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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 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'))

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

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

@@ -620,6 +620,7 @@ construct_axis_grob = function(axis_param, which, data_scale) {

 # -axis_param parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters.

 # -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.

+# -... Other arguments.

 #

 # == value

 # An annotation function which can be used in `HeatmapAnnotation`.

@@ -634,7 +635,17 @@ construct_axis_grob = function(axis_param, which, data_scale) {

 # draw(anno, test = "matrix")

 anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16, 

 	size = unit(2, "mm"), ylim = NULL, extend = 0.05, axis = TRUE,

-	axis_param = default_axis_param(which), width = NULL, height = NULL) {

+	axis_param = default_axis_param(which), width = NULL, height = NULL, ...) {

+

+	other_args = list(...)

+	if(length(other_args)) {

+		if("axis_gp" %in% names(other_args)) {

+			stop_wrap("`axis_gp` is removed from the arguments. Use `axis_param = list(gp = ...)` instead.")

+		}

+		if("axis_direction" %in% names(other_args)) {

+			stop_wrap("`axis_direction` is not supported any more.")

+		}

+	}

 	if(is.null(.ENV$current_annotation_which)) {

 		which = match.arg(which)[1]

@@ -1020,6 +1031,7 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),

 # -axis_param parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters.

 # -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.

+# -... Other arguments.

 #

 # == value

 # An annotation function which can be used in `HeatmapAnnotation`.

@@ -1038,7 +1050,20 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),

 anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6,

 	gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE, 

 	axis_param = default_axis_param(which),

-	width = NULL, height = NULL) {

+	width = NULL, height = NULL, ...) {

+

+	other_args = list(...)

+	if(length(other_args)) {

+		if("axis_gp" %in% names(other_args)) {

+			stop_wrap("`axis_gp` is removed from the arguments. Use `axis_param = list(gp = ...)` instead.")

+		}

+		if("axis_side" %in% names(other_args)) {

+			stop_wrap("`axis_side` is removed from the arguments. Use `axis_param = list(side = ...)` instead.")

+		}

+		if("axis_direction" %in% names(other_args)) {

+			stop_wrap("`axis_direction` is not supported any more.")

+		}

+	}

 	if(inherits(x, "list")) x = do.call("cbind", x)

 	if(inherits(x, "data.frame")) x = as.matrix(x)

@@ -1193,6 +1218,7 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 # -axis_param parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters.

 # -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.

+# -... Other arguments.

 #

 # == value

 # An annotation function which can be used in `HeatmapAnnotation`.

@@ -1210,7 +1236,20 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

 	gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6,

 	pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which),

-	width = NULL, height = NULL) {

+	width = NULL, height = NULL, ...) {

+

+	other_args = list(...)

+	if(length(other_args)) {

+		if("axis_gp" %in% names(other_args)) {

+			stop_wrap("`axis_gp` is removed from the arguments. Use `axis_param = list(gp = ...)` instead.")

+		}

+		if("axis_side" %in% names(other_args)) {

+			stop_wrap("`axis_side` is removed from the arguments. Use `axis_param = list(side = ...)` instead.")

+		}

+		if("axis_direction" %in% names(other_args)) {

+			stop_wrap("`axis_direction` is not supported any more.")

+		}

+	}

 	if(is.null(.ENV$current_annotation_which)) {

 		which = match.arg(which)[1]

@@ -293,6 +293,16 @@ Heatmap = function(matrix, col, name,

         }

     }

+    if("top_annotation_height" %in% called_args) {

+        stop_wrap("`top_annotation_height` is removed. Set the height directly in `HeatmapAnnotation()`.")

+    }

+    if("bottom_annotation_height" %in% called_args) {

+        stop_wrap("`bottom_annotation_height` is removed. Set the height directly in `HeatmapAnnotation()`.")

+    }

+    if("combined_name_fun" %in% called_args) {

+        stop_wrap("`combined_name_fun` is removed. Please directly set `row_names_title`. See https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#titles-for-splitting")

+    }

+

     if("heatmap_legend_param" %in% called_args) {

         for(opt_name in setdiff(c("title_gp", "title_position", "labels_gp", "grid_width", "grid_height", "border"), names(heatmap_legend_param))) {

             opt_name2 = paste0("legend_", opt_name)

@@ -250,7 +250,7 @@ SingleAnnotation = function(name, value, col, fun,

     } else {

         name_offset = unit(1, "mm")

     }

-    name_rot = ifelse(which == "column", 0, 90)

+    if(is.null(name_rot)) name_rot = ifelse(which == "column", 0, 90)

     anno_name = name

     if(which == "column") {

@@ -94,6 +94,9 @@ densityHeatmap = function(data,

 		if(any(grepl("row", names(arg_list)))) {

 			stop_wrap("density heatmaps do not allow to set rows.")

 		}

+		if("anno" %in% names(arg_list)) {

+			stop_wrap("`anno` is removed from the argument. Please directly construct a `HeatmapAnnotation` object and set to `top_annotation` or `bottom_annotation`.")

+		}

 	}

 	ylab = ylab

@@ -88,6 +88,28 @@ oncoPrint = function(mat,

 	arg_list = as.list(match.call())[-1]

 	arg_names = names(arg_list)

+	if("alter_fun_list" %in% arg_names) {

+		stop_wrap("`alter_fun_list` is removed from the arguments.")

+	}

+	if("axis_gp" %in% arg_names) {

+		stop_wrap("`axis_gp` is removed from the arguments. Please set `axis_param(gp = ...)` in `anno_oncoprint_barplot()` when you define the `top_annotation` or `right_annotation`.")

+	}

+	if("show_row_names" %in% arg_names) {

+		stop_wrap("`show_row_names` is removed from the arguments. Please directly remove `anno_oncoprint_barplot()` in `right_annotation` to remove barplots on the left of the oncoPrint.")

+	}

+	if("row_barplot_width" %in% arg_names) {

+		stop_wrap("`row_barplot_width` is removed from the arguments. Please directly set `width` in `anno_oncoprint_barplot()` in `right_annotation`.")

+	}

+	if("top_annotation_height" %in% arg_names) {

+		stop_wrap("`top_annotation_height` is removed from the arguments. Please directly set `height` in `anno_oncoprint_barplot()` in `top_annotation`.")

+	}

+	if("bottom_annotation_height" %in% arg_names) {

+		stop_wrap("`bottom_annotation_height` is removed from the arguments. Please directly set `height` in `bottom_annotation`.")

+	}

+	if("barplot_ignore" %in% arg_names) {

+		stop_wrap("`barplot_ignore` is removed from the arguments. The subset of alterations now can be controlled in `anno_oncoprint_barplot()`.")

+	}

+

 	# convert mat to mat_list

 	if(inherits(mat, "data.frame")) {

 		mat = as.matrix(mat)

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

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

 }

 }

 \examples{

@@ -10,7 +10,7 @@ Barplot Annotation

 anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6,

     gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE,

     axis_param = default_axis_param(which),

-    width = NULL, height = NULL)

+    width = NULL, height = NULL, ...)

 }

 \arguments{

@@ -26,6 +26,7 @@ anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_wid

   \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}

   \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.}

+  \item{...}{Other arguments.}

 }

 \value{

@@ -10,7 +10,7 @@ Boxplot Annotation

 anno_boxplot(x, which = c("column", "row"), border = TRUE,

     gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6,

     pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which),

-    width = NULL, height = NULL)

+    width = NULL, height = NULL, ...)

 }

 \arguments{

@@ -28,6 +28,7 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,

   \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}

   \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.}

+  \item{...}{Other arguments.}

 }

 \value{

@@ -9,7 +9,7 @@ Points Annotation

 \usage{

 anno_points(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16,

     size = unit(2, "mm"), ylim = NULL, extend = 0.05, axis = TRUE,

-    axis_param = default_axis_param(which), width = NULL, height = NULL)

+    axis_param = default_axis_param(which), width = NULL, height = NULL, ...)

 }

 \arguments{

@@ -25,6 +25,7 @@ anno_points(x, which = c("column", "row"), border = TRUE, gp = gpar(), pch = 16,

   \item{axis_param}{parameters for controlling axis. See \code{\link{default_axis_param}} for all possible settings and default parameters.}

   \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.}

+  \item{...}{Other arguments.}

 }

 \value{

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

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

 \itemize{

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

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

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

 \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

 }

 }

 \examples{

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

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

 \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

 }

 }

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

 \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

 }

 }

 \examples{

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

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

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

 }

 }

 \examples{