@@ -1,54 +1,54 @@

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

-

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

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

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

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

-

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

-

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

-

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

-

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

+

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

+

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

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

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

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

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

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

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

+

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

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

+

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

+

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

@@ -70,7 +70,7 @@ Heatmap(matrix, col, name,

     heatmap_legend_param = list(title = name),

     use_raster = FALSE,

     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),

-    raster_quality = 1,

+    raster_quality = 2,

     raster_device_param = list())

 }

 \arguments{

@@ -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{

@@ -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{

@@ -10,9 +10,9 @@ 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,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-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

 }

 }

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

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

 \itemize{

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

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

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

 }

 }