@@ -1,31 +1,31 @@

-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))

-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

-setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))

+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))

+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))

 setGeneric('re_size', function(object, ...) standardGeneric('re_size'))

-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))

-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))

+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))

 setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))

-setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))

-setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))

-setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))

-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))

-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))

-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))

-setGeneric('draw', function(object, ...) standardGeneric('draw'))

 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

 setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))

-setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))

+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))

+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))

+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))

 setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))

-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))

+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

+setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))

 setGeneric('column_order', function(object, ...) standardGeneric('column_order'))

-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))

 setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))

-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))

-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))

+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))

+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))

+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))

+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

 setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))

-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))

+setGeneric('draw', function(object, ...) standardGeneric('draw'))

+setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))

+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))

+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))

+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))

+setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))

+setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))

+setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))

@@ -125,6 +125,7 @@ subset_vector = function(x, i) x[i]

 #          the value of ``pt_size`` can be a vector, while if ``x`` is a matrix, ``pt_size`` can

 #          only be a single value.

 # -pt_gp Graphic parameters for points/symbols. The length setting is same as ``pt_size``.

+#     If ``pch`` is set as letters, the fontsize should be set as ``pt_gp = gpar(fontsize = ...)``.

 # -anno_simple_size size of the simple annotation.

 # -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.

 # -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}.

 \itemize{

 \item \code{\link{add_heatmap,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

-\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{add_heatmap,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{add_heatmap,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -23,7 +23,7 @@ anno_simple(x, col, na_col = "grey",

   \item{gp}{Graphic parameters for grid borders. The \code{fill} parameter is disabled.}

   \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.}

   \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.}

-  \item{pt_gp}{Graphic parameters for points/symbols. The length setting is same as \code{pt_size}.}

+  \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 = ...)}.}

   \item{anno_simple_size}{size of the simple annotation.}

   \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}

   \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}.

 \code{column_order} can be dispatched on following classes:

 \itemize{

-\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{column_order,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{column_order,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -10,8 +10,8 @@ Method dispatch page for \code{component_height}.

 \code{component_height} can be dispatched on following classes:

 \itemize{

-\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{component_height,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{component_height,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -10,8 +10,8 @@ Method dispatch page for \code{component_width}.

 \code{component_width} can be dispatched on following classes:

 \itemize{

-\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{component_width,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{component_width,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -10,8 +10,8 @@ Method dispatch page for \code{copy_all}.

 \code{copy_all} can be dispatched on following classes:

 \itemize{

-\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

 \item \code{\link{copy_all,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

+\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

 }

 }

 \examples{

@@ -10,12 +10,12 @@ Method dispatch page for \code{draw}.

 \code{draw} can be dispatched on following classes:

 \itemize{

-\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

 \item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method

 \item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

-\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{draw,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{draw,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -10,8 +10,8 @@ Method dispatch page for \code{row_dend}.

 \code{row_dend} can be dispatched on following classes:

 \itemize{

-\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{row_dend,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{row_dend,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{

@@ -10,12 +10,12 @@ Method dispatch page for \code{show}.

 \code{show} can be dispatched on following classes:

 \itemize{

+\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method

 \item \code{\link{show,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

-\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 \item \code{\link{show,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

 \item \code{\link{show,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

-\item \code{\link{show,ColorMapping-method}}, \code{\link{ColorMapping-class}} class method

+\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

+\item \code{\link{show,Heatmap-method}}, \code{\link{Heatmap-class}} class method

 }

 }

 \examples{