@@ -2,7 +2,7 @@ Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

 Version: 2.9.4

-Date: 2021-09-08

+Date: 2021-10-17

 Author: Zuguang Gu

 Maintainer: Zuguang Gu <z.gu@dkfz.de>

 Depends: R (>= 3.5.0), methods, grid, graphics, stats, grDevices

@@ -139,6 +139,7 @@ export("alter_graphic")

 export("anno_barplot")

 export("anno_block")

 export("anno_boxplot")

+export("anno_customize")

 export("anno_density")

 export("anno_empty")

 export("anno_histogram")

@@ -224,6 +225,7 @@ export("set_size")

 export("smartAlign2")

 export("subset_gp")

 export("subset_matrix_by_row")

+export("subset_no")

 export("subset_vector")

 export("test_alter_fun")

 export("unify_mat_list")

@@ -5,6 +5,7 @@ CHANGES in VERSION 2.9.4

 * Rasterization: the default maximal size for temporary image is set to 30000 px (both for width and height).

 * add a new argument `beside` in `anno_barplot()` to position bars beside each other.

 * add `plot()` method for `Heatmap` and `HeatmapList` classes.

+* add `anno_customize()`.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -101,6 +101,18 @@ subset_matrix_by_row = function(x, i) x[i, , drop = FALSE]

 #

 subset_vector = function(x, i) x[i]

+# == title

+# Do not do subseting

+#

+# == param

+# -x A vector.

+# -i The indices.

+#

+# == details

+# Mainly used for constructing the `AnnotationFunction-class` object.

+#

+subset_no = function(x, i) x

+

 # == title

 # Simple Annotation

 #

@@ -4073,4 +4085,119 @@ anno_zoom = function(align_to, panel_fun = function(index, nm = NULL) { grid.rec

 	return(anno)

 }

+# == title

+# Customized annotation

+#

+# == param

+# -x A categorical variable.

+# -graphics A list of functions that define graphics for each level in ``x``.

+# -which Is it a row annotation or a column annotation?

+# -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.

+# -border Whether to draw border.

+# -verbose Whether to print messages.

+#

+# == details

+# Functions in ``graphics`` define simple graphics drawn in each annotation cell. The function takes four arguments:

+#

+# -x,y Center of the annotation cell.

+# -w,h Width and height of the annotation cell.

+#

+# == value

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

+#

+# == example

+# x = sort(sample(letters[1:3], 10, replace = TRUE))

+# graphics = list(

+#     "a" = function(x, y, w, h) grid.points(x, y, pch = 16),

+#     "b" = function(x, y, w, h) grid.rect(x, y, w*0.8, h*0.8, gp = gpar(fill = "red")),

+#     "c" = function(x, y, w, h) grid.segments(x - 0.5*w, y - 0.5*h, x + 0.5*w, y + 0.5*h, gp = gpar(lty = 2))

+# )

+#

+# anno = anno_customize(x, graphics = graphics)

+#

+# m = matrix(rnorm(100), 10)

+# Heatmap(m, top_annotation = HeatmapAnnotation(bar = x, foo = anno))

+#

+# # Add legends for `foo`

+# ht = Heatmap(m, top_annotation = HeatmapAnnotation(bar = x, foo = anno))

+# lgd = Legend(title = "foo", at = names(graphics), graphics = graphics)

+# draw(ht, annotation_legend_list = list(lgd))

+anno_customize = function(x, graphics = list(), which = c("column", "row"),  

+	border = TRUE, width = NULL, height = NULL, verbose = TRUE) {

+

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

+		which = match.arg(which)[1]

+	} else {

+		which = .ENV$current_annotation_which

+	}

+

+	anno_size = anno_width_and_height(which, width, height, unit(5, "mm"))

+

+	value = as.character(x)

+	n = length(value)

+

+	if(verbose) {

+		nm = setdiff(value, names(graphics))

+		if(length(nm)) {

+			message(qq("Note: following levels in `x` have no graphics defined:\n    @{paste(nm, collapse = ', ')}.\nSet `verbose = FALSE` in `anno_customize()` to turn off this message."))

+		}

+	}

+

+	row_fun = function(index, k = 1, N = 1) {

+		

+		n = length(index)

+

+		pushViewport(viewport(yscale = c(0.5, n+0.5)))

+		for(i in seq_len(n)) {

+			if(!is.null(graphics[[ value[index[i]] ]])) {

+				fun = graphics[[ value[index[i]] ]]

+				pushViewport(viewport(y = n-i+1, height = 1, default.units = "native"))

+				fun(unit(0.5, "npc"), unit(0.5, "npc"), unit(1, "npc"), unit(1, "npc"))

+				popViewport()

+			}

+		}

+		if(border) grid.rect(gp = gpar(fill = "transparent"))

+		popViewport()

+	}

+

+	column_fun = function(index, k = 1, N = 1) {

+		

+		n = length(index)

+

+		pushViewport(viewport(xscale = c(0.5, n+0.5)))

+		for(i in seq_len(n)) {

+			if(!is.null(graphics[[ value[index[i]] ]])) {

+				fun = graphics[[ value[index[i]] ]]

+				pushViewport(viewport(x = i, width = 1, default.units = "native"))

+				fun(unit(0.5, "npc"), unit(0.5, "npc"), unit(1, "npc"), unit(1, "npc"))

+				popViewport()

+			}

+		}

+		if(border) grid.rect(gp = gpar(fill = "transparent"))

+		popViewport()

+	}

+

+	if(which == "row") {

+		fun = row_fun

+	} else if(which == "column") {

+		fun = column_fun

+	}

+

+	anno = AnnotationFunction(

+		fun = fun,

+		fun_name = "anno_customize",

+		which = which,

+		width = anno_size$width,

+		height = anno_size$height,

+		n = n,

+		var_import = list(value, border, graphics)

+	)

+

+	anno@subset_rule$value = subset_vector

+

+	anno@subsetable = TRUE

+		

+	return(anno) 

+}

@@ -360,7 +360,10 @@ Heatmap = function(matrix, col, name,

     if(is.data.frame(matrix)) {

         if(verbose) qqcat("convert data frame to matrix\n")

-        warning_wrap("The input is a data frame, convert it to the matrix.")

+        warning_wrap("The input is a data frame, convert it to a matrix.")

+        if(!all(sapply(matrix, is.numeric))) {

+            warning_wrap("Note: not all columns in the data frame are numeric. The data frame will be converted into a character matrix.")

+        }

         matrix = as.matrix(matrix)

     }

     fa_level = NULL

@@ -135,7 +135,7 @@ oncoPrint = function(mat, name,

 		## check whether there are NA values in the matrix

 		if(any(is.na(mat))) {

-			message_wrap("Found NA values in the matrix and treat as no alteration. If `NA` means no alteration, you can explicitly set it to empty strings like ''. If `NA` is an alteration type, you should format it to a string like `'NA'` and define a graphic for it.")

+			message_wrap("Found NA values in the matrix and treat as no alteration. If `NA` means no alteration, you can explicitly set it to empty strings like ''. If `NA` is an alteration type, you should format it to a string like `'NA'` and define graphics for it.")

 		}

 		mat_list = lapply(all_type, function(type) {

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

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

 }

 }

 \examples{

new file mode 100644

@@ -0,0 +1,52 @@

+\name{anno_customize}

+\alias{anno_customize}

+\title{

+Customized annotation

+}

+\description{

+Customized annotation

+}

+\usage{

+anno_customize(x, graphics = list(), which = c("column", "row"),

+    border = TRUE, width = NULL, height = NULL, verbose = TRUE)

+}

+\arguments{

+

+  \item{x}{A categorical variable.}

+  \item{graphics}{A list of functions that define graphics for each level in \code{x}.}

+  \item{which}{Is it a row annotation or a column annotation?}

+  \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{border}{Whether to draw border.}

+  \item{verbose}{Whether to print messages.}

+

+}

+\details{

+Functions in \code{graphics} define simple graphics drawn in each annotation cell. The function takes four arguments:

+

+\describe{

+  \item{x,y}{Center of the annotation cell.}

+  \item{w,h}{Width and height of the annotation cell.}

+}

+}

+\value{

+An annotation function which can be used in \code{\link{HeatmapAnnotation}}.

+}

+\examples{

+x = sort(sample(letters[1:3], 10, replace = TRUE))

+graphics = list(

+    "a" = function(x, y, w, h) grid.points(x, y, pch = 16),

+    "b" = function(x, y, w, h) grid.rect(x, y, w*0.8, h*0.8, gp = gpar(fill = "red")),

+    "c" = function(x, y, w, h) grid.segments(x - 0.5*w, y - 0.5*h, x + 0.5*w, y + 0.5*h, gp = gpar(lty = 2))

+)

+

+anno = anno_customize(x, graphics = graphics)

+

+m = matrix(rnorm(100), 10)

+Heatmap(m, top_annotation = HeatmapAnnotation(bar = x, foo = anno))

+

+# Add legends for `foo`

+ht = Heatmap(m, top_annotation = HeatmapAnnotation(bar = x, foo = anno))

+lgd = Legend(title = "foo", at = names(graphics), graphics = graphics)

+draw(ht, annotation_legend_list = list(lgd))

+}

@@ -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{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{

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

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

 \itemize{

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

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

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

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

 }

 }

@@ -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{

@@ -18,4 +18,5 @@ Draw heatmap annotations

 \examples{

 # There is no example

 NULL

+

 }

@@ -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{

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

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

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

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

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

 }

 }

new file mode 100644

@@ -0,0 +1,25 @@

+\name{subset_no}

+\alias{subset_no}

+\title{

+Do not do subseting

+}

+\description{

+Do not do subseting

+}

+\usage{

+subset_no(x, i)

+}

+\arguments{

+

+  \item{x}{A vector.}

+  \item{i}{The indices.}

+

+}

+\details{

+Mainly used for constructing the \code{\link{AnnotationFunction-class}} object.

+}

+\examples{

+# There is no example

+NULL

+

+}

@@ -659,3 +659,19 @@ dev.new(width = 3.938326, height = 4.502203)

 draw(Heatmap(mat, right_annotation = rowAnnotation(foo = anno), 

 	row_split = row_split))

+

+

+#### anno_custome ###

+x = sort(sample(letters[1:3], 10, replace = TRUE))

+graphics = list(

+	"a" = function(x, y, w, h) grid.points(x, y, pch = 16),

+	"b" = function(x, y, w, h) grid.rect(x, y, w*0.8, h*0.8, gp = gpar(fill = "red")),

+	"c" = function(x, y, w, h) grid.segments(x - 0.5*w, y - 0.5*h, x + 0.5*w, y + 0.5*h, gp = gpar(lty = 2))

+)

+

+anno = anno_customize(x, graphics = graphics)

+draw(anno, index = 1:10, test = "")

+

+anno = anno_customize(c(x, "d"), graphics = graphics)

+

+