@@ -48,8 +48,8 @@ S3method("heightDetails", "legend_body")

 export("heightDetails.legend_body")

 S3method("heightDetails", "packed_legends")

 export("heightDetails.packed_legends")

-S3method("heightDetails", "text_box")

-export("heightDetails.text_box")

+S3method("heightDetails", "textbox")

+export("heightDetails.textbox")

 S3method("length", "HeatmapAnnotation")

 export("length.HeatmapAnnotation")

 S3method("length", "HeatmapList")

@@ -124,8 +124,8 @@ S3method("widthDetails", "legend_body")

 export("widthDetails.legend_body")

 S3method("widthDetails", "packed_legends")

 export("widthDetails.packed_legends")

-S3method("widthDetails", "text_box")

-export("widthDetails.text_box")

+S3method("widthDetails", "textbox")

+export("widthDetails.textbox")

 export("%v%")

 export("AdditiveUnit")

 export("AnnotationFunction")

@@ -159,7 +159,7 @@ export("anno_points")

 export("anno_simple")

 export("anno_summary")

 export("anno_text")

-export("anno_text_box")

+export("anno_textbox")

 export("anno_zoom")

 export("annotation_axis_grob")

 export("bar3D")

@@ -199,7 +199,7 @@ export("getXY_in_parent_vp")

 export("grid.annotation_axis")

 export("grid.boxplot")

 export("grid.dendrogram")

-export("grid.text_box")

+export("grid.textbox")

 export("gt_render")

 export("ht_global_opt")

 export("ht_opt")

@@ -235,7 +235,7 @@ export("subset_matrix_by_row")

 export("subset_no")

 export("subset_vector")

 export("test_alter_fun")

-export("text_box_grob")

+export("textbox_grob")

 export("unify_mat_list")

 export("upset_left_annotation")

 export("upset_right_annotation")

@@ -290,7 +290,6 @@ exportMethods("set_component_height")

 exportMethods("set_component_width")

 import(digest)

-import(parallel)

 import(doParallel)

 import(foreach)

 import(grDevices)

@@ -298,6 +297,7 @@ import(graphics)

 import(grid)

 import(matrixStats)

 import(methods)

+import(parallel)

 import(png)

 import(stats)

 importFrom("GetoptLong", qq)

@@ -324,5 +324,4 @@ importFrom("utils", "combn")

 importFrom("utils", "getFromNamespace")

 importFrom("utils", "packageDescription")

 importFrom("utils", "str")

-importFrom("utils", "sessionInfo")

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -410,6 +410,7 @@ setMethod(f = "draw",

     show_parent_dend_line = NULL

     ) {

+    .ENV$IS_UNDER_JUPYTER = is_under_jupyter()

     if(.ENV$IS_UNDER_JUPYTER && !.ENV$IS_UNDER_JUPYTER_IGNORE) {

         .ENV$IS_UNDER_JUPYTER_IGNORE = TRUE

similarity index 89%

rename from R/anno_text_box.R

rename to R/anno_textbox.R

@@ -28,15 +28,15 @@

 # == example

 # words = sapply(1:30, function(x) strrep(sample(letters, 1), sample(3:10, 1)))

 # grid.newpage()

-# grid.text_box(words, gp = gpar(fontsize = runif(30, min = 5, max = 30)))

+# grid.textbox(words, gp = gpar(fontsize = runif(30, min = 5, max = 30)))

 #

 # sentenses = c("This is sentense 1", "This is a long long long long long long long sentense.")

 # grid.newpage()

-# grid.text_box(sentenses)

-# grid.text_box(sentenses, word_wrap = TRUE)

-# grid.text_box(sentenses, word_wrap = TRUE, add_new_line = TRUE)

+# grid.textbox(sentenses)

+# grid.textbox(sentenses, word_wrap = TRUE)

+# grid.textbox(sentenses, word_wrap = TRUE, add_new_line = TRUE)

 #

-text_box_grob = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "centre", 

+textbox_grob = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "centre", 

 	gp = gpar(), background_gp = gpar(col = "black", fill = "transparent"), round_corners = FALSE, r = unit(0.1, "snpc"),

 	line_space = unit(4, "pt"), text_space = unit(4, "pt"), max_width = unit(100, "mm"), 

 	padding = unit(4, "pt"), first_text_from = "top", add_new_line = FALSE, word_wrap = FALSE) { # width in mm

@@ -203,33 +203,33 @@ text_box_grob = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just

 		# rectGrob(x = x, y = y, width = text_width, height = text_height, default.units = "mm", just = c(0, 0))

 	)

-	gb = gTree(children = gl, cl = "text_box", 

+	gb = gTree(children = gl, cl = "textbox", 

 		vp = viewport(x = vp_x, y = vp_y, just = vp_just, width = unit(w, "mm"), 

 			          height = unit(h, "mm")))

 	return(gb)

 }

 # == title

-# Width for text_box grob

+# Width for textbox grob

 #

 # == param

-# -x The ``text_box`` grob returned by `text_box_grob`.

+# -x The ``textbox`` grob returned by `textbox_grob`.

 #

 # == value

 # A `grid::unit` object.

-widthDetails.text_box = function(x) {

+widthDetails.textbox = function(x) {

 	x$vp$width

 }

 # == title

-# Height for text_box grob

+# Height for textbox grob

 #

 # == param

-# -x The ``text_box`` grob returned by `text_box_grob`.

+# -x The ``textbox`` grob returned by `textbox_grob`.

 #

 # == value

 # A `grid::unit` object.

-heightDetails.text_box = function(x) {

+heightDetails.textbox = function(x) {

 	x$vp$height

 }

@@ -241,13 +241,13 @@ heightDetails.text_box = function(x) {

 # -x X position.

 # -y Y position.

 # -gp Graphics parameters of texts.

-# -... Pass to `text_box_grob`.

+# -... Pass to `textbox_grob`.

 #

 # == details

-# All details can be found in the help page of `text_box_grob`.

+# All details can be found in the help page of `textbox_grob`.

 #

-grid.text_box = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp = gpar(), ...) {

-	gb = text_box_grob(text, x = x, y = y, gp = gp, ...)

+grid.textbox = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp = gpar(), ...) {

+	gb = textbox_grob(text, x = x, y = y, gp = gp, ...)

 	grid.draw(gb)

 }

@@ -257,7 +257,7 @@ grid.text_box = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp =

 #

 # == param

 # -align_to It controls how the text boxes are aligned to the heatmap rows. The value can be a categorical vector which have the same

-#      length as heatmap rows, or a list of row indices.

+#      length as heatmap rows, or a list of row indices. It does not necessarily include all row indices.

 # -text The corresponding texts. The value should be a list of texts. To control graphics parameters of texts in the boxes, The value

 #    of ``text`` can also be set as a list of data frames where the first column contains the text, from the second column contains

 #    graphics parameters for each text. The column names should be "col", "fontsize", "fontfamily" and "fontface".

@@ -265,7 +265,7 @@ grid.text_box = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp =

 # -which Only "row" is allowed.

 # -by Are text boxed arranged by `anno_link` or by `anno_block`?

 # -side Side of the annotation to the heatmap.

-# -... Pass to `text_box_grob`.

+# -... Pass to `textbox_grob`.

 #

 # == example

 # require(circlize)

@@ -278,9 +278,9 @@ grid.text_box = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), gp =

 # names(text) = unique(split)

 #

 # Heatmap(mat, cluster_rows = FALSE, row_split = split,

-#     right_annotation = rowAnnotation(wc = anno_text_box(split, text))

+#     right_annotation = rowAnnotation(wc = anno_textbox(split, text))

 # )

-anno_text_box = function(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"),

+anno_textbox = function(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"),

 	which = c("row", "column"), by = "anno_link", side = c("right", "left"), ...) {

 	if(is.null(background_gp$fill)) background_gp$fill = "#DDDDDD"

@@ -290,7 +290,7 @@ anno_text_box = function(align_to, text, background_gp = gpar(fill = "#DDDDDD",

 	which = match.arg(which)[1]

 	if(which == "column") {

-		stop_wrap("`anno_text_box()` can only be used as row annotation.")

+		stop_wrap("`anno_textbox()` can only be used as row annotation.")

 	}

 	# 1. align_to numeric index, text: a data frame

@@ -328,12 +328,12 @@ anno_text_box = function(align_to, text, background_gp = gpar(fill = "#DDDDDD",

 		stop_wrap("Format of `align_to` or `text` is wrong.")

 	}

-	# a list of text_box grobs

+	# a list of textbox grobs

 	dev.null()

 	gbl = lapply(text, function(x) {

 		if(is.atomic(x)) {

-			text_box_grob(text = x, background_gp = gpar(col = NA, fill = "transparent"), ...)

+			textbox_grob(text = x, background_gp = gpar(col = NA, fill = "transparent"), ...)

 		} else if(is.data.frame(x)) {

 			if("col" %in% colnames(x)) {

 				col = x$col

@@ -358,7 +358,7 @@ anno_text_box = function(align_to, text, background_gp = gpar(fill = "#DDDDDD",

 			} else {

 				fontface = get.gpar("fontface")[[1]]

 			}

-			text_box_grob(text = x[[1]], gp = gpar(col = col, fontsize = fontsize, fontfamily = fontfamily, fontface = fontface), 

+			textbox_grob(text = x[[1]], gp = gpar(col = col, fontsize = fontsize, fontfamily = fontfamily, fontface = fontface), 

 				background_gp = gpar(col = NA, fill = "transparent"), ...)

 		}

 	})

@@ -247,8 +247,7 @@ GLOBAL_PADDING = unit(rep(5.5, 4), "points")

 is_under_jupyter = function() {

-    s = sessionInfo()

-    "IRkernel" %in% c(names(s$otherPkgs), names(s$loadedOnly))

+    "IRkernel" %in% loadedNamespaces()

 }

 .ENV$IS_UNDER_JUPYTER = FALSE

@@ -29,9 +29,6 @@ This message can be suppressed by:

     packageStartupMessage(msg)

-

-    .ENV$IS_UNDER_JUPYTER = is_under_jupyter()

-    .ENV$IS_UNDER_JUPYTER_IGNORE = FALSE

 }

 rv = R.Version()

@@ -15,5 +15,4 @@ method and the \code{\%v\%v} method so that above three classes can be appended

 \examples{

 # There is no example

 NULL

-

 }

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

 \examples{

 # There is no example

 NULL

-

 }

@@ -22,5 +22,4 @@ See \code{\link{AnnotationFunction}} constructor for details.

 \examples{

 # There is no example

 NULL

-

 }

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

 \examples{

 # There is no example

 NULL

-

 }

@@ -40,5 +40,4 @@ The complete reference of ComplexHeatmap package is available at \url{http://jok

 \examples{

 # There is no example

 NULL

-

 }

@@ -22,5 +22,4 @@ Internally used.

 \examples{

 # There is no example

 NULL

-

 }

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

 \examples{

 # There is no example

 NULL

-

 }

@@ -181,8 +181,8 @@ Heatmap(matrix, col, name,

   \item{raster_quality}{A value larger than 1.}

   \item{raster_device_param}{A list of further parameters for the selected graphic device. For raster image support, please check \url{https://jokergoo.github.io/ComplexHeatmap-reference/book/a-single-heatmap.html#heatmap-as-raster-image} .}

   \item{raster_resize_mat}{Whether resize the matrix to let the dimension of the matrix the same as the dimension of the raster image? The value can be logical. If it is \code{TRUE}, \code{\link[base]{mean}} is used to summarize the sub matrix which corresponds to a single pixel. The value can also be a summary function, e.g. \code{\link[base:Extremes]{max}}.}

-  \item{raster_by_magick}{Whether to use \code{\link[magick:transform]{image_resize}} to scale the image.}

-  \item{raster_magick_filter}{Pass to \code{filter} argument of \code{\link[magick:transform]{image_resize}}. A character scalar and all possible values are in \code{\link[magick:options]{filter_types}}. The default is \code{"Lanczos"}.}

+  \item{raster_by_magick}{Whether to use \code{\link[magick]{image_resize}} to scale the image.}

+  \item{raster_magick_filter}{Pass to \code{filter} argument of \code{\link[magick]{image_resize}}. A character scalar and all possible values are in \code{\link[magick]{filter_types}}. The default is \code{"Lanczos"}.}

   \item{post_fun}{A function which will be executed after the heatmap list is drawn.}

 }

@@ -212,5 +212,4 @@ 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

-

 }

@@ -84,5 +84,4 @@ 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

-

 }

@@ -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,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

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

 }

 }

 \examples{

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

 \name{adjust_heatmap_list-HeatmapList-method}

 \alias{adjust_heatmap_list,HeatmapList-method}

-\alias{adjust_heatmap_list}

 \title{

 Adjust Heatmap List

 }

@@ -24,8 +23,8 @@ 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 @@ This function is the same as \code{\link{anno_zoom}}. It links subsets of rows o

 \examples{

 # There is no example

 NULL

-

 }

@@ -36,5 +36,4 @@ Zuguang Gu <z.gu@dkfz.de>

 \examples{

 # There is no example

 NULL

-

 }

similarity index 84%

rename from man/anno_text_box.Rd

rename to man/anno_textbox.Rd

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

-\name{anno_text_box}

-\alias{anno_text_box}

+\name{anno_textbox}

+\alias{anno_textbox}

 \title{

 Text box annotations

 }

@@ -7,7 +7,7 @@ Text box annotations

 Text box annotations

 }

 \usage{

-anno_text_box(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"),

+anno_textbox(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"),

     which = c("row", "column"), by = "anno_link", side = c("right", "left"), ...)

 }

 \arguments{

@@ -18,7 +18,7 @@ anno_text_box(align_to, text, background_gp = gpar(fill = "#DDDDDD", col = "#AAA

   \item{which}{Only "row" is allowed.}

   \item{by}{Are text boxed arranged by \code{\link{anno_link}} or by \code{\link{anno_block}}?}

   \item{side}{Side of the annotation to the heatmap.}

-  \item{...}{Pass to \code{\link{text_box_grob}}.}

+  \item{...}{Pass to \code{\link{textbox_grob}}.}

 }

 \examples{

@@ -32,6 +32,6 @@ text = lapply(unique(split), function(x) {

 names(text) = unique(split)

 Heatmap(mat, cluster_rows = FALSE, row_split = split,

-    right_annotation = rowAnnotation(wc = anno_text_box(split, text))

+    right_annotation = rowAnnotation(wc = anno_textbox(split, text))

 )

 }

@@ -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 Legends

 }

@@ -28,8 +27,8 @@ 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{attach_annotation-Heatmap-method}

 \alias{attach_annotation,Heatmap-method}

-\alias{attach_annotation}

 \title{

 Attach heatmap annotations to the heatmap

 }

@@ -29,3 +28,4 @@ ha2 = HeatmapAnnotation(bar = letters[1:10])

 ht = attach_annotation(ht, ha2)

 ht

 }

+\alias{attach_annotation}

@@ -23,5 +23,4 @@ A \code{\link[GenomicRanges:GRanges-class]{GRanges}} object of the genomic bins.

 \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

 }

@@ -70,8 +69,8 @@ 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

-

 }

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

 \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

 }

 }

 \examples{

@@ -20,5 +20,4 @@ If there is no complement set, it returns zero.

 \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

-

 }

@@ -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{

@@ -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

-

 }

@@ -27,5 +27,4 @@ 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

-

 }

@@ -27,5 +27,4 @@ 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

-

 }

@@ -27,5 +27,4 @@ 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

-

 }

@@ -20,5 +20,4 @@ It recognizes following separators: \code{;:,|}.

 \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 contructed by \code{\link[grid:grid.segment

 \examples{

 # There is no example

 NULL

-

 }

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

 \examples{

 # There is no example

 NULL

-

 }

@@ -28,5 +28,4 @@ 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

-

 }

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

 \examples{

 # There is no example

 NULL

-

 }

@@ -209,5 +209,4 @@ 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

-

 }

@@ -10,11 +10,11 @@ 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,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method

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

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

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

 }

 }

@@ -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 Annotations

 }

@@ -32,8 +31,8 @@ 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