... | ... |
@@ -1,31 +1,31 @@ |
1 |
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors')) |
|
2 |
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height')) |
|
3 |
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) |
|
4 |
-setGeneric('component_height', function(object, ...) standardGeneric('component_height')) |
|
5 |
-setGeneric('re_size', function(object, ...) standardGeneric('re_size')) |
|
6 |
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout')) |
|
7 | 1 |
setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size')) |
2 |
+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list')) |
|
3 |
+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height')) |
|
8 | 4 |
setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list')) |
5 |
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend')) |
|
6 |
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation')) |
|
7 |
+setGeneric('re_size', function(object, ...) standardGeneric('re_size')) |
|
8 |
+setGeneric('row_order', function(object, ...) standardGeneric('row_order')) |
|
9 |
+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend')) |
|
9 | 10 |
setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend')) |
10 | 11 |
setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster')) |
11 |
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend')) |
|
12 |
-setGeneric('row_order', function(object, ...) standardGeneric('row_order')) |
|
12 |
+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title')) |
|
13 |
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout')) |
|
13 | 14 |
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 | 15 |
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')) |
|
16 |
+setGeneric('draw', function(object, ...) standardGeneric('draw')) |
|
20 | 17 |
setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size')) |
21 |
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation')) |
|
18 |
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend')) |
|
19 |
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend')) |
|
20 |
+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all')) |
|
21 |
+setGeneric('component_height', function(object, ...) standardGeneric('component_height')) |
|
22 |
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors')) |
|
23 |
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width')) |
|
22 | 24 |
setGeneric('prepare', function(object, ...) standardGeneric('prepare')) |
23 |
-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames')) |
|
24 |
-setGeneric('draw', function(object, ...) standardGeneric('draw')) |
|
25 |
-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title')) |
|
25 |
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap')) |
|
26 | 26 |
setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster')) |
27 |
-setGeneric('component_width', function(object, ...) standardGeneric('component_width')) |
|
27 |
+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames')) |
|
28 |
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend')) |
|
28 | 29 |
setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list')) |
29 |
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend')) |
|
30 |
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list')) |
|
31 |
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all')) |
|
30 |
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) |
|
31 |
+setGeneric('component_width', function(object, ...) standardGeneric('component_width')) |
... | ... |
@@ -620,6 +620,7 @@ construct_axis_grob = function(axis_param, which, data_scale) { |
620 | 620 |
# -axis_param parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters. |
621 | 621 |
# -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
622 | 622 |
# -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
623 |
+# -... Other arguments. |
|
623 | 624 |
# |
624 | 625 |
# == value |
625 | 626 |
# An annotation function which can be used in `HeatmapAnnotation`. |
... | ... |
@@ -634,7 +635,17 @@ construct_axis_grob = function(axis_param, which, data_scale) { |
634 | 635 |
# draw(anno, test = "matrix") |
635 | 636 |
anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16, |
636 | 637 |
size = unit(2, "mm"), ylim = NULL, extend = 0.05, axis = TRUE, |
637 |
- axis_param = default_axis_param(which), width = NULL, height = NULL) { |
|
638 |
+ axis_param = default_axis_param(which), width = NULL, height = NULL, ...) { |
|
639 |
+ |
|
640 |
+ other_args = list(...) |
|
641 |
+ if(length(other_args)) { |
|
642 |
+ if("axis_gp" %in% names(other_args)) { |
|
643 |
+ stop_wrap("`axis_gp` is removed from the arguments. Use `axis_param = list(gp = ...)` instead.") |
|
644 |
+ } |
|
645 |
+ if("axis_direction" %in% names(other_args)) { |
|
646 |
+ stop_wrap("`axis_direction` is not supported any more.") |
|
647 |
+ } |
|
648 |
+ } |
|
638 | 649 |
|
639 | 650 |
if(is.null(.ENV$current_annotation_which)) { |
640 | 651 |
which = match.arg(which)[1] |
... | ... |
@@ -1020,6 +1031,7 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(), |
1020 | 1031 |
# -axis_param parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters. |
1021 | 1032 |
# -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
1022 | 1033 |
# -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
1034 |
+# -... Other arguments. |
|
1023 | 1035 |
# |
1024 | 1036 |
# == value |
1025 | 1037 |
# An annotation function which can be used in `HeatmapAnnotation`. |
... | ... |
@@ -1038,7 +1050,20 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(), |
1038 | 1050 |
anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6, |
1039 | 1051 |
gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE, |
1040 | 1052 |
axis_param = default_axis_param(which), |
1041 |
- width = NULL, height = NULL) { |
|
1053 |
+ width = NULL, height = NULL, ...) { |
|
1054 |
+ |
|
1055 |
+ other_args = list(...) |
|
1056 |
+ if(length(other_args)) { |
|
1057 |
+ if("axis_gp" %in% names(other_args)) { |
|
1058 |
+ stop_wrap("`axis_gp` is removed from the arguments. Use `axis_param = list(gp = ...)` instead.") |
|
1059 |
+ } |
|
1060 |
+ if("axis_side" %in% names(other_args)) { |
|
1061 |
+ stop_wrap("`axis_side` is removed from the arguments. Use `axis_param = list(side = ...)` instead.") |
|
1062 |
+ } |
|
1063 |
+ if("axis_direction" %in% names(other_args)) { |
|
1064 |
+ stop_wrap("`axis_direction` is not supported any more.") |
|
1065 |
+ } |
|
1066 |
+ } |
|
1042 | 1067 |
|
1043 | 1068 |
if(inherits(x, "list")) x = do.call("cbind", x) |
1044 | 1069 |
if(inherits(x, "data.frame")) x = as.matrix(x) |
... | ... |
@@ -1193,6 +1218,7 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR |
1193 | 1218 |
# -axis_param parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters. |
1194 | 1219 |
# -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
1195 | 1220 |
# -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
1221 |
+# -... Other arguments. |
|
1196 | 1222 |
# |
1197 | 1223 |
# == value |
1198 | 1224 |
# An annotation function which can be used in `HeatmapAnnotation`. |
... | ... |
@@ -1210,7 +1236,20 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR |
1210 | 1236 |
anno_boxplot = function(x, which = c("column", "row"), border = TRUE, |
1211 | 1237 |
gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6, |
1212 | 1238 |
pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which), |
1213 |
- width = NULL, height = NULL) { |
|
1239 |
+ width = NULL, height = NULL, ...) { |
|
1240 |
+ |
|
1241 |
+ other_args = list(...) |
|
1242 |
+ if(length(other_args)) { |
|
1243 |
+ if("axis_gp" %in% names(other_args)) { |
|
1244 |
+ stop_wrap("`axis_gp` is removed from the arguments. Use `axis_param = list(gp = ...)` instead.") |
|
1245 |
+ } |
|
1246 |
+ if("axis_side" %in% names(other_args)) { |
|
1247 |
+ stop_wrap("`axis_side` is removed from the arguments. Use `axis_param = list(side = ...)` instead.") |
|
1248 |
+ } |
|
1249 |
+ if("axis_direction" %in% names(other_args)) { |
|
1250 |
+ stop_wrap("`axis_direction` is not supported any more.") |
|
1251 |
+ } |
|
1252 |
+ } |
|
1214 | 1253 |
|
1215 | 1254 |
if(is.null(.ENV$current_annotation_which)) { |
1216 | 1255 |
which = match.arg(which)[1] |
... | ... |
@@ -293,6 +293,16 @@ Heatmap = function(matrix, col, name, |
293 | 293 |
} |
294 | 294 |
} |
295 | 295 |
|
296 |
+ if("top_annotation_height" %in% called_args) { |
|
297 |
+ stop_wrap("`top_annotation_height` is removed. Set the height directly in `HeatmapAnnotation()`.") |
|
298 |
+ } |
|
299 |
+ if("bottom_annotation_height" %in% called_args) { |
|
300 |
+ stop_wrap("`bottom_annotation_height` is removed. Set the height directly in `HeatmapAnnotation()`.") |
|
301 |
+ } |
|
302 |
+ if("combined_name_fun" %in% called_args) { |
|
303 |
+ stop_wrap("`combined_name_fun` is removed. Please directly set `row_names_title`. See https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#titles-for-splitting") |
|
304 |
+ } |
|
305 |
+ |
|
296 | 306 |
if("heatmap_legend_param" %in% called_args) { |
297 | 307 |
for(opt_name in setdiff(c("title_gp", "title_position", "labels_gp", "grid_width", "grid_height", "border"), names(heatmap_legend_param))) { |
298 | 308 |
opt_name2 = paste0("legend_", opt_name) |
... | ... |
@@ -250,7 +250,7 @@ SingleAnnotation = function(name, value, col, fun, |
250 | 250 |
} else { |
251 | 251 |
name_offset = unit(1, "mm") |
252 | 252 |
} |
253 |
- name_rot = ifelse(which == "column", 0, 90) |
|
253 |
+ if(is.null(name_rot)) name_rot = ifelse(which == "column", 0, 90) |
|
254 | 254 |
|
255 | 255 |
anno_name = name |
256 | 256 |
if(which == "column") { |
... | ... |
@@ -94,6 +94,9 @@ densityHeatmap = function(data, |
94 | 94 |
if(any(grepl("row", names(arg_list)))) { |
95 | 95 |
stop_wrap("density heatmaps do not allow to set rows.") |
96 | 96 |
} |
97 |
+ if("anno" %in% names(arg_list)) { |
|
98 |
+ stop_wrap("`anno` is removed from the argument. Please directly construct a `HeatmapAnnotation` object and set to `top_annotation` or `bottom_annotation`.") |
|
99 |
+ } |
|
97 | 100 |
} |
98 | 101 |
|
99 | 102 |
ylab = ylab |
... | ... |
@@ -88,6 +88,28 @@ oncoPrint = function(mat, |
88 | 88 |
arg_list = as.list(match.call())[-1] |
89 | 89 |
arg_names = names(arg_list) |
90 | 90 |
|
91 |
+ if("alter_fun_list" %in% arg_names) { |
|
92 |
+ stop_wrap("`alter_fun_list` is removed from the arguments.") |
|
93 |
+ } |
|
94 |
+ if("axis_gp" %in% arg_names) { |
|
95 |
+ stop_wrap("`axis_gp` is removed from the arguments. Please set `axis_param(gp = ...)` in `anno_oncoprint_barplot()` when you define the `top_annotation` or `right_annotation`.") |
|
96 |
+ } |
|
97 |
+ if("show_row_names" %in% arg_names) { |
|
98 |
+ stop_wrap("`show_row_names` is removed from the arguments. Please directly remove `anno_oncoprint_barplot()` in `right_annotation` to remove barplots on the left of the oncoPrint.") |
|
99 |
+ } |
|
100 |
+ if("row_barplot_width" %in% arg_names) { |
|
101 |
+ stop_wrap("`row_barplot_width` is removed from the arguments. Please directly set `width` in `anno_oncoprint_barplot()` in `right_annotation`.") |
|
102 |
+ } |
|
103 |
+ if("top_annotation_height" %in% arg_names) { |
|
104 |
+ stop_wrap("`top_annotation_height` is removed from the arguments. Please directly set `height` in `anno_oncoprint_barplot()` in `top_annotation`.") |
|
105 |
+ } |
|
106 |
+ if("bottom_annotation_height" %in% arg_names) { |
|
107 |
+ stop_wrap("`bottom_annotation_height` is removed from the arguments. Please directly set `height` in `bottom_annotation`.") |
|
108 |
+ } |
|
109 |
+ if("barplot_ignore" %in% arg_names) { |
|
110 |
+ stop_wrap("`barplot_ignore` is removed from the arguments. The subset of alterations now can be controlled in `anno_oncoprint_barplot()`.") |
|
111 |
+ } |
|
112 |
+ |
|
91 | 113 |
# convert mat to mat_list |
92 | 114 |
if(inherits(mat, "data.frame")) { |
93 | 115 |
mat = as.matrix(mat) |
... | ... |
@@ -10,9 +10,9 @@ Method dispatch page for \code{add_heatmap}. |
10 | 10 |
\code{add_heatmap} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
|
14 | 13 |
\item \code{\link{add_heatmap,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
15 | 14 |
\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
15 |
+\item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
|
16 | 16 |
} |
17 | 17 |
} |
18 | 18 |
\examples{ |
... | ... |
@@ -10,7 +10,7 @@ Barplot Annotation |
10 | 10 |
anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6, |
11 | 11 |
gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE, |
12 | 12 |
axis_param = default_axis_param(which), |
13 |
- width = NULL, height = NULL) |
|
13 |
+ width = NULL, height = NULL, ...) |
|
14 | 14 |
} |
15 | 15 |
\arguments{ |
16 | 16 |
|
... | ... |
@@ -26,6 +26,7 @@ anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_wid |
26 | 26 |
\item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.} |
27 | 27 |
\item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.} |
28 | 28 |
\item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.} |
29 |
+ \item{...}{Other arguments.} |
|
29 | 30 |
|
30 | 31 |
} |
31 | 32 |
\value{ |
... | ... |
@@ -10,7 +10,7 @@ Boxplot Annotation |
10 | 10 |
anno_boxplot(x, which = c("column", "row"), border = TRUE, |
11 | 11 |
gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6, |
12 | 12 |
pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which), |
13 |
- width = NULL, height = NULL) |
|
13 |
+ width = NULL, height = NULL, ...) |
|
14 | 14 |
} |
15 | 15 |
\arguments{ |
16 | 16 |
|
... | ... |
@@ -28,6 +28,7 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE, |
28 | 28 |
\item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.} |
29 | 29 |
\item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.} |
30 | 30 |
\item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.} |
31 |
+ \item{...}{Other arguments.} |
|
31 | 32 |
|
32 | 33 |
} |
33 | 34 |
\value{ |
... | ... |
@@ -9,7 +9,7 @@ Points Annotation |
9 | 9 |
\usage{ |
10 | 10 |
anno_points(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16, |
11 | 11 |
size = unit(2, "mm"), ylim = NULL, extend = 0.05, axis = TRUE, |
12 |
- axis_param = default_axis_param(which), width = NULL, height = NULL) |
|
12 |
+ axis_param = default_axis_param(which), width = NULL, height = NULL, ...) |
|
13 | 13 |
} |
14 | 14 |
\arguments{ |
15 | 15 |
|
... | ... |
@@ -25,6 +25,7 @@ anno_points(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16, |
25 | 25 |
\item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.} |
26 | 26 |
\item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.} |
27 | 27 |
\item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.} |
28 |
+ \item{...}{Other arguments.} |
|
28 | 29 |
|
29 | 30 |
} |
30 | 31 |
\value{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{column_dend}. |
10 | 10 |
\code{column_dend} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{column_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
14 | 13 |
\item \code{\link{column_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
14 |
+\item \code{\link{column_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}. |
10 | 10 |
\code{component_width} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
14 | 13 |
\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
14 |
+\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -10,12 +10,12 @@ Method dispatch page for \code{draw}. |
10 | 10 |
\code{draw} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
|
14 |
-\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method |
|
15 |
-\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
|
16 | 13 |
\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
14 |
+\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method |
|
17 | 15 |
\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
18 | 16 |
\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
17 |
+\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
|
18 |
+\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
|
19 | 19 |
} |
20 | 20 |
} |
21 | 21 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{draw_title}. |
10 | 10 |
\code{draw_title} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{draw_title,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
14 | 13 |
\item \code{\link{draw_title,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
14 |
+\item \code{\link{draw_title,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{make_layout}. |
10 | 10 |
\code{make_layout} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{make_layout,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
14 | 13 |
\item \code{\link{make_layout,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
14 |
+\item \code{\link{make_layout,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -11,11 +11,11 @@ Method dispatch page for \code{show}. |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 | 13 |
\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method |
14 |
-\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
|
15 | 14 |
\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
16 |
-\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
|
17 |
-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
15 |
+\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
|
18 | 16 |
\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
17 |
+\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
18 |
+\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
|
19 | 19 |
} |
20 | 20 |
} |
21 | 21 |
\examples{ |