Browse code

add NEWs

Zuguang Gu authored on 30/12/2018 08:12:22
Showing129 changed files

... ...
@@ -2,7 +2,7 @@ Package: ComplexHeatmap
2 2
 Type: Package
3 3
 Title: Make Complex Heatmaps
4 4
 Version: 1.99.5
5
-Date: 2018-12-26
5
+Date: 2018-12-30
6 6
 Author: Zuguang Gu
7 7
 Maintainer: Zuguang Gu <z.gu@dkfz.de>
8 8
 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices
... ...
@@ -1,3 +1,8 @@
1
+CHANGES in VERSION 1.99.5
2
+
3
+* add `UpSet()` and some related functions to make Upset plots
4
+
5
+========================
1 6
 
2 7
 CHANGES in VERSION 1.99.4
3 8
 
... ...
@@ -955,7 +955,7 @@ order.comb_mat = function(m, decreasing = TRUE, on = "comb_set") {
955 955
 #
956 956
 upset_top_annotation = function(m, 
957 957
 	gp = gpar(fill = "black"), 
958
-	height = unit(ifelse(set_on_rows, 2, 3), "cm"),
958
+	height = unit(ifelse(set_on_rows, 3, 2), "cm"),
959 959
 	show_annotation_name = TRUE,
960 960
 	annotation_name_gp = gpar(),
961 961
 	annotation_name_offset = NULL,
... ...
@@ -1013,7 +1013,7 @@ upset_top_annotation = function(m,
1013 1013
 #
1014 1014
 upset_right_annotation = function(m,
1015 1015
 	gp = gpar(fill = "black"),  
1016
-	width = unit(ifelse(set_on_rows, 3, 2), "cm"),
1016
+	width = unit(ifelse(set_on_rows, 2, 3), "cm"),
1017 1017
 	show_annotation_name = TRUE,
1018 1018
 	annotation_name_gp = gpar(),
1019 1019
 	annotation_name_offset = NULL,
... ...
@@ -15,5 +15,4 @@ method and the \code{\%v\%v} method so that above three classes can be appended
15 15
 \examples{
16 16
 # There is no example
17 17
 NULL
18
-
19 18
 }
... ...
@@ -26,5 +26,4 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
-
30 29
 }
... ...
@@ -22,5 +22,4 @@ See \code{\link{AnnotationFunction}} constructor for details.
22 22
 \examples{
23 23
 # There is no example
24 24
 NULL
25
-
26 25
 }
... ...
@@ -26,5 +26,4 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
-
30 29
 }
... ...
@@ -40,5 +40,4 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok
40 40
 \examples{
41 41
 # There is no example
42 42
 NULL
43
-
44 43
 }
... ...
@@ -30,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
-
34 33
 }
... ...
@@ -196,5 +196,4 @@ Zuguang Gu <z.gu@dkfz.de>
196 196
 \examples{
197 197
 # There is no example
198 198
 NULL
199
-
200 199
 }
... ...
@@ -25,5 +25,4 @@ Zuguang Gu <z.gu@dkfz.de>
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -80,5 +80,4 @@ Zuguang Gu <z.gu@dkfz.de>
80 80
 \examples{
81 81
 # There is no example
82 82
 NULL
83
-
84 83
 }
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -26,5 +26,4 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
-
30 29
 }
... ...
@@ -26,5 +26,4 @@ Zuguang Gu <z.gu@dkfz.de>
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
-
30 29
 }
... ...
@@ -28,5 +28,4 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
-
32 31
 }
... ...
@@ -40,5 +40,4 @@ Zuguang Gu <z.gu@dkfz.de>
40 40
 \examples{
41 41
 # There is no example
42 42
 NULL
43
-
44 43
 }
... ...
@@ -28,5 +28,4 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
-
32 31
 }
... ...
@@ -28,5 +28,4 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
-
32 31
 }
... ...
@@ -28,5 +28,4 @@ Zuguang Gu <z.gu@dkfz.de>
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
-
32 31
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{adjust_heatmap_list-HeatmapList-method}
2 2
 \alias{adjust_heatmap_list,HeatmapList-method}
3
-\alias{adjust_heatmap_list}
4 3
 \title{
5 4
 Adjust Heatmap List
6 5
 }
... ...
@@ -24,8 +23,8 @@ This function is only for internal use.
24 23
 \author{
25 24
 Zuguang Gu <z.gu@dkfz.de>
26 25
 }
26
+\alias{adjust_heatmap_list}
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -20,5 +20,4 @@ anno_link(...)
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
-
24 23
 }
... ...
@@ -33,5 +33,4 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
-
37 36
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{annotation_legend_size-HeatmapList-method}
2 2
 \alias{annotation_legend_size,HeatmapList-method}
3
-\alias{annotation_legend_size}
4 3
 \title{
5 4
 Size of the Annotation Legends
6 5
 }
... ...
@@ -28,8 +27,8 @@ A \code{\link[grid]{unit}} object.
28 27
 \author{
29 28
 Zuguang Gu <z.gu@dkfz.de>
30 29
 }
30
+\alias{annotation_legend_size}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
-
35 34
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{color_mapping_legend-ColorMapping-method}
2 2
 \alias{color_mapping_legend,ColorMapping-method}
3
-\alias{color_mapping_legend}
4 3
 \title{
5 4
 Draw Legend Based on Color Mapping
6 5
 }
... ...
@@ -66,8 +65,8 @@ A \code{\link{Legends-class}} object.
66 65
 \author{
67 66
 Zuguang Gu <z.gu@dkfz.de>
68 67
 }
68
+\alias{color_mapping_legend}
69 69
 \examples{
70 70
 # There is no example
71 71
 NULL
72
-
73 72
 }
... ...
@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
-
33 32
 }
... ...
@@ -31,5 +31,4 @@ Zuguang Gu <z.gu@dkfz.de>
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
-
35 34
 }
... ...
@@ -24,5 +24,4 @@ Zuguang Gu <z.gu@dkfz.de>
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
-
28 27
 }
... ...
@@ -30,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
-
34 33
 }
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -26,5 +26,4 @@ The environment is at \code{object@var_env}.
26 26
 \examples{
27 27
 # There is no example
28 28
 NULL
29
-
30 29
 }
... ...
@@ -21,5 +21,4 @@ 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
-
25 24
 }
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -17,5 +17,4 @@ default_get_type(x)
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -17,5 +17,4 @@ dend_heights(x)
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -28,5 +28,4 @@ A \code{\link{grob}} object which is contructed by \code{\link[grid:grid.segment
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
-
32 31
 }
... ...
@@ -17,5 +17,4 @@ Dimension of the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -28,5 +28,4 @@ which is generally for testing purpose.
28 28
 \examples{
29 29
 # There is no example
30 30
 NULL
31
-
32 31
 }
... ...
@@ -33,5 +33,4 @@ Zuguang Gu <z.gu@dkfz.de>
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
-
37 36
 }
... ...
@@ -30,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
-
34 33
 }
... ...
@@ -175,5 +175,4 @@ Zuguang Gu <z.gu@dkfz.de>
175 175
 \examples{
176 176
 # There is no example
177 177
 NULL
178
-
179 178
 }
... ...
@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
-
33 32
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{draw_annotation-Heatmap-method}
2 2
 \alias{draw_annotation,Heatmap-method}
3
-\alias{draw_annotation}
4 3
 \title{
5 4
 Draw Heatmap Annotations on the Heatmap
6 5
 }
... ...
@@ -31,8 +30,8 @@ This function returns no value.
31 30
 \author{
32 31
 Zuguang Gu <z.gu@dkfz.de>
33 32
 }
33
+\alias{draw_annotation}
34 34
 \examples{
35 35
 # There is no example
36 36
 NULL
37
-
38 37
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{draw_annotation_legend-HeatmapList-method}
2 2
 \alias{draw_annotation_legend,HeatmapList-method}
3
-\alias{draw_annotation_legend}
4 3
 \title{
5 4
 Draw legends for All Annotations
6 5
 }
... ...
@@ -32,8 +31,8 @@ This function returns no value.
32 31
 \author{
33 32
 Zuguang Gu <z.gu@dkfz.de>
34 33
 }
34
+\alias{draw_annotation_legend}
35 35
 \examples{
36 36
 # There is no example
37 37
 NULL
38
-
39 38
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{draw_dend-Heatmap-method}
2 2
 \alias{draw_dend,Heatmap-method}
3
-\alias{draw_dend}
4 3
 \title{
5 4
 Draw Heatmap Dendrograms
6 5
 }
... ...
@@ -34,8 +33,8 @@ This function returns no value.
34 33
 \author{
35 34
 Zuguang Gu <z.gu@dkfz.de>
36 35
 }
36
+\alias{draw_dend}
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
-
41 40
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{draw_dimnames-Heatmap-method}
2 2
 \alias{draw_dimnames,Heatmap-method}
3
-\alias{draw_dimnames}
4 3
 \title{
5 4
 Draw row names or column names
6 5
 }
... ...
@@ -30,8 +29,8 @@ This function returns no value.
30 29
 \author{
31 30
 Zuguang Gu <z.gu@dkfz.de>
32 31
 }
32
+\alias{draw_dimnames}
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
-
37 36
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{draw_heatmap_body-Heatmap-method}
2 2
 \alias{draw_heatmap_body,Heatmap-method}
3
-\alias{draw_heatmap_body}
4 3
 \title{
5 4
 Draw Heatmap Body
6 5
 }
... ...
@@ -29,8 +28,8 @@ This function returns no value.
29 28
 \author{
30 29
 Zuguang Gu <z.gu@dkfz.de>
31 30
 }
31
+\alias{draw_heatmap_body}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
-
36 35
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{draw_heatmap_legend-HeatmapList-method}
2 2
 \alias{draw_heatmap_legend,HeatmapList-method}
3
-\alias{draw_heatmap_legend}
4 3
 \title{
5 4
 Draw legends for All Heatmaps
6 5
 }
... ...
@@ -33,8 +32,8 @@ This function returns no value.
33 32
 \author{
34 33
 Zuguang Gu <z.gu@dkfz.de>
35 34
 }
35
+\alias{draw_heatmap_legend}
36 36
 \examples{
37 37
 # There is no example
38 38
 NULL
39
-
40 39
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{draw_heatmap_list-HeatmapList-method}
2 2
 \alias{draw_heatmap_list,HeatmapList-method}
3
-\alias{draw_heatmap_list}
4 3
 \title{
5 4
 Draw the List of Heatmaps
6 5
 }
... ...
@@ -26,8 +25,8 @@ This function returns no value.
26 25
 \author{
27 26
 Zuguang Gu <z.gu@dkfz.de>
28 27
 }
28
+\alias{draw_heatmap_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
-
33 32
 }
... ...
@@ -32,5 +32,4 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
-
36 35
 }
... ...
@@ -30,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>
30 30
 \examples{
31 31
 # There is no example
32 32
 NULL
33
-
34 33
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{get_color_mapping_list-HeatmapAnnotation-method}
2 2
 \alias{get_color_mapping_list,HeatmapAnnotation-method}
3
-\alias{get_color_mapping_list}
4 3
 \title{
5 4
 Get a List of ColorMapping objects
6 5
 }
... ...
@@ -26,8 +25,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list.
26 25
 \author{
27 26
 Zuguang Gu <z.gu@dkfz.de>
28 27
 }
28
+\alias{get_color_mapping_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
-
33 32
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{get_legend_param_list-HeatmapAnnotation-method}
2 2
 \alias{get_legend_param_list,HeatmapAnnotation-method}
3
-\alias{get_legend_param_list}
4 3
 \title{
5 4
 Get a List of Annotation Legend Parameters
6 5
 }
... ...
@@ -26,8 +25,8 @@ A list.
26 25
 \author{
27 26
 Zuguang Gu <z.gu@dkfz.de>
28 27
 }
28
+\alias{get_legend_param_list}
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
-
33 32
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{heatmap_legend_size-HeatmapList-method}
2 2
 \alias{heatmap_legend_size,HeatmapList-method}
3
-\alias{heatmap_legend_size}
4 3
 \title{
5 4
 Size of the Heatmap Legends
6 5
 }
... ...
@@ -28,8 +27,8 @@ A \code{\link[grid]{unit}} object.
28 27
 \author{
29 28
 Zuguang Gu <z.gu@dkfz.de>
30 29
 }
30
+\alias{heatmap_legend_size}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
-
35 34
 }
... ...
@@ -18,5 +18,4 @@ Height of the Heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
-
22 21
 }
... ...
@@ -21,5 +21,4 @@ Internally used.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
-
25 24
 }
... ...
@@ -18,5 +18,4 @@ Height of the Heatmap List
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
-
22 21
 }
... ...
@@ -21,5 +21,4 @@ Internally used.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
-
25 24
 }
... ...
@@ -23,5 +23,4 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -23,5 +23,4 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -23,5 +23,4 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -20,5 +20,4 @@ The physical height of the grob can be get by \code{convertWidth(grobHeight(axis
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
-
24 23
 }
... ...
@@ -17,5 +17,4 @@ Grob height for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -17,5 +17,4 @@ Grob height for legend_body
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -17,5 +17,4 @@ Grob height for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -25,5 +25,4 @@ will also be sychronized in \code{\link{ht_opt}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -17,5 +17,4 @@ Number of Annotations
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -17,5 +17,4 @@ Length of the HeatmapList object
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -15,5 +15,4 @@ A vector of viewport names.
15 15
 \examples{
16 16
 # There is no example
17 17
 NULL
18
-
19 18
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{make_column_cluster-Heatmap-method}
2 2
 \alias{make_column_cluster,Heatmap-method}
3
-\alias{make_column_cluster}
4 3
 \title{
5 4
 Make Cluster on Columns
6 5
 }
... ...
@@ -29,8 +28,8 @@ A \code{\link{Heatmap-class}} object.
29 28
 \author{
30 29
 Zuguang Gu <z.gu@dkfz.de>
31 30
 }
31
+\alias{make_column_cluster}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
-
36 35
 }
... ...
@@ -32,5 +32,4 @@ Zuguang Gu <z.gu@dkfz.de>
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
-
36 35
 }
... ...
@@ -130,5 +130,4 @@ Zuguang Gu <z.gu@dkfz.de>
130 130
 \examples{
131 131
 # There is no example
132 132
 NULL
133
-
134 133
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{make_row_cluster-Heatmap-method}
2 2
 \alias{make_row_cluster,Heatmap-method}
3
-\alias{make_row_cluster}
4 3
 \title{
5 4
 Make Cluster on Rows
6 5
 }
... ...
@@ -28,8 +27,8 @@ A \code{\link{Heatmap-class}} object.
28 27
 \author{
29 28
 Zuguang Gu <z.gu@dkfz.de>
30 29
 }
30
+\alias{make_row_cluster}
31 31
 \examples{
32 32
 # There is no example
33 33
 NULL
34
-
35 34
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{map_to_colors-ColorMapping-method}
2 2
 \alias{map_to_colors,ColorMapping-method}
3
-\alias{map_to_colors}
4 3
 \title{
5 4
 Map Values to Colors
6 5
 }
... ...
@@ -35,3 +34,4 @@ col_fun = colorRamp2(c(0, 1), c("white", "red"))
35 34
 cm = ColorMapping(col_fun = col_fun)
36 35
 map_to_colors(cm, runif(10))
37 36
 }
37
+\alias{map_to_colors}
... ...
@@ -17,5 +17,4 @@ Names of the heatmaps/annotations
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -17,5 +17,4 @@ Number of Columns in the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -22,5 +22,4 @@ it returns \code{NA}.
22 22
 \examples{
23 23
 # There is no example
24 24
 NULL
25
-
26 25
 }
... ...
@@ -21,5 +21,4 @@ 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
-
25 24
 }
... ...
@@ -22,5 +22,4 @@ The sets (by \code{\link{set_name}}) from all combination matrice should be the
22 22
 \examples{
23 23
 # There is no example
24 24
 NULL
25
-
26 25
 }
... ...
@@ -17,5 +17,4 @@ Number of Rows in the Heatmap
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -90,5 +90,4 @@ Zuguang Gu <z.gu@dkfz.de>
90 90
 \examples{
91 91
 # There is no example
92 92
 NULL
93
-
94 93
 }
... ...
@@ -23,5 +23,4 @@ by the combination matrix.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -39,5 +39,4 @@ Zuguang Gu <z.gu@dkfz.de>
39 39
 \examples{
40 40
 # There is no example
41 41
 NULL
42
-
43 42
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{prepare-Heatmap-method}
2 2
 \alias{prepare,Heatmap-method}
3
-\alias{prepare}
4 3
 \title{
5 4
 Prepare the Heatmap
6 5
 }
... ...
@@ -34,8 +33,8 @@ The \code{\link{Heatmap-class}} object.
34 33
 \author{
35 34
 Zuguang Gu <z.gu@dkfz.de>
36 35
 }
36
+\alias{prepare}
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
-
41 40
 }
... ...
@@ -18,5 +18,4 @@ Print the comb_mat Object
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
-
22 21
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{re_size-HeatmapAnnotation-method}
2 2
 \alias{re_size,HeatmapAnnotation-method}
3
-\alias{re_size}
4 3
 \title{
5 4
 Resize the Width or Height of Heatmap Annotations
6 5
 }
... ...
@@ -42,8 +41,8 @@ The basic rules are (take \code{height} and \code{annotation_height} for example
42 41
      and \code{anno_simple_size} is disabled.
43 42
 6. If \code{simple_anno_size_adjust} is \code{FALSE}, the size of the simple annotations will not change.
44 43
 }
44
+\alias{re_size}
45 45
 \examples{
46 46
 # There is no example
47 47
 NULL
48
-
49 48
 }
... ...
@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>
29 29
 \examples{
30 30
 # There is no example
31 31
 NULL
32
-
33 32
 }
... ...
@@ -25,5 +25,4 @@ See help page of \code{\link{anno_barplot}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -25,5 +25,4 @@ See help page of \code{\link{anno_boxplot}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -25,5 +25,4 @@ See help page of \code{\link{anno_density}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -25,5 +25,4 @@ See help page of \code{\link{anno_histogram}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -25,5 +25,4 @@ See help page of \code{\link{anno_link}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -25,5 +25,4 @@ See help page of \code{\link{anno_points}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -25,5 +25,4 @@ See help page of \code{\link{anno_text}}.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{set_component_height-Heatmap-method}
2 2
 \alias{set_component_height,Heatmap-method}
3
-\alias{set_component_height}
4 3
 \title{
5 4
 Set Height of Heatmap Component
6 5
 }
... ...
@@ -30,8 +29,8 @@ The \code{\link{Heatmap-class}} object.
30 29
 \author{
31 30
 Zuguang Gu <z.gu@dkfz.de>
32 31
 }
32
+\alias{set_component_height}
33 33
 \examples{
34 34
 # There is no example
35 35
 NULL
36
-
37 36
 }
... ...
@@ -1,6 +1,5 @@
1 1
 \name{set_component_width-Heatmap-method}
2 2
 \alias{set_component_width,Heatmap-method}
3
-\alias{set_component_width}
4 3
 \title{
5 4
 Set Width of Heatmap Component
6 5
 }
... ...
@@ -29,8 +28,8 @@ The \code{\link{Heatmap-class}} object.
29 28
 \author{
30 29
 Zuguang Gu <z.gu@dkfz.de>
31 30
 }
31
+\alias{set_component_width}
32 32
 \examples{
33 33
 # There is no example
34 34
 NULL
35
-
36 35
 }
... ...
@@ -17,5 +17,4 @@ Print the AnnotationFunction Object
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -23,5 +23,4 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -23,5 +23,4 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -24,5 +24,4 @@ This function returns no value.
24 24
 \examples{
25 25
 # There is no example
26 26
 NULL
27
-
28 27
 }
... ...
@@ -23,5 +23,4 @@ Zuguang Gu <z.gu@dkfz.de>
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -23,5 +23,4 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -23,5 +23,4 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -25,5 +25,4 @@ Internally used.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -25,5 +25,4 @@ Internally used.
25 25
 \examples{
26 26
 # There is no example
27 27
 NULL
28
-
29 28
 }
... ...
@@ -21,5 +21,4 @@ Mainly used for constructing the \code{\link{AnnotationFunction-class}} object.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
-
25 24
 }
... ...
@@ -21,5 +21,4 @@ Mainly used for constructing the \code{\link{AnnotationFunction-class}} object.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
-
25 24
 }
... ...
@@ -18,5 +18,4 @@ Print the Summary of a Heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
-
22 21
 }
... ...
@@ -18,5 +18,4 @@ Summary of a Heatmap List
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
-
22 21
 }
... ...
@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>
27 27
 \examples{
28 28
 # There is no example
29 29
 NULL
30
-
31 30
 }
... ...
@@ -9,7 +9,7 @@ Default UpSet Right Annotation
9 9
 \usage{
10 10
 upset_right_annotation(m,
11 11
     gp = gpar(fill = "black"),
12
-    width = unit(ifelse(set_on_rows, 3, 2), "cm"),
12
+    width = unit(ifelse(set_on_rows, 2, 3), "cm"),
13 13
     show_annotation_name = TRUE,
14 14
     annotation_name_gp = gpar(),
15 15
     annotation_name_offset = NULL,
... ...
@@ -37,5 +37,4 @@ how to set the right annotation or left annotation in \code{\link{UpSet}}, pleas
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
-
41 40
 }
... ...
@@ -9,7 +9,7 @@ Default UpSet Top Annotation
9 9
 \usage{
10 10
 upset_top_annotation(m,
11 11
     gp = gpar(fill = "black"),
12
-    height = unit(ifelse(set_on_rows, 2, 3), "cm"),
12
+    height = unit(ifelse(set_on_rows, 3, 2), "cm"),
13 13
     show_annotation_name = TRUE,
14 14
     annotation_name_gp = gpar(),
15 15
     annotation_name_offset = NULL,
... ...
@@ -37,5 +37,4 @@ how to set the top annotation or bottom annotation in \code{\link{UpSet}}, pleas
37 37
 \examples{
38 38
 # There is no example
39 39
 NULL
40
-
41 40
 }
... ...
@@ -18,5 +18,4 @@ Width of the Heatmap
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
-
22 21
 }
... ...
@@ -21,5 +21,4 @@ Internally used.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
-
25 24
 }
... ...
@@ -18,5 +18,4 @@ Width of the Heatmap List
18 18
 \examples{
19 19
 # There is no example
20 20
 NULL
21
-
22 21
 }
... ...
@@ -21,5 +21,4 @@ Internally used.
21 21
 \examples{
22 22
 # There is no example
23 23
 NULL
24
-
25 24
 }
... ...
@@ -23,5 +23,4 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -23,5 +23,4 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -23,5 +23,4 @@ Internally used.
23 23
 \examples{
24 24
 # There is no example
25 25
 NULL
26
-
27 26
 }
... ...
@@ -20,5 +20,4 @@ The physical width of the grob can be get by \code{convertWidth(grobWidth(axis_g
20 20
 \examples{
21 21
 # There is no example
22 22
 NULL
23
-
24 23
 }
... ...
@@ -17,5 +17,4 @@ Grob width for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -17,5 +17,4 @@ Grob width for legend_body
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }
... ...
@@ -17,5 +17,4 @@ Grob width for packed_legends
17 17
 \examples{
18 18
 # There is no example
19 19
 NULL
20
-
21 20
 }