@@ -149,7 +149,7 @@ export("height<-")

 export("ht_global_opt")

 export("ht_opt")

 export("is_abs_unit")

-export("list_component")

+export("list_components")

 export("max_text_height")

 export("max_text_width")

 export("merge_dendrogram")

@@ -405,13 +405,16 @@ anno_oncoprint_barplot = function(type = all_type, which = c("column", "row"),

 	if(which == "column") {

 		count = apply(arr, c(2, 3), sum)

-		anno_barplot(count, gp = gpar(fill = col, col = NA), which = "column",

+		fun = anno_barplot(count, gp = gpar(fill = col, col = NA), which = "column",

 			baseline = 0, height = anno_size$height, border = border, ...)

 	} else {

 		count = apply(arr, c(1, 3), sum)

-		anno_barplot(count, gp = gpar(fill = col, col = NA), which = "row",

+		fun = anno_barplot(count, gp = gpar(fill = col, col = NA), which = "row",

 			baseline = 0, width = anno_size$width, border = border, ...)

 	}

+	

+	fun@show_name = FALSE

+	return(fun)

 }

 guess_alter_fun_is_vectorized = function(alter_fun) {

@@ -289,7 +289,7 @@ rep.list = function(x, n) {

 # == value

 # A vector of viewport names.

 #

-list_component = function() {

+list_components = function() {

     vp = grid.ls(viewports = TRUE, grobs = FALSE, flatten = FALSE, print = FALSE)

     vp = unlist(vp)

     attributes(vp) = NULL

@@ -15,5 +15,4 @@ method so that above three classes can be appended to each other.

 \examples{

 # There is no example

 NULL

-

 }

@@ -26,5 +26,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -23,5 +23,4 @@ See \code{\link{AnnotationFunction}} constructor for details.

 \examples{

 # There is no example

 NULL

-

 }

@@ -121,5 +121,4 @@ ComplexHeatmap Complete Reference ().

 \examples{

 # There is no example

 NULL

-

 }

@@ -26,5 +26,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -36,5 +36,4 @@ You can refer to the ComplexHeatmap Complete Reference for all the information o

 \examples{

 # There is no example

 NULL

-

 }

@@ -23,5 +23,4 @@ If the heatmap list is horizontal, \code{i} is the real row indices and \code{j}

 \examples{

 # There is no example

 NULL

-

 }

@@ -30,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -185,5 +185,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -25,5 +25,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -74,5 +74,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -26,5 +26,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -26,5 +26,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -28,5 +28,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -40,5 +40,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -28,5 +28,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -28,5 +28,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -28,5 +28,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{adjust_heatmap_list-HeatmapList-method}

 \alias{adjust_heatmap_list,HeatmapList-method}

-\alias{adjust_heatmap_list}

 \title{

 Adjust heatmap list

 }

@@ -23,8 +22,8 @@ This function is only for internal use.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{adjust_heatmap_list}

 \examples{

 # There is no example

 NULL

-

 }

@@ -20,5 +20,4 @@ anno_link(...)

 \examples{

 # There is no example

 NULL

-

 }

@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -26,5 +26,4 @@ A \code{\link[grid]{grob}} object.

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{annotation_legend_size-HeatmapList-method}

 \alias{annotation_legend_size,HeatmapList-method}

-\alias{annotation_legend_size}

 \title{

 Size of the annotation legend viewport

 }

@@ -29,8 +28,8 @@ A \code{\link[grid]{unit}} object.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{annotation_legend_size}

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{color_mapping_legend-ColorMapping-method}

 \alias{color_mapping_legend,ColorMapping-method}

-\alias{color_mapping_legend}

 \title{

 Draw Legend Based on Color Mapping

 }

@@ -66,8 +65,8 @@ A \code{\link{Legends-class}} object.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{color_mapping_legend}

 \examples{

 # There is no example

 NULL

-

 }

@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -31,5 +31,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -24,5 +24,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -30,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -26,5 +26,4 @@ The environment is at \code{object@var_env}.

 \examples{

 # There is no example

 NULL

-

 }

@@ -21,5 +21,4 @@ it calls \code{\link{copy_all,AnnotationFunction-method}} to hard copy the varia

 \examples{

 # There is no example

 NULL

-

 }

@@ -17,5 +17,4 @@ dend_heights(x)

 \examples{

 # There is no example

 NULL

-

 }

@@ -28,5 +28,4 @@ A \code{\link{grob}} object which is generally contructed by \code{\link[grid]{s

 \examples{

 # There is no example

 NULL

-

 }

@@ -17,5 +17,4 @@ Dimension of the Heatmap

 \examples{

 # There is no example

 NULL

-

 }

@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -27,5 +27,4 @@ which is generally for testing purpose.

 \examples{

 # There is no example

 NULL

-

 }

@@ -33,5 +33,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -29,5 +29,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -174,5 +174,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -27,5 +27,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{draw_annotation-Heatmap-method}

 \alias{draw_annotation,Heatmap-method}

-\alias{draw_annotation}

 \title{

 Draw Heatmap Annotations on the Heatmap

 }

@@ -31,8 +30,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{draw_annotation}

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{draw_annotation_legend-HeatmapList-method}

 \alias{draw_annotation_legend,HeatmapList-method}

-\alias{draw_annotation_legend}

 \title{

 Draw legends for all column annotations

 }

@@ -28,8 +27,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{draw_annotation_legend}

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{draw_dend-Heatmap-method}

 \alias{draw_dend,Heatmap-method}

-\alias{draw_dend}

 \title{

 Draw Heatmap Dendrograms

 }

@@ -34,8 +33,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{draw_dend}

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{draw_dimnames-Heatmap-method}

 \alias{draw_dimnames,Heatmap-method}

-\alias{draw_dimnames}

 \title{

 Draw row names or column names

 }

@@ -30,8 +29,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{draw_dimnames}

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{draw_heatmap_body-Heatmap-method}

 \alias{draw_heatmap_body,Heatmap-method}

-\alias{draw_heatmap_body}

 \title{

 Draw the Heatmap Body

 }

@@ -29,8 +28,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{draw_heatmap_body}

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{draw_heatmap_legend-HeatmapList-method}

 \alias{draw_heatmap_legend,HeatmapList-method}

-\alias{draw_heatmap_legend}

 \title{

 Draw legends for all heatmaps

 }

@@ -28,8 +27,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{draw_heatmap_legend}

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{draw_heatmap_list-HeatmapList-method}

 \alias{draw_heatmap_list,HeatmapList-method}

-\alias{draw_heatmap_list}

 \title{

 Draw the list of heatmaps

 }

@@ -26,8 +25,8 @@ This function returns no value.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{draw_heatmap_list}

 \examples{

 # There is no example

 NULL

-

 }

@@ -32,5 +32,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -30,5 +30,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{get_color_mapping_list-HeatmapAnnotation-method}

 \alias{get_color_mapping_list,HeatmapAnnotation-method}

-\alias{get_color_mapping_list}

 \title{

 Get a List of ColorMapping objects

 }

@@ -26,8 +25,8 @@ A list of \code{\link{ColorMapping-class}} objects or an empty list.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{get_color_mapping_list}

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{get_legend_param_list-HeatmapAnnotation-method}

 \alias{get_legend_param_list,HeatmapAnnotation-method}

-\alias{get_legend_param_list}

 \title{

 Get a List of Annotation Legend Parameters

 }

@@ -26,8 +25,8 @@ A list.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{get_legend_param_list}

 \examples{

 # There is no example

 NULL

-

 }

@@ -29,5 +29,4 @@ All the values are measured with \code{native} coordinate.

 \examples{

 # There is no example

 NULL

-

 }

@@ -22,5 +22,4 @@ general method. It applies \code{\link[grid]{grid.draw}} on the \code{grob} slot

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{heatmap_legend_size-HeatmapList-method}

 \alias{heatmap_legend_size,HeatmapList-method}

-\alias{heatmap_legend_size}

 \title{

 Size of the heatmap legend viewport

 }

@@ -26,8 +25,8 @@ A \code{\link[grid]{unit}} object.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{heatmap_legend_size}

 \examples{

 # There is no example

 NULL

-

 }

@@ -18,5 +18,4 @@ Height of the HeatmapAnnotation Object

 \examples{

 # There is no example

 NULL

-

 }

@@ -21,5 +21,4 @@ The returned unit x is always in \code{mm}.

 \examples{

 # There is no example

 NULL

-

 }

@@ -18,5 +18,4 @@ Height of the SingleAnnotation object

 \examples{

 # There is no example

 NULL

-

 }

@@ -18,5 +18,4 @@ height(x, ...)

 \examples{

 # There is no example

 NULL

-

 }

@@ -20,5 +20,4 @@ Assign the Height to the AnnotationFunction Object

 \examples{

 # There is no example

 NULL

-

 }

@@ -20,5 +20,4 @@ Assign the Height to the HeatmapAnnotation Object

 \examples{

 # There is no example

 NULL

-

 }

@@ -20,5 +20,4 @@ Assign the Height to the SingleAnnotation Object

 \examples{

 # There is no example

 NULL

-

 }

@@ -20,5 +20,4 @@ height(x, ...) <- value

 \examples{

 # There is no example

 NULL

-

 }

@@ -17,5 +17,4 @@ Grob width for annotation_axis

 \examples{

 # There is no example

 NULL

-

 }

@@ -17,5 +17,4 @@ Grob height for packed_legends

 \examples{

 # There is no example

 NULL

-

 }

@@ -17,5 +17,4 @@ Grob height for legend_body

 \examples{

 # There is no example

 NULL

-

 }

@@ -17,5 +17,4 @@ Grob height for packed_legends

 \examples{

 # There is no example

 NULL

-

 }

@@ -25,5 +25,4 @@ will also be sychronized in \code{\link{ht_opt}}.

 \examples{

 # There is no example

 NULL

-

 }

@@ -17,5 +17,4 @@ Number of Annotations

 \examples{

 # There is no example

 NULL

-

 }

@@ -17,5 +17,4 @@ Length of the HeatmapList object

 \examples{

 # There is no example

 NULL

-

 }

similarity index 72%

rename from man/list_component.rd

rename to man/list_components.rd

@@ -1,5 +1,5 @@

-\name{list_component}

-\alias{list_component}

+\name{list_components}

+\alias{list_components}

 \title{

 List All Heatmap Components

 }

@@ -7,7 +7,7 @@ List All Heatmap Components

 List All Heatmap Components

 }

 \usage{

-list_component()

+list_components()

 }

 \value{

 A vector of viewport names.

@@ -15,5 +15,4 @@ A vector of viewport names.

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{make_column_cluster-Heatmap-method}

 \alias{make_column_cluster,Heatmap-method}

-\alias{make_column_cluster}

 \title{

 Make Cluster on Columns

 }

@@ -29,8 +28,8 @@ A \code{\link{Heatmap-class}} object.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{make_column_cluster}

 \examples{

 # There is no example

 NULL

-

 }

@@ -32,5 +32,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -133,5 +133,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{make_row_cluster-Heatmap-method}

 \alias{make_row_cluster,Heatmap-method}

-\alias{make_row_cluster}

 \title{

 Make Cluster on Rows

 }

@@ -28,8 +27,8 @@ A \code{\link{Heatmap-class}} object.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{make_row_cluster}

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{map_to_colors-ColorMapping-method}

 \alias{map_to_colors,ColorMapping-method}

-\alias{map_to_colors}

 \title{

 Map Values to Colors

 }

@@ -35,3 +34,4 @@ col_fun = colorRamp2(c(0, 1), c("white", "red"))

 cm = ColorMapping(col_fun = col_fun)

 map_to_colors(cm, runif(10))

 }

+\alias{map_to_colors}

@@ -17,5 +17,4 @@ Names of the heatmaps/annotations

 \examples{

 # There is no example

 NULL

-

 }

@@ -17,5 +17,4 @@ Number of Columns in the Heatmap

 \examples{

 # There is no example

 NULL

-

 }

@@ -18,5 +18,4 @@ Number of Observations

 \examples{

 # There is no example

 NULL

-

 }

@@ -21,5 +21,4 @@ It returns the \code{n} slot of the annotaton function. If it does not exist, it

 \examples{

 # There is no example

 NULL

-

 }

@@ -17,5 +17,4 @@ Number of Rows in the Heatmap

 \examples{

 # There is no example

 NULL

-

 }

@@ -76,5 +76,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -39,5 +39,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{prepare-Heatmap-method}

 \alias{prepare,Heatmap-method}

-\alias{prepare}

 \title{

 Prepare the Heatmap

 }

@@ -34,8 +33,8 @@ The \code{\link{Heatmap-class}} object.

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

+\alias{prepare}

 \examples{

 # There is no example

 NULL

-

 }

@@ -1,6 +1,5 @@

 \name{resize-HeatmapAnnotation-method}

 \alias{resize,HeatmapAnnotation-method}

-\alias{resize}

 \title{

 Resize the Width or Height of Heatmap Annotations

 }

@@ -41,8 +40,8 @@ the basic rule is:

      and \code{anno_simple_size} is disabled.

 6. If \code{simple_anno_size_adjust} is \code{FALSE}, the size of the simple annotations will not change.

 }

+\alias{resize}

 \examples{

 # There is no example

 NULL

-