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regenerate docs

Zuguang Gu authored on 17/10/2017 21:31:32
Showing7 changed files

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@@ -1,54 +1,54 @@
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-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
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-
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-setGeneric('get_color_mapping_param_list', function(object, ...) standardGeneric('get_color_mapping_param_list'))
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+setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
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 setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
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-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
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-
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-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
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-
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-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
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-
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-setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
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-
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-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
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+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
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-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
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+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
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-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
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+setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
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-setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
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+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
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-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
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+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
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-setGeneric('draw', function(object, ...) standardGeneric('draw'))
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+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
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-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
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+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
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-setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
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+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
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-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
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+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
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-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
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+setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
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 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
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-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
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+setGeneric('get_color_mapping_param_list', function(object, ...) standardGeneric('get_color_mapping_param_list'))
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-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
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+setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
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 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
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+setGeneric('draw', function(object, ...) standardGeneric('draw'))
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+
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+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
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+
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 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
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 setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
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-setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
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+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
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 setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
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-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
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+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
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+
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+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
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 setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
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+
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+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
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+
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+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
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@@ -70,7 +70,7 @@ Heatmap(matrix, col, name,
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     heatmap_legend_param = list(title = name),
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     use_raster = FALSE,
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     raster_device = c("png", "jpeg", "tiff", "CairoPNG", "CairoJPEG", "CairoTIFF"),
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-    raster_quality = 1,
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+    raster_quality = 2,
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     raster_device_param = list())
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 }
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 \arguments{
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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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@@ -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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@@ -10,9 +10,9 @@ 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,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-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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@@ -10,10 +10,10 @@ 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,HeatmapList-method}}, \code{\link{HeatmapList-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,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,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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 }