... | ... |
@@ -1,31 +1,31 @@ |
1 |
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout')) |
|
2 |
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list')) |
|
3 |
-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title')) |
|
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')) |
|
4 | 5 |
setGeneric('re_size', function(object, ...) standardGeneric('re_size')) |
5 |
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend')) |
|
6 |
-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list')) |
|
6 |
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout')) |
|
7 |
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size')) |
|
7 | 8 |
setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list')) |
8 |
-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend')) |
|
9 |
-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width')) |
|
10 |
-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list')) |
|
11 |
-setGeneric('component_height', function(object, ...) standardGeneric('component_height')) |
|
12 |
-setGeneric('component_width', function(object, ...) standardGeneric('component_width')) |
|
13 |
-setGeneric('prepare', function(object, ...) standardGeneric('prepare')) |
|
14 |
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend')) |
|
15 |
-setGeneric('row_order', function(object, ...) standardGeneric('row_order')) |
|
16 |
-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size')) |
|
17 |
-setGeneric('draw', function(object, ...) standardGeneric('draw')) |
|
18 | 9 |
setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend')) |
19 | 10 |
setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster')) |
20 |
-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all')) |
|
11 |
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend')) |
|
12 |
+setGeneric('row_order', function(object, ...) standardGeneric('row_order')) |
|
13 |
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list')) |
|
21 | 14 |
setGeneric('row_dend', function(object, ...) standardGeneric('row_dend')) |
22 |
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation')) |
|
15 |
+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap')) |
|
16 |
+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width')) |
|
23 | 17 |
setGeneric('column_order', function(object, ...) standardGeneric('column_order')) |
24 |
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height')) |
|
25 | 18 |
setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend')) |
26 |
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster')) |
|
27 |
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body')) |
|
28 |
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors')) |
|
19 |
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend')) |
|
20 |
+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size')) |
|
21 |
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation')) |
|
22 |
+setGeneric('prepare', function(object, ...) standardGeneric('prepare')) |
|
29 | 23 |
setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames')) |
30 |
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size')) |
|
31 |
-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap')) |
|
24 |
+setGeneric('draw', function(object, ...) standardGeneric('draw')) |
|
25 |
+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title')) |
|
26 |
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster')) |
|
27 |
+setGeneric('component_width', function(object, ...) standardGeneric('component_width')) |
|
28 |
+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')) |
... | ... |
@@ -125,6 +125,7 @@ subset_vector = function(x, i) x[i] |
125 | 125 |
# the value of ``pt_size`` can be a vector, while if ``x`` is a matrix, ``pt_size`` can |
126 | 126 |
# only be a single value. |
127 | 127 |
# -pt_gp Graphic parameters for points/symbols. The length setting is same as ``pt_size``. |
128 |
+# If ``pch`` is set as letters, the fontsize should be set as ``pt_gp = gpar(fontsize = ...)``. |
|
128 | 129 |
# -anno_simple_size size of the simple annotation. |
129 | 130 |
# -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation. |
130 | 131 |
# -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation. |
... | ... |
@@ -11,8 +11,8 @@ Method dispatch page for \code{add_heatmap}. |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 | 13 |
\item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
14 |
-\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
15 | 14 |
\item \code{\link{add_heatmap,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
15 |
+\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
16 | 16 |
} |
17 | 17 |
} |
18 | 18 |
\examples{ |
... | ... |
@@ -23,7 +23,7 @@ anno_simple(x, col, na_col = "grey", |
23 | 23 |
\item{gp}{Graphic parameters for grid borders. The \code{fill} parameter is disabled.} |
24 | 24 |
\item{pch}{Points/symbols that are added on top of the annotation grids. The value can be numeric or single letters. It can be a vector if \code{x} is a vector and a matrix if \code{x} is a matrix. No points are drawn if the corresponding values are NA.} |
25 | 25 |
\item{pt_size}{Size of the points/symbols. It should be a \code{\link[grid]{unit}} object. If \code{x} is a vector, the value of \code{pt_size} can be a vector, while if \code{x} is a matrix, \code{pt_size} can only be a single value.} |
26 |
- \item{pt_gp}{Graphic parameters for points/symbols. The length setting is same as \code{pt_size}.} |
|
26 |
+ \item{pt_gp}{Graphic parameters for points/symbols. The length setting is same as \code{pt_size}. If \code{pch} is set as letters, the fontsize should be set as \code{pt_gp = gpar(fontsize = ...)}.} |
|
27 | 27 |
\item{anno_simple_size}{size of the simple annotation.} |
28 | 28 |
\item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.} |
29 | 29 |
\item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.} |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{column_order}. |
10 | 10 |
\code{column_order} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
14 | 13 |
\item \code{\link{column_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
14 |
+\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{component_height}. |
10 | 10 |
\code{component_height} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
14 | 13 |
\item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
14 |
+\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-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,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
14 | 13 |
\item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
14 |
+\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{copy_all}. |
10 | 10 |
\code{copy_all} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
|
14 | 13 |
\item \code{\link{copy_all,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
14 |
+\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-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,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
14 | 13 |
\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
15 | 14 |
\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method |
16 | 15 |
\item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
17 |
-\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
18 | 16 |
\item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
17 |
+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
18 |
+\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
19 | 19 |
} |
20 | 20 |
} |
21 | 21 |
\examples{ |
... | ... |
@@ -10,8 +10,8 @@ Method dispatch page for \code{row_dend}. |
10 | 10 |
\code{row_dend} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
-\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
14 | 13 |
\item \code{\link{row_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
14 |
+\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
15 | 15 |
} |
16 | 16 |
} |
17 | 17 |
\examples{ |
... | ... |
@@ -10,12 +10,12 @@ Method dispatch page for \code{show}. |
10 | 10 |
\code{show} can be dispatched on following classes: |
11 | 11 |
|
12 | 12 |
\itemize{ |
13 |
+\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method |
|
13 | 14 |
\item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method |
14 |
-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
15 |
-\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
16 | 15 |
\item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method |
17 | 16 |
\item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method |
18 |
-\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method |
|
17 |
+\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method |
|
18 |
+\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method |
|
19 | 19 |
} |
20 | 20 |
} |
21 | 21 |
\examples{ |