 1100
 
1101
+
1055 1102
 # assume x is ordered
1056 1103
 is_diff_equal = function(x) {
1057 1104
 	all(abs(diff(diff(x)))/mean(diff(x)) < 1e-4)
1058 1105
deleted file mode 100644
1059 1106
deleted file mode 100755
... ...
@@ -1,3 +0,0 @@
1
-[Dolphin]
2
-Timestamp=2016,3,17,15,14,24
3
-ViewMode=1
... ...
@@ -14,4 +14,5 @@ It is only designed for \code{+} generic method so that above three classes can
14 14
 \examples{
15 15
 # There is no example
16 16
 NULL
17
+
17 18
 }
... ...
@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -21,4 +21,5 @@ See \code{\link{AnnotationFunction}} constructor for details.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -105,4 +105,5 @@ are all subsettable.
105 105
 \examples{
106 106
 # There is no example
107 107
 NULL
108
+
108 109
 }
... ...
@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -36,4 +36,5 @@ The vignette provides detailed explanation of how to use this package.
36 36
 \examples{
37 37
 # There is no example
38 38
 NULL
39
+
39 40
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{[.AnnotationFunction}
2 2
 \alias{[.AnnotationFunction}
3
+\alias{Extract.AnnotationFunction}
3 4
 \title{
4 5
 Subset an AnnotationFunction Object
5 6
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{[.Heatmap}
2 2
 \alias{[.Heatmap}
3
+\alias{Extract.Heatmap}
3 4
 \title{
4 5
 Subset a Heatmap
5 6
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{[.HeatmapAnnotation}
2 2
 \alias{[.HeatmapAnnotation}
3
+\alias{Extract.HeatmapAnnotation}
3 4
 \title{
4 5
 Subset the HeatmapAnnotation object
5 6
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{[.SingleAnnotation}
2 2
 \alias{[.SingleAnnotation}
3
+\alias{Extract.SingleAnnotation}
3 4
 \title{
4 5
 Subset an SingleAnnotation Object
5 6
 }
... ...
@@ -71,4 +71,5 @@ Zuguang Gu <z.gu@dkfz.de>
71 71
 \examples{
72 72
 # There is no example
73 73
 NULL
74
+
74 75
 }
... ...
@@ -186,4 +186,5 @@ Zuguang Gu <z.gu@dkfz.de>
186 186
 \examples{
187 187
 # There is no example
188 188
 NULL
189
+
189 190
 }
... ...
@@ -25,4 +25,5 @@ Zuguang Gu <z.gu@dkfz.de>
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -66,4 +66,5 @@ Zuguang Gu <z.gu@dkfz.de>
66 66
 \examples{
67 67
 # There is no example
68 68
 NULL
69
+
69 70
 }
... ...
@@ -67,4 +67,5 @@ Zuguang Gu <z.gu@dkfz.de>
67 67
 \examples{
68 68
 # There is no example
69 69
 NULL
70
+
70 71
 }
... ...
@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -9,7 +9,6 @@ The Class for Legends
9 9
 }
10 10
 \details{
11 11
 This is a very simple class for legends that it only has one slot which is the real \code{\link[grid]{grob}} of the legends.
12
-The design of the \code{Legends} class is to support more helper functions such as \code{\link{width.Legends}} to get 
13 12
 more information of the legends grob.
14 13
 }
15 14
 \examples{
... ...
@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{+.AdditiveUnit}
2 2
 \alias{+.AdditiveUnit}
3
+\alias{add.AdditiveUnit}
3 4
 \title{
4 5
 Horizontally Add Heatmaps or Annotations to a Heatmap List
5 6
 }
... ...
@@ -25,7 +26,7 @@ The \code{\link{HeatmapAnnotation-class}} object to be added should only be row
25 26
 A \code{\link{HeatmapList-class}} object.
26 27
 }
27 28
 \seealso{
28
-\code{\link{\%v\%}} operator is used for vertical heatmap list.
29
+\code{\link[=pct_v_pct]{\%v\%}} operator is used for vertical heatmap list.
29 30
 }
30 31
 \author{
31 32
 Zuguang Gu <z.gu@dkfz.de>
... ...
@@ -33,4 +34,5 @@ Zuguang Gu <z.gu@dkfz.de>
33 34
 \examples{
34 35
 # There is no example
35 36
 NULL
37
+
36 38
 }
... ...
@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -17,7 +17,7 @@ Add row annotations or heatmaps as a heatmap list
17 17
 
18 18
 }
19 19
 \details{
20
-There is a helper function \code{+.AdditiveUnit} for horizontal add or \code{\link{\%v\%}} for vertical add.
20
+There is a helper function \code{+.AdditiveUnit} for horizontal add or \code{\link[=pct_v_pct]{\%v\%}} for vertical add.
21 21
 }
22 22
 \value{
23 23
 A \code{\link{HeatmapList-class}} object.
... ...
@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -28,4 +28,5 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{adjust_heatmap_list-HeatmapList-method}
2 2
 \alias{adjust_heatmap_list,HeatmapList-method}
3
+\alias{adjust_heatmap_list}
3 4
 \title{
4 5
 Adjust heatmap list
5 6
 }
... ...
@@ -14,8 +15,8 @@ Adjust heatmap list
14 15
   \item{object}{A \code{\link{HeatmapList-class}} object}
15 16
 
16 17
 }
17
-\alias{adjust_heatmap_list}
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -20,4 +20,5 @@ anno_link(...)
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
+
23 24
 }
... ...
@@ -26,4 +26,5 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
+
29 30
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{annotation_legend_size-HeatmapList-method}
2 2
 \alias{annotation_legend_size,HeatmapList-method}
3
+\alias{annotation_legend_size}
3 4
 \title{
4 5
 Size of the annotation legend viewport
5 6
 }
... ...
@@ -28,8 +29,8 @@ A \code{\link[grid]{unit}} object.
28 29
 \author{
29 30
 Zuguang Gu <z.gu@dkfz.de>
30 31
 }
31
-\alias{annotation_legend_size}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{color_mapping_legend-ColorMapping-method}
2 2
 \alias{color_mapping_legend,ColorMapping-method}
3
+\alias{color_mapping_legend}
3 4
 \title{
4 5
 Draw Legend Based on Color Mapping
5 6
 }
... ...
@@ -65,8 +66,8 @@ A \code{\link{Legends-class}} object.
65 66
 \author{
66 67
 Zuguang Gu <z.gu@dkfz.de>
67 68
 }
68
-\alias{color_mapping_legend}
69 69
 \examples{
70 70
 # There is no example
71 71
 NULL
72
+
72 73
 }
... ...
@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -31,4 +31,5 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -24,4 +24,5 @@ Zuguang Gu <z.gu@dkfz.de>
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
+
27 28
 }
... ...
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
+
33 34
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -24,4 +24,5 @@ The environment is at \code{object@var_env}.
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
+
27 28
 }
... ...
@@ -21,4 +21,5 @@ it calls \code{\link{copy_all,AnnotationFunction-method}} to hard copy the varia
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -17,4 +17,5 @@ dend_heights(x)
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -28,4 +28,5 @@ A \code{\link{grob}} object which is generally contructed by \code{\link[grid]{s
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
+
31 32
 }
... ...
@@ -17,4 +17,5 @@ Dimension of the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -27,4 +27,5 @@ which is generally for testing purpose.
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -33,4 +33,5 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
+
36 37
 }
... ...
@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -164,4 +164,5 @@ Zuguang Gu <z.gu@dkfz.de>
164 164
 \examples{
165 165
 # There is no example
166 166
 NULL
167
+
167 168
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_annotation-Heatmap-method}
2 2
 \alias{draw_annotation,Heatmap-method}
3
+\alias{draw_annotation}
3 4
 \title{
4 5
 Draw Heatmap Annotations on the Heatmap
5 6
 }
... ...
@@ -30,8 +31,8 @@ This function returns no value.
30 31
 \author{
31 32
 Zuguang Gu <z.gu@dkfz.de>
32 33
 }
33
-\alias{draw_annotation}
34 34
 \examples{
35 35
 # There is no example
36 36
 NULL
37
+
37 38
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_annotation_legend-HeatmapList-method}
2 2
 \alias{draw_annotation_legend,HeatmapList-method}
3
+\alias{draw_annotation_legend}
3 4
 \title{
4 5
 Draw legends for all column annotations
5 6
 }
... ...
@@ -27,8 +28,8 @@ This function returns no value.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{draw_annotation_legend}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_dend-Heatmap-method}
2 2
 \alias{draw_dend,Heatmap-method}
3
+\alias{draw_dend}
3 4
 \title{
4 5
 Draw Heatmap Dendrograms
5 6
 }
... ...
@@ -33,8 +34,8 @@ This function returns no value.
33 34
 \author{
34 35
 Zuguang Gu <z.gu@dkfz.de>
35 36
 }
36
-\alias{draw_dend}
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
+
40 41
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_dimnames-Heatmap-method}
2 2
 \alias{draw_dimnames,Heatmap-method}
3
+\alias{draw_dimnames}
3 4
 \title{
4 5
 Draw row names or column names
5 6
 }
... ...
@@ -29,8 +30,8 @@ This function returns no value.
29 30
 \author{
30 31
 Zuguang Gu <z.gu@dkfz.de>
31 32
 }
32
-\alias{draw_dimnames}
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
+
36 37
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_heatmap_body-Heatmap-method}
2 2
 \alias{draw_heatmap_body,Heatmap-method}
3
+\alias{draw_heatmap_body}
3 4
 \title{
4 5
 Draw the heatmap body
5 6
 }
... ...
@@ -28,8 +29,8 @@ This function returns no value.
28 29
 \author{
29 30
 Zuguang Gu <z.gu@dkfz.de>
30 31
 }
31
-\alias{draw_heatmap_body}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_heatmap_legend-HeatmapList-method}
2 2
 \alias{draw_heatmap_legend,HeatmapList-method}
3
+\alias{draw_heatmap_legend}
3 4
 \title{
4 5
 Draw legends for all heatmaps
5 6
 }
... ...
@@ -27,8 +28,8 @@ This function returns no value.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{draw_heatmap_legend}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{draw_heatmap_list-HeatmapList-method}
2 2
 \alias{draw_heatmap_list,HeatmapList-method}
3
+\alias{draw_heatmap_list}
3 4
 \title{
4 5
 Draw the list of heatmaps
5 6
 }
... ...
@@ -25,8 +26,8 @@ This function returns no value.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{draw_heatmap_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -32,4 +32,5 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -30,4 +30,5 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
+
33 34
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{get_color_mapping_list-HeatmapAnnotation-method}
2 2
 \alias{get_color_mapping_list,HeatmapAnnotation-method}
3
+\alias{get_color_mapping_list}
3 4
 \title{
4 5
 Get a List of ColorMapping objects
5 6
 }
... ...
@@ -25,8 +26,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{get_color_mapping_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{get_legend_param_list-HeatmapAnnotation-method}
2 2
 \alias{get_legend_param_list,HeatmapAnnotation-method}
3
+\alias{get_legend_param_list}
3 4
 \title{
4 5
 Get a List of Annotation Legend Parameters
5 6
 }
... ...
@@ -25,8 +26,8 @@ A list.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{get_legend_param_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -22,4 +22,5 @@ general method. It applies \code{\link[grid]{grid.draw}} on the \code{grob} slot
22 22
 \examples{
23 23
 # There is no example
24 24
 NULL
25
+
25 26
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{heatmap_legend_size-HeatmapList-method}
2 2
 \alias{heatmap_legend_size,HeatmapList-method}
3
+\alias{heatmap_legend_size}
3 4
 \title{
4 5
 Size of the heatmap legend viewport
5 6
 }
... ...
@@ -25,8 +26,8 @@ A \code{\link[grid]{unit}} object.
25 26
 \author{
26 27
 Zuguang Gu <z.gu@dkfz.de>
27 28
 }
28
-\alias{heatmap_legend_size}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -18,4 +18,5 @@ Height of the HeatmapAnnotation x
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ The returned unit x is in \code{mm}.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ Height of the SingleAnnotation x
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ height(x, ...)
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{height<-.AnnotationFunction}
2 2
 \alias{height<-.AnnotationFunction}
3
+\alias{heightAssign.AnnotationFunction}
3 4
 \title{
4 5
 Assign the Height to the AnnotationFunction x
5 6
 }
... ...
@@ -19,4 +20,5 @@ Assign the Height to the AnnotationFunction x
19 20
 \examples{
20 21
 # There is no example
21 22
 NULL
23
+
22 24
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{height<-.HeatmapAnnotation}
2 2
 \alias{height<-.HeatmapAnnotation}
3
+\alias{heightAssign.HeatmapAnnotation}
3 4
 \title{
4 5
 Assign the Height to the HeatmapAnnotation x
5 6
 }
... ...
@@ -19,4 +20,5 @@ Assign the Height to the HeatmapAnnotation x
19 20
 \examples{
20 21
 # There is no example
21 22
 NULL
23
+
22 24
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{height<-.SingleAnnotation}
2 2
 \alias{height<-.SingleAnnotation}
3
+\alias{heightAssign.SingleAnnotation}
3 4
 \title{
4 5
 Assign the Height to the SingleAnnotation x
5 6
 }
... ...
@@ -19,4 +20,5 @@ Assign the Height to the SingleAnnotation x
19 20
 \examples{
20 21
 # There is no example
21 22
 NULL
23
+
22 24
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{height<-}
2 2
 \alias{height<-}
3
+\alias{heightAssign}
3 4
 \title{
4 5
 Generic assignment method for height
5 6
 }
... ...
@@ -19,4 +20,5 @@ height(x, ...) <- value
19 20
 \examples{
20 21
 # There is no example
21 22
 NULL
23
+
22 24
 }
23 25
new file mode 100644
... ...
@@ -0,0 +1,21 @@
1
+\name{heightDetails.legend}
2
+\alias{heightDetails.legend}
3
+\title{
4
+Grob height for packed_legends
5
+}
6
+\description{
7
+Grob height for packed_legends
8
+}
9
+\usage{
10
+\method{heightDetails}{legend}(x)
11
+}
12
+\arguments{
13
+
14
+  \item{x}{legend body}
15
+
16
+}
17
+\examples{
18
+# There is no example
19
+NULL
20
+
21
+}
0 22
new file mode 100644
... ...
@@ -0,0 +1,21 @@
1
+\name{heightDetails.annotation_axis}
2
+\alias{heightDetails.annotation_axis}
3
+\title{
4
+Grob width for annotation_axis
5
+}
6
+\description{
7
+Grob width for annotation_axis
8
+}
9
+\usage{
10
+\method{heightDetails}{annotation_axis}(x)
11
+}
12
+\arguments{
13
+
14
+  \item{x}{legend body}
15
+
16
+}
17
+\examples{
18
+# There is no example
19
+NULL
20
+
21
+}
0 22
new file mode 100644
... ...
@@ -0,0 +1,21 @@
1
+\name{heightDetails.legend_body}
2
+\alias{heightDetails.legend_body}
3
+\title{
4
+Grob height for legend_body
5
+}
6
+\description{
7
+Grob height for legend_body
8
+}
9
+\usage{
10
+\method{heightDetails}{legend_body}(x)
11
+}
12
+\arguments{
13
+
14
+  \item{x}{legend body}
15
+
16
+}
17
+\examples{
18
+# There is no example
19
+NULL
20
+
21
+}
0 22
new file mode 100644
... ...
@@ -0,0 +1,21 @@
1
+\name{heightDetails.packed_legends}
2
+\alias{heightDetails.packed_legends}
3
+\title{
4
+Grob height for packed_legends
5
+}
6
+\description{
7
+Grob height for packed_legends
8
+}
9
+\usage{
10
+\method{heightDetails}{packed_legends}(x)
11
+}
12
+\arguments{
13
+
14
+  \item{x}{legend body}
15
+
16
+}
17
+\examples{
18
+# There is no example
19
+NULL
20
+
21
+}
... ...
@@ -25,4 +25,5 @@ will also sychronized in \code{\link{ht_opt}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -17,4 +17,5 @@ Number of Annotations
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{make_column_cluster-Heatmap-method}
2 2
 \alias{make_column_cluster,Heatmap-method}
3
+\alias{make_column_cluster}
3 4
 \title{
4 5
 Make Cluster on Columns
5 6
 }
... ...
@@ -27,8 +28,8 @@ A \code{\link{Heatmap-class}} object.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{make_column_cluster}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -32,4 +32,5 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -125,4 +125,5 @@ Zuguang Gu <z.gu@dkfz.de>
125 125
 \examples{
126 126
 # There is no example
127 127
 NULL
128
+
128 129
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{make_row_cluster-Heatmap-method}
2 2
 \alias{make_row_cluster,Heatmap-method}
3
+\alias{make_row_cluster}
3 4
 \title{
4 5
 Make Cluster on Rows
5 6
 }
... ...
@@ -27,8 +28,8 @@ A \code{\link{Heatmap-class}} object.
27 28
 \author{
28 29
 Zuguang Gu <z.gu@dkfz.de>
29 30
 }
30
-\alias{make_row_cluster}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
+
34 35
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{map_to_colors-ColorMapping-method}
2 2
 \alias{map_to_colors,ColorMapping-method}
3
+\alias{map_to_colors}
3 4
 \title{
4 5
 Map Values to Colors
5 6
 }
... ...
@@ -34,4 +35,3 @@ col_fun = colorRamp2(c(0, 1), c("white", "red"))
34 35
 cm = ColorMapping(col_fun = col_fun)
35 36
 map_to_colors(cm, runif(10))
36 37
 }
37
-\alias{map_to_colors}
... ...
@@ -1,5 +1,6 @@
1 1
 \name{names<-.HeatmapAnnotation}
2 2
 \alias{names<-.HeatmapAnnotation}
3
+\alias{namesAssign.HeatmapAnnotation}
3 4
 \title{
4 5
 Assign Annotation Names
5 6
 }
... ...
@@ -17,4 +17,5 @@ Number of Columns in the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -18,4 +18,5 @@ Number of Observations
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ It returns the \code{n} slot of the annotaton function. If it does not exist, it
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -17,4 +17,5 @@ Number of Rows in the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -74,4 +74,5 @@ Zuguang Gu <z.gu@dkfz.de>
74 74
 \examples{
75 75
 # There is no example
76 76
 NULL
77
+
77 78
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{\%v\%}
2 2
 \alias{\%v\%}
3
+\alias{pct_v_pct}
3 4
 \title{
4 5
 Vertically Add Heatmaps or Annotations to a Heatmap List
5 6
 }
... ...
@@ -25,7 +26,7 @@ The \code{\link{HeatmapAnnotation-class}} object to be added should only be colu
25 26
 A \code{\link{HeatmapList-class}} object.
26 27
 }
27 28
 \seealso{
28
-\code{\link{+.AdditiveUnit}} operator is used for vertical heatmap list.
29
+\code{\link[=add.AdditiveUnit]{+.AdditiveUnit}} operator is used for vertical heatmap list.
29 30
 }
30 31
 \author{
31 32
 Zuguang Gu <z.gu@dkfz.de>
... ...
@@ -33,4 +34,5 @@ Zuguang Gu <z.gu@dkfz.de>
33 34
 \examples{
34 35
 # There is no example
35 36
 NULL
37
+
36 38
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{prepare-Heatmap-method}
2 2
 \alias{prepare,Heatmap-method}
3
+\alias{prepare}
3 4
 \title{
4 5
 Prepare the Heatmap
5 6
 }
... ...
@@ -33,8 +34,8 @@ The \code{\link{Heatmap-class}} object.
33 34
 \author{
34 35
 Zuguang Gu <z.gu@dkfz.de>
35 36
 }
36
-\alias{prepare}
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
+
40 41
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{resize-HeatmapAnnotation-method}
2 2
 \alias{resize,HeatmapAnnotation-method}
3
+\alias{resize}
3 4
 \title{
4 5
 Resize the Width or Height of Heatmap Annotations
5 6
 }
... ...
@@ -40,8 +41,8 @@ the basic rule is:
40 41
      and \code{anno_simple_row_size} is disabled.
41 42
 6. If \code{simple_anno_size_adjust} is \code{FALSE}, the size of the simple annotations will not change.
42 43
 }
43
-\alias{resize}
44 44
 \examples{
45 45
 # There is no example
46 46
 NULL
47
+
47 48
 }
... ...
@@ -29,4 +29,5 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
+
32 33
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_barplot}}
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_boxplot}}
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_density}}
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_histogram}}
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_link}}
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_points}}
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -25,4 +25,5 @@ See help page of \code{\link{anno_text}}
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
+
28 29
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{set_component_height-Heatmap-method}
2 2
 \alias{set_component_height,Heatmap-method}
3
+\alias{set_component_height}
3 4
 \title{
4 5
 Set Height of Heatmap Component
5 6
 }
... ...
@@ -29,8 +30,8 @@ The \code{\link{Heatmap-class}} object.
29 30
 \author{
30 31
 Zuguang Gu <z.gu@dkfz.de>
31 32
 }
32
-\alias{set_component_height}
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
+
36 37
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{set_component_width-Heatmap-method}
2 2
 \alias{set_component_width,Heatmap-method}
3
+\alias{set_component_width}
3 4
 \title{
4 5
 Set Width of Heatmap Component
5 6
 }
... ...
@@ -28,8 +29,8 @@ The \code{\link{Heatmap-class}} object.
28 29
 \author{
29 30
 Zuguang Gu <z.gu@dkfz.de>
30 31
 }
31
-\alias{set_component_width}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
+
35 36
 }
... ...
@@ -17,4 +17,5 @@ Print the AnnotationFunction object
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
+
20 21
 }
... ...
@@ -23,4 +23,5 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -23,4 +23,5 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -24,4 +24,5 @@ This function returns no value.
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
+
27 28
 }
... ...
@@ -23,4 +23,5 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
+
26 27
 }
... ...
@@ -21,4 +21,5 @@ It returns the width if it is a row annotation and the height if it is a column
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -21,4 +21,5 @@ It returns the width if it is a row annotation and the height if it is a column
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ size(x, ...)
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{size<-.AnnotationFunction}
2 2
 \alias{size<-.AnnotationFunction}
3
+\alias{sizeAssign.AnnotationFunction}
3 4
 \title{
4 5
 Assign the Size to the AnnotationFunction x
5 6
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{size<-.HeatmapAnnotation}
2 2
 \alias{size<-.HeatmapAnnotation}
3
+\alias{sizeAssign.HeatmapAnnotation}
3 4
 \title{
4 5
 Assign the Size to the HeatmapAnnotation x
5 6
 }
... ...
@@ -22,4 +23,5 @@ It assigns the width if it is a row annotation and the height if it is a column
22 23
 \examples{
23 24
 # There is no example
24 25
 NULL
26
+
25 27
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{size<-.SingleAnnotation}
2 2
 \alias{size<-.SingleAnnotation}
3
+\alias{sizeAssign.SingleAnnotation}
3 4
 \title{
4 5
 Assign the Size of the SingleAnnotation x
5 6
 }
... ...
@@ -22,4 +23,5 @@ It assigns the width if it is a row annotation and the height if it is a column
22 23
 \examples{
23 24
 # There is no example
24 25
 NULL
26
+
25 27
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{size<-}
2 2
 \alias{size<-}
3
+\alias{sizeAssign}
3 4
 \title{
4 5
 Generic assignment method for size
5 6
 }
... ...
@@ -19,4 +20,5 @@ size(x, ...) <- value
19 20
 \examples{
20 21
 # There is no example
21 22
 NULL
23
+
22 24
 }
... ...
@@ -18,4 +18,5 @@ subset_matrix_by_row(x, i)
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ subset_vector(x, i)
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ Print the Summary of a Heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -27,4 +27,5 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
+
30 31
 }
... ...
@@ -18,4 +18,5 @@ Width of the HeatmapAnnotation x
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -21,4 +21,5 @@ The returned unit x is in \code{mm}.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
+
24 25
 }
... ...
@@ -18,4 +18,5 @@ Width of the SingleAnnotation x
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -18,4 +18,5 @@ width(x, ...)
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
+
21 22
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{width<-.AnnotationFunction}
2 2
 \alias{width<-.AnnotationFunction}
3
+\alias{widthAssign.AnnotationFunction}
3 4
 \title{
4 5
 Assign the Width to the AnnotationFunction x
5 6
 }
... ...
@@ -19,4 +20,5 @@ Assign the Width to the AnnotationFunction x
19 20
 \examples{
20 21
 # There is no example
21 22
 NULL
23
+
22 24
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{width<-.HeatmapAnnotation}
2 2
 \alias{width<-.HeatmapAnnotation}
3
+\alias{widthAssign.HeatmapAnnotation}
3 4
 \title{
4 5
 Assign the Width to the HeatmapAnnotation x
5 6
 }
... ...
@@ -19,4 +20,5 @@ Assign the Width to the HeatmapAnnotation x
19 20
 \examples{
20 21
 # There is no example
21 22
 NULL
23
+
22 24
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{width<-.SingleAnnotation}
2 2
 \alias{width<-.SingleAnnotation}
3
+\alias{widthAssign.SingleAnnotation}
3 4
 \title{
4 5
 Assign the Width to the SingleAnnotation x
5 6
 }
... ...
@@ -19,4 +20,5 @@ Assign the Width to the SingleAnnotation x
19 20
 \examples{
20 21
 # There is no example
21 22
 NULL
23
+
22 24
 }
... ...
@@ -1,5 +1,6 @@
1 1
 \name{width<-}
2 2
 \alias{width<-}
3
+\alias{widthAssign}
3 4
 \title{
4 5
 Generic assignment method for width
5 6
 }
... ...
@@ -19,4 +20,5 @@ width(x, ...) <- value
19 20
 \examples{
20 21
 # There is no example
21 22
 NULL
23
+
22 24
 }
23 25
new file mode 100644
... ...
@@ -0,0 +1,21 @@
1
+\name{widthDetails.legend}
2
+\alias{widthDetails.legend}
3
+\title{
4
+Grob width for packed_legends
5
+}
6
+\description{
7
+Grob width for packed_legends
8
+}
9
+\usage{
10
+\method{widthDetails}{legend}(x)
11
+}
12
+\arguments{
13
+
14
+  \item{x}{legend body}
15
+
16
+}
17
+\examples{
18
+# There is no example
19
+NULL
20
+
21
+}
0 22
new file mode 100644
... ...
@@ -0,0 +1,21 @@
1
+\name{widthDetails.annotation_axis}
2
+\alias{widthDetails.annotation_axis}
3
+\title{
4
+Grob width for annotation_axis
5
+}
6
+\description{
7
+Grob width for annotation_axis
8
+}
9
+\usage{
10
+\method{widthDetails}{annotation_axis}(x)
11
+}
12
+\arguments{
13
+
14
+  \item{x}{legend body}
15
+
16
+}
17
+\examples{
18
+# There is no example
19
+NULL
20
+
21
+}
0 22
new file mode 100644
... ...
@@ -0,0 +1,21 @@
1
+\name{widthDetails.legend_body}
2
+\alias{widthDetails.legend_body}
3
+\title{
4
+Grob width for legend_body
5
+}
6
+\description{
7
+Grob width for legend_body
8
+}
9
+\usage{
10
+\method{widthDetails}{legend_body}(x)
11
+}
12
+\arguments{
13
+
14
+  \item{x}{legend body}
15
+
16
+}
17
+\examples{
18
+# There is no example
19
+NULL
20
+
21
+}
0 22
new file mode 100644
... ...
@@ -0,0 +1,21 @@
1
+\name{widthDetails.packed_legends}
2
+\alias{widthDetails.packed_legends}
3
+\title{
4
+Grob width for packed_legends
5
+}
6
+\description{
7
+Grob width for packed_legends
8
+}
9
+\usage{
10
+\method{widthDetails}{packed_legends}(x)
11
+}
12
+\arguments{
13
+
14
+  \item{x}{legend body}
15
+
16
+}
17
+\examples{
18
+# There is no example
19
+NULL
20
+
21
+}
0 22
new file mode 100755
... ...
@@ -0,0 +1,167 @@
1
+#toc {
2
+  position: fixed;
3
+  left: 0;
4
+  top: 20px;
5
+  width: 200px;
6
+  height: 100%;
7
+  overflow:auto;
8
+  padding: 0px 10px 0px 10px;
9
+}
10
+#toc_header {
11
+  display: none;
12
+}
13
+#toc ul {
14
+  margin: 0px;
15
+  padding: 0px;
16
+}
17
+#toc ul li {
18
+  list-style-type: none;
19
+}
20
+
21
+#toc ul li ul li {
22
+  margin-left: 15px;
23
+  list-style-type: circle;
24
+}
25
+body, td {
26
+   font-family: Arial,Helvetica,sans-serif;
27
+   background-color: white;
28
+   font-size: 13px;
29
+  max-width: 800px;
30
+  margin: auto;
31
+  margin-left:210px;
32
+  padding: 0px 10px 0px 10px;
33
+  border-left: 1px solid #EEEEEE;
34
+  line-height: 150%;
35
+}
36
+
37
+tt, code, pre {
38
+   font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, 
39
+
40
+monospace;
41
+}
42
+
43
+h1 {
44
+   font-size:2.2em;
45
+}
46
+
47
+h2 {
48
+   font-size:1.8em;
49
+}
50
+
51
+h3 {
52
+   font-size:1.4em;
53
+}
54
+
55
+h4 {
56
+   font-size:1.0em;
57
+}
58
+
59
+h5 {
60
+   font-size:0.9em;
61
+}
62
+
63
+h6 {
64
+   font-size:0.8em;
65
+}
66
+
67
+a {
68
+  text-decoration: none;
69
+}
70
+
71
+a:hover {
72
+  text-decoration: underline;
73
+}
74
+
75
+a:visited {
76
+   color: rgb(50%, 0%, 50%);
77
+}
78
+
79
+pre, img {
80
+  max-width: 100%;
81
+}
82
+pre {
83
+  overflow-x: auto;
84
+}
85
+pre code {
86
+   display: block; padding: 0.5em;
87
+}
88
+
89
+code {
90
+  font-size: 92%;
91
+  border: 1px solid #ccc;
92
+}
93
+
94
+code[class] {
95
+  background-color: #F8F8F8;
96
+}
97
+
98
+table, td, th {
99
+  border: none;
100
+}
101
+
102
+blockquote {
103
+   color:#666666;
104
+   margin:0;
105
+   padding-left: 1em;
106
+   border-left: 0.5em #EEE solid;
107
+}
108
+
109
+hr {
110
+   height: 0px;
111
+   border-bottom: none;
112
+   border-top-width: thin;
113
+   border-top-style: dotted;
114
+   border-top-color: #999999;
115
+}
116
+
117
+@media print {
118
+   * {
119
+      background: transparent !important;
120
+      color: black !important;
121
+      filter:none !important;
122
+      -ms-filter: none !important;
123
+   }
124
+
125
+   body {
126
+      font-size:12pt;
127
+      max-width:100%;
128
+   }
129
+
130
+   a, a:visited {
131
+      text-decoration: underline;
132
+   }
133
+
134
+   hr {
135
+      visibility: hidden;
136
+      page-break-before: always;
137
+   }
138
+
139
+   pre, blockquote {
140
+      padding-right: 1em;
141
+      page-break-inside: avoid;
142
+   }
143
+
144
+   tr, img {
145
+      page-break-inside: avoid;
146
+   }
147
+
148
+   img {
149
+      max-width: 100% !important;
150
+   }
151
+
152
+   @page :left {
153
+      margin: 15mm 20mm 15mm 10mm;
154
+   }
155
+
156
+   @page :right {
157
+      margin: 15mm 10mm 15mm 20mm;
158
+   }
159
+
160
+   p, h2, h3 {
161
+      orphans: 3; widows: 3;
162
+   }
163
+
164
+   h2, h3 {
165
+      page-break-after: avoid;
166
+   }
167
+}
0 168
new file mode 100644
... ...
@@ -0,0 +1,124 @@
1
+
2
+set.seed(888)
3
+
4
+type = c(rep("Tumor", 10), rep("Control", 10))
5
+gender = sample(c("F", "M"), 20, replace = TRUE)
6
+gender[sample(1:20, 2)] = NA
7
+age = runif(20, min = 30, max = 80)
8
+mutation = data.frame(mut1 = sample(c(TRUE, FALSE), 20, p = c(0.2, 0.8), replace = TRUE),
9
+    mut2 = sample(c(TRUE, FALSE), 20, p = c(0.3, 0.7), replace = TRUE))
10
+anno = data.frame(type = type, gender = gender, age = age, mutation, stringsAsFactors = FALSE) 
11
+
12
+anno_col = list(type = c("Tumor" = "red", "Control" = "blue"),
13
+    gender = c("F" = "pink", "M" = "darkgreen"),
14
+    mutation = c("TRUE" = "black", "FALSE" = "white"))
15
+
16
+######################################
17
+# generate methylation matrix
18
+rand_meth = function(k, mean) {
19
+    (runif(k) - 0.5)*min(c(1-mean), mean) + mean
20
+}
21
+
22
+mean_meth = c(rand_meth(300, 0.3), rand_meth(700, 0.7))
23
+mat_meth = as.data.frame(lapply(mean_meth, function(m) {
24
+    if(m < 0.3) {
25
+        c(rand_meth(10, m), rand_meth(10, m + 0.2))
26
+    } else if(m > 0.7) {
27
+        c(rand_meth(10, m), rand_meth(10, m - 0.2))
28
+    } else {
29
+        c(rand_meth(10, m), rand_meth(10, m + sample(c(1, -1), 1)*0.2))
30
+    }
31
+
32
+}))
33
+mat_meth = t(mat_meth)
34
+rownames(mat_meth) = NULL
35
+colnames(mat_meth) = paste0("sample", 1:20)
36
+
37
+######################################
38
+# generate directions for methylation
39
+direction = rowMeans(mat_meth[, 1:10]) - rowMeans(mat_meth[, 11:20])
40
+direction = ifelse(direction > 0, "hyper", "hypo")
41
+library(circlize)
42
+
43
+#######################################
44
+# generate expression matrix
45
+mat_expr = t(apply(mat_meth, 1, function(x) {
46
+    x = x + rnorm(length(x), sd = abs(runif(1)-0.5)*0.4 + 0.1)
47
+    -scale(x)
48
+}))
49
+dimnames(mat_expr) = dimnames(mat_meth)
50
+
51
+#############################################################
52
+# matrix for correlation between methylation and expression
53
+cor_pvalue = -log10(sapply(seq_len(nrow(mat_meth)), function(i) {
54
+    cor.test(mat_meth[i, ], mat_expr[i, ])$p.value
55
+}))
56
+
57
+#####################################################
58
+# matrix for types of genes
59
+gene_type = sample(c("protein_coding", "lincRNA", "microRNA", "psedo-gene", "others"), 
60
+    nrow(mat_meth), replace = TRUE, prob = c(6, 1, 1, 1, 1))
61
+
62
+#################################################
63
+# annotation to genes
64
+anno_gene = sapply(mean_meth, function(m) {
65
+    if(m > 0.6) {
66
+        if(runif(1) < 0.8) return("intragenic")
67
+    }
68
+    if(m < 0.4) {
69
+        if(runif(1) < 0.4) return("TSS")
70
+    }
71
+    return("intergenic")
72
+})
73
+
74
+anno_gene_col = c("intragenic" = "blue", "TSS" = "red", "intergenic" = "grey")
75
+
76
+############################################
77
+# distance to genes
78
+tss_dist = sapply(mean_meth, function(m) {
79
+    if(m < 0.3) {
80
+        if(runif(1) < 0.5) {
81
+            return(round( (runif(1) - 0.5)*1000 + 500))
82
+        } else {
83
+            return(round( (runif(1) - 0.5)*10000 + 500))
84
+        }
85
+    } else if(m < 0.6) {
86
+        if(runif(1) < 0.8) {
87
+            return(round( (runif(1)-0.5)*100000 + 50000 ))
88
+        } else {
89
+            return(round( (runif(1)-0.5)*1000000 + 500000 ))
90
+        }
91
+    }
92
+    return(round( (runif(1) - 0.5)*1000000 + 500000))    
93
+})
94
+
95
+
96
+#######################################
97
+# annotation to enhancers
98
+rand_tss = function(m) {
99
+    if(m < 0.4) {
100
+        if(runif(1) < 0.25) return(runif(1))
101
+    } else if (runif(1) < 0.1) {
102
+        return(runif(1))
103
+    } 
104
+    return(0)
105
+}
106
+rand_enhancer = function(m) {
107
+    if(m < 0.4) {
108
+        if(runif(1) < 0.6) return(runif(1))
109
+    } else if (runif(1) < 0.1) {
110
+        return(runif(1))
111
+    } 
112
+    return(0)
113
+}
114
+rand_repressive = function(m) {
115
+    if(m > 0.4) {
116
+        if(runif(1) < 0.8) return(runif(1))
117
+    }
118
+    return(0)
119
+}
120
+anno_states = data.frame(
121
+    tss = sapply(mean_meth, rand_tss), 
122
+    enhancer = sapply(mean_meth, rand_enhancer), 
123
+    rand_repressive = sapply(mean_meth, rand_repressive))
124
+
0 125
new file mode 100644
... ...
@@ -0,0 +1,115 @@
1
+<!--
2
+%\VignetteEngine{knitr}
3
+%\VignetteIndexEntry{Common use of ComplexHeatmap package}
4
+-->
5
+
6
+Common use of ComplexHeatmap package
7
+========================================
8
+
9
+**Author**: Zuguang Gu ( z.gu@dkfz.de )
10
+
11
+**Date**: `r Sys.Date()`
12
+
13
+-------------------------------------------------------------
14
+
15
+```{r global_settings, echo = FALSE, message = FALSE}
16
+library(markdown)
17
+options(markdown.HTML.options = c(options('markdown.HTML.options')[[1]], "toc"))
18
+
19
+library(knitr)
20
+knitr::opts_chunk$set(
21
+    error = FALSE,
22
+    tidy  = FALSE,
23
+    message = FALSE,
24
+    fig.align = "center"
25
+)
26
+options(markdown.HTML.stylesheet = "custom.css")
27
+
28
+options(width = 100)
29
+```
30
+
31
+```{r}
32
+library(circlize)
33
+library(ComplexHeatmap)
34
+
35
+source("generate_random_dataset.R")
36
+```
37
+
38
+# A Single Heatmap with annotations
39
+
40
+```{r}
41
+Heatmap(mat_meth, name = "methylation",
42
+	top_annotation = HeatmapAnnotation(
43
+		type = anno$type,
44
+		gender = anno$gender,
45
+		age = anno_points(anno$age, ylim = c(0, 80)),
46
+		mutation = as.matrix(anno[, c("mut1", "mut2")]),
47
+		col = anno_col
48
+	), column_title = "Differential Methylated Regions")
49
+```
50
+
51
+```{r}
52
+Heatmap(mat_meth, name = "methylation",
53
+	top_annotation = HeatmapAnnotation(
54
+		df = anno,
55
+		annotation_name_side = "left"
56
+	), column_title = "Differential Methylated Regions")
57
+```
58
+
59
+```{r}
60
+Heatmap(mat_meth, name = "methylation",
61
+	top_annotation = HeatmapAnnotation(
62
+		df = anno,
63
+		col = anno_col,
64
+		annotation_name_side = "left"
65
+	), 
66
+	right_annotation = rowAnnotation(
67
+		anno_gene = anno_gene,
68
+		tss_dist = anno_points(tss_dist),
69
+		col = list(anno_gene = anno_gene_col)
70
+	),
71
+	column_title = "Differential Methylated Regions")
72
+```
73
+
74
+
75
+```{r}
76
+Heatmap(mat_meth, name = "methylation",
77
+	top_annotation = HeatmapAnnotation(
78
+		type = anno$type,
79
+		gender = anno$gender,
80
+		age = anno_points(anno$age, ylim = c(0, 80)),
81
+		mutation = as.matrix(anno[, c("mut1", "mut2")]),
82
+		col = anno_col
83
+	), 
84
+	right_annotation = rowAnnotation(
85
+		anno_gene = anno_gene,
86
+		tss_dist = anno_points(tss_dist),
87
+		col = list(anno_gene = anno_gene_col)
88
+	),
89
+	show_column_names = FALSE,
90
+	column_title = "Differential Methylated Regions",
91
+	column_km = 2, row_km = 4)
92
+```
93
+
94
+
95
+## Heatmap List
96
+
97
+```{r}
98
+meth_col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red"))
99
+expr_col_fun = colorRamp2(c(-2, 0, 2), c("green", "white", "red"))
100
+ht_list = Heatmap(mat_meth, name = "methylation", col = meth_col_fun) + 
101
+	Heatmap(mat_expr, name = "epxression", col = expr_col_fun)
102
+draw(ht_list, row_km = 4)
103
+```
104
+
105
+
106
+```{r}
107
+ht_list = Heatmap(mat_meth[1:40, ], name = "methylation", col = meth_col_fun) %v%
108
+	Heatmap(mat_expr[1:40, ], name = "epxression", col = expr_col_fun)
109
+draw(ht_list, column_km = 2)
110
+```
111
+
112
+## OncoPrint
113
+
114
+## Density as a heatmap
115
+