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revised documentation

Zuguang Gu authored on 03/03/2019 22:06:13
Showing11 changed files

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@@ -1,31 +1,31 @@
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-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
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-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
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-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
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+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
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+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
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+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
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+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
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 setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
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-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
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-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
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+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
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+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
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 setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
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-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
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-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
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-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
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-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
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-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
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-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
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-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
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-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
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-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
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-setGeneric('draw', function(object, ...) standardGeneric('draw'))
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 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
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 setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
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-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
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+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
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+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
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+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
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 setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
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-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
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+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
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+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
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 setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
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-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
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 setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
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-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
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-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
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-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
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+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
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+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
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+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
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+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
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 setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
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-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
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-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
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+setGeneric('draw', function(object, ...) standardGeneric('draw'))
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+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
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+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
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+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
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+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
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+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
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+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
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+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
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@@ -125,6 +125,7 @@ subset_vector = function(x, i) x[i]
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 #          the value of ``pt_size`` can be a vector, while if ``x`` is a matrix, ``pt_size`` can
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 #          only be a single value.
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 # -pt_gp Graphic parameters for points/symbols. The length setting is same as ``pt_size``.
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+#     If ``pch`` is set as letters, the fontsize should be set as ``pt_gp = gpar(fontsize = ...)``.
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 # -anno_simple_size size of the simple annotation.
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 # -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.
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 # -height Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.
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@@ -11,8 +11,8 @@ Method dispatch page for \code{add_heatmap}.
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 \itemize{
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 \item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
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-\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 \item \code{\link{add_heatmap,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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+\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 }
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 }
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 \examples{
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@@ -23,7 +23,7 @@ anno_simple(x, col, na_col = "grey",
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   \item{gp}{Graphic parameters for grid borders. The \code{fill} parameter is disabled.}
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   \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.}
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   \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.}
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-  \item{pt_gp}{Graphic parameters for points/symbols. The length setting is same as \code{pt_size}.}
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+  \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 = ...)}.}
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   \item{anno_simple_size}{size of the simple annotation.}
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   \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}
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   \item{height}{Height of the annotation. The value should be an absolute unit. Height is not allowed to be set for row annotation.}
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@@ -10,8 +10,8 @@ Method dispatch page for \code{column_order}.
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 \code{column_order} can be dispatched on following classes:
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 \itemize{
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-\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 \item \code{\link{column_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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+\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 }
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 }
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 \examples{
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@@ -10,8 +10,8 @@ Method dispatch page for \code{component_height}.
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 \code{component_height} can be dispatched on following classes:
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 \itemize{
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-\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 \item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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+\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 }
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 }
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 \examples{
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@@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}.
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 \code{component_width} can be dispatched on following classes:
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 \itemize{
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-\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 \item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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+\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 }
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 }
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 \examples{
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@@ -10,8 +10,8 @@ Method dispatch page for \code{copy_all}.
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 \code{copy_all} can be dispatched on following classes:
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 \itemize{
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-\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
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 \item \code{\link{copy_all,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
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+\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
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 }
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 }
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 \examples{
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@@ -10,12 +10,12 @@ Method dispatch page for \code{draw}.
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 \code{draw} can be dispatched on following classes:
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 \itemize{
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-\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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 \item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
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 \item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method
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 \item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
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-\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 \item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
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+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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+\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 }
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 }
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 \examples{
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@@ -10,8 +10,8 @@ Method dispatch page for \code{row_dend}.
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 \code{row_dend} can be dispatched on following classes:
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 \itemize{
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-\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 \item \code{\link{row_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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+\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 }
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 }
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 \examples{
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@@ -10,12 +10,12 @@ Method dispatch page for \code{show}.
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 \code{show} can be dispatched on following classes:
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 \itemize{
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+\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
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 \item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
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-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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-\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 \item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
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 \item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
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-\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method
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+\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
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+\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method
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 }
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 }
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 \examples{