@@ -2,6 +2,7 @@ CHANGES in VERSION 2.13.2

 * `HeatmapAnnotation()`: fixed a bug where annotation legends are not all generated when `df` is set.

 * `UpSet()`: now `bg_col` can be a vector of length more than two.

+* `oncoPrint()`: Add `pct_include` argument.

 ========================

@@ -1,32 +1,32 @@

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -23,6 +23,7 @@

 # -pct_gp Graphic paramters for percent values

 # -pct_digits Digits for the percent values.

 # -pct_side Side of the percent values to the oncoPrint. This argument is currently disabled.

+# -pct_include Alteration types that are included for the calculation of percent values.

 # -row_labels Labels as the row names of the oncoPrint.

 # -show_row_names Whether show row names?

 # -row_names_side Side of the row names to the oncoPrint. This argument is currently disabled.

@@ -69,6 +70,7 @@ oncoPrint = function(mat, name,

 	pct_gp = gpar(fontsize = 10), 

 	pct_digits = 0,

 	pct_side = "left",

+	pct_include = NULL,

 	row_labels = NULL,

 	show_row_names = TRUE,

@@ -368,7 +370,10 @@ oncoPrint = function(mat, name,

 	}

 	# for each gene, percent of samples that have alterations

-	pct_num = rowSums(apply(arr, 1:2, any)) / ncol(mat_list[[1]])

+	if(is.null(pct_include)) {

+		pct_include = dimnames(arr)[[3]]

+	}

+	pct_num = rowSums(apply(arr[, , dimnames(arr)[[3]] %in% pct_include, drop = FALSE], 1:2, any)) / ncol(mat_list[[1]])

 	pct = paste0(round(pct_num * 100, digits = pct_digits), "%")

 	### now the annotations

@@ -10,9 +10,9 @@ Method dispatch page for \code{add_heatmap}.

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

 \itemize{

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

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

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

 }

 }

 \examples{

@@ -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,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

 \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

 }

 }

 \examples{

@@ -11,10 +11,10 @@ Method dispatch page for \code{draw}.

 \itemize{

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

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

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

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

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

 }

 }

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

@@ -22,6 +22,7 @@ oncoPrint(mat, name,

     pct_gp = gpar(fontsize = 10),

     pct_digits = 0,

     pct_side = "left",

+    pct_include = NULL,

     row_labels = NULL,

     show_row_names = TRUE,

@@ -60,6 +61,7 @@ oncoPrint(mat, name,

   \item{pct_gp}{Graphic paramters for percent values}

   \item{pct_digits}{Digits for the percent values.}

   \item{pct_side}{Side of the percent values to the oncoPrint. This argument is currently disabled.}

+  \item{pct_include}{Alteration types that are included for the calculation of percent values.}

   \item{row_labels}{Labels as the row names of the oncoPrint.}

   \item{show_row_names}{Whether show row names?}

   \item{row_names_side}{Side of the row names to the oncoPrint. This argument is currently disabled.}

@@ -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,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method

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

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

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

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

 }

 }

 \examples{