@@ -106,6 +106,7 @@ export("Legends")

 export("SingleAnnotation")

 export("adjust_dend_by_x")

 export("anno_barplot")

+export("anno_block")

 export("anno_boxplot")

 export("anno_density")

 export("anno_empty")

@@ -215,7 +215,8 @@ anno_simple = function(x, col, na_col = "grey",

                 if(!is.null(pch)) {

 					l = !is.na(pch[, i])

 					grid.points(x = rep((i-0.5)/nc, sum(l)), y = y[l], pch = pch[l, i], 

-						size = pt_size[i], gp = subset_gp(pt_gp, i))

+						size = {if(length(pt_size) == 1) pt_size else pt_size[i]}, 

+						gp = subset_gp(pt_gp, i))

 				}

             }

         } else {

@@ -246,7 +247,8 @@ anno_simple = function(x, col, na_col = "grey",

                 	pch = pch[index, , drop = FALSE]

 					l = !is.na(pch[, i])

 					grid.points(x[l], y = rep((nc-i +0.5)/nc, sum(l)), pch = pch[l, i], 

-						size = pt_size[i], gp = subset_gp(pt_gp, i))

+						size = {if(length(pt_size) == 1) pt_size else pt_size[i]}, 

+						gp = subset_gp(pt_gp, i))

 				}

             }

         } else {

@@ -375,7 +375,7 @@ setMethod(f = "make_layout",

     layout_size = object@layout$layout_size

     if(is_abs_unit(object@heatmap_param$width)) {

         # recalcualte the width of heatmap body

-        object@matrix_param$width = object@heatmap_param$width -

+        object@matrix_param$width = convertWidth(object@heatmap_param$width -

             sum(layout_size$row_title_left_width,

                 layout_size$row_dend_left_width,

                 layout_size$row_anno_left_width,

@@ -383,9 +383,12 @@ setMethod(f = "make_layout",

                 layout_size$row_dend_right_width,

                 layout_size$row_anno_right_width,

                 layout_size$row_names_right_width,

-                layout_size$row_title_right_width)   

+                layout_size$row_title_right_width), "mm")

+        if(object@matrix_param$width[[1]] <= 0) {

+            stop_wrap("width of the heatmap body is negative, maybe `heatmap_width` you set is too small. Note `heatmap_width` is the width of the complete heatmap.")

+        }

     } else if(is_abs_unit(object@matrix_param$width)) {  # e.g. unit(1, "npc")

-        object@heatmap_param$width = sum(

+        object@heatmap_param$width = convertWidth(sum(

             layout_size$row_title_left_width,

             layout_size$row_dend_left_width,

             layout_size$row_names_left_width,

@@ -394,7 +397,7 @@ setMethod(f = "make_layout",

             layout_size$row_title_right_width,

             layout_size$row_anno_left_width,

             layout_size$row_anno_right_width

-        ) + object@matrix_param$width

+        ) + object@matrix_param$width, "mm")

         if(nc_slice > 1) {

             object@heatmap_param$width = object@heatmap_param$width + sum(column_gap[seq_len(nc_slice-1)])

         }

@@ -403,7 +406,7 @@ setMethod(f = "make_layout",

     }

     if(is_abs_unit(object@heatmap_param$height)) {

-        object@matrix_param$height = object@heatmap_param$height - 

+        object@matrix_param$height = convertHeight(object@heatmap_param$height - 

             sum(layout_size$column_title_top_height,

                 layout_size$column_dend_top_height,

                 layout_size$column_anno_top_height,

@@ -411,9 +414,12 @@ setMethod(f = "make_layout",

                 layout_size$column_title_bottom_height,

                 layout_size$column_dend_bottom_height,

                 layout_size$column_anno_bottom_height,

-                layout_size$column_names_bottom_height)

+                layout_size$column_names_bottom_height), "mm")

+        if(object@matrix_param$height[[1]] <= 0) {

+            stop_wrap("height of the heatmap body is negative, maybe `heatmap_height` you set is too small. Note `heatmap_height` is the height of the complete heatmap.")

+        }

     } else if(is_abs_unit(object@matrix_param$height)) {

-        object@heatmap_param$height = sum(

+        object@heatmap_param$height = convertHeight(sum(

             layout_size$column_title_top_height,

             layout_size$column_dend_top_height,

             layout_size$column_anno_top_height,

@@ -422,7 +428,7 @@ setMethod(f = "make_layout",

             layout_size$column_dend_bottom_height,

             layout_size$column_anno_bottom_height,

             layout_size$column_names_bottom_height

-        ) + object@matrix_param$height

+        ) + object@matrix_param$height, "mm")

         if(nr_slice > 1) {

             object@heatmap_param$height = object@heatmap_param$height + sum(row_gap[seq_len(nr_slice-1)])

         }

@@ -107,6 +107,9 @@ HeatmapAnnotation = function(...,

 	simple_anno_size_adjust = FALSE

 	) {

+	dev.null()

+	on.exit(dev.off2())

+

 	.ENV$current_annotation_which = NULL

 	which = match.arg(which)[1]

 	.ENV$current_annotation_which = which

@@ -271,7 +274,7 @@ HeatmapAnnotation = function(...,

     len = len[len > 0]

     if(length(len)) {

 	    if(length(unique(len)) > 1) {

-	    	stop_wrap("Length of annotations differs.")

+	    	stop_wrap(paste0("Length of annotations differs. ", paste(qq("@{names(len)}: @{len}", collapse = FALSE), collapse = ", ")))

 	    }

 	}

@@ -361,9 +361,9 @@ setMethod(f = "column_dend",

-proper_format_lt = function(lt) {

+proper_format_lt = function(lt) {	

 	n_ht = length(lt)

-	# for a single heatmap 

+	

 	if(n_ht == 1) {

 		if(length(lt[[1]]) == 1) {

 			return(lt[[1]][[1]])

@@ -371,7 +371,13 @@ proper_format_lt = function(lt) {

 			return(lt[[1]])

 		}

 	} else {

-		has_splitting = any(sapply(lt, function(x) length(x) != 1))

+		l_empty = sapply(lt, function(x) length(x) == 0)

+		lt = lt[!l_empty]

+		if(length(lt) == 0) {

+			return(NULL)

+		}

+	

+		has_splitting = any(sapply(lt, function(x) length(x) > 1))

 		if(has_splitting) {

 			return(lt)

 		} else {

@@ -23,6 +23,8 @@

 # -column_names_gp Pass to `Heatmap`.

 # -column_names_rot Pass to `Heatmap`.

 # -cluster_columns Whether cluster columns (here clustered by density values)? Normally we don't cluster columns.

+# - clustering_distance_columns

+# -clustering_method_columns

 # -... pass to `Heatmap`.

 #

 # == details

@@ -97,7 +99,7 @@ densityHeatmap = function(data,

 	density_param$na.rm = TRUE

-	if(!is.matrix(data) && !is.data.frame(matrix) && !is.list(matrix)) {

+	if(!is.matrix(data) && !is.data.frame(data) && !is.list(data)) {

 		stop("only matrix and list are allowed.")

 	}

 	if(is.matrix(data)) {

@@ -185,5 +185,3 @@ ht_global_opt = ht_opt

 GLOBAL_PADDING = unit(c(2, 2, 2, 2), "mm")

-

-

@@ -104,6 +104,9 @@ Legend = function(at, labels = at, col_fun, nrow = NULL, ncol = 1, by_row = FALS

 	title = "", title_gp = gpar(fontsize = 10, fontface = "bold"),

 	title_position = c("topleft", "topcenter", "leftcenter", "lefttop", "leftcenter-rot", "lefttop-rot")) {

+	dev.null()

+	on.exit(dev.off2())

+

 	if(missing(at) && !missing(labels)) {

 		at = seq_along(labels)

 	}

@@ -758,6 +761,9 @@ packLegend = function(...,gap = unit(2, "mm"), row_gap = unit(2, "mm"), column_g

 	direction = c("vertical", "horizontal"),

 	max_width = NULL, max_height = NULL, list = NULL) {

+	dev.null()

+	on.exit(dev.off2())

+

 	if(!is.null(list)) {

 		legend_list = list

 	} else {

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{adjust_heatmap_list-HeatmapList-method}

 \alias{adjust_heatmap_list,HeatmapList-method}

+\alias{adjust_heatmap_list}

 \title{

 Adjust heatmap list

 }

@@ -22,8 +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

+

 }

new file mode 100644

@@ -0,0 +1,28 @@

+\name{anno_block}

+\alias{anno_block}

+\title{

+Block annotation

+}

+\description{

+Block annotation

+}

+\usage{

+anno_block(gp = gpar(), labels = NULL, labels_gp = gpar(), labels_rot = ifelse(which == "row", 90, 0),

+    which = c("column", "row"), width = NULL, height = NULL)

+}

+\arguments{

+

+  \item{gp}{Graphic parameters}

+  \item{labels}{-labels}

+  \item{labels_gp}{-labels_gp}

+  \item{labels_rot}{-labels_rot}

+  \item{which}{-which}

+  \item{width}{-width}

+  \item{height}{-height}

+

+}

+\examples{

+# There is no example

+NULL

+

+}

@@ -22,7 +22,7 @@ anno_horizon(x, which = c("column", "row"),

   \item{n_slice}{Number of slices on y-axis.}

   \item{slice_size}{Height of the slice. If the value is not \code{NULL}, \code{n_slice} will be recalculated. }

   \item{negative_from_top}{Whether the areas for negative values start from the top or the bottom of the plotting region?}

-  \item{normalize}{Whether normalize \code{x} to let data range of each observation in (0, 1)?}

+  \item{normalize}{Whether normalize \code{x} by max(abs(x)).}

   \item{gap}{Gap size of neighbouring horizon chart.}

   \item{axis}{Whether to add axis?}

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

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{annotation_legend_size-HeatmapList-method}

 \alias{annotation_legend_size,HeatmapList-method}

+\alias{annotation_legend_size}

 \title{

 Size of the annotation legend viewport

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{annotation_legend_size}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{color_mapping_legend-ColorMapping-method}

 \alias{color_mapping_legend,ColorMapping-method}

+\alias{color_mapping_legend}

 \title{

 Draw Legend Based on Color Mapping

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{color_mapping_legend}

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

@@ -31,6 +31,9 @@ densityHeatmap(data,

     column_names_rot = 90,

     cluster_columns = FALSE,

+    clustering_distance_columns = "ks",

+    clustering_method_columns = "complete",

+    

     ...)

 }

 \arguments{

@@ -54,7 +57,8 @@ densityHeatmap(data,

   \item{column_names_max_height}{Pass to \code{\link{Heatmap}}.}

   \item{column_names_gp}{Pass to \code{\link{Heatmap}}.}

   \item{column_names_rot}{Pass to \code{\link{Heatmap}}.}

-  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns.}

+  \item{cluster_columns}{Whether cluster columns (here clustered by density values)? Normally we don't cluster columns. - clustering_distance_columns}

+  \item{clustering_method_columns}{-clustering_method_columns}

   \item{...}{pass to \code{\link{Heatmap}}.}

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_annotation-Heatmap-method}

 \alias{draw_annotation,Heatmap-method}

+\alias{draw_annotation}

 \title{

 Draw Heatmap Annotations on the Heatmap

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_annotation}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_annotation_legend-HeatmapList-method}

 \alias{draw_annotation_legend,HeatmapList-method}

+\alias{draw_annotation_legend}

 \title{

 Draw legends for all column annotations

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_annotation_legend}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_dend-Heatmap-method}

 \alias{draw_dend,Heatmap-method}

+\alias{draw_dend}

 \title{

 Draw Heatmap Dendrograms

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_dend}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_dimnames-Heatmap-method}

 \alias{draw_dimnames,Heatmap-method}

+\alias{draw_dimnames}

 \title{

 Draw row names or column names

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_dimnames}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_heatmap_body-Heatmap-method}

 \alias{draw_heatmap_body,Heatmap-method}

+\alias{draw_heatmap_body}

 \title{

 Draw the Heatmap Body

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_heatmap_body}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_heatmap_legend-HeatmapList-method}

 \alias{draw_heatmap_legend,HeatmapList-method}

+\alias{draw_heatmap_legend}

 \title{

 Draw legends for all heatmaps

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_heatmap_legend}

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{draw_heatmap_list-HeatmapList-method}

 \alias{draw_heatmap_list,HeatmapList-method}

+\alias{draw_heatmap_list}

 \title{

 Draw the list of heatmaps

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{draw_heatmap_list}

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \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

 }

@@ -25,8 +26,8 @@ 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

+

 }

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

 \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

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{get_legend_param_list}

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \name{heatmap_legend_size-HeatmapList-method}

 \alias{heatmap_legend_size,HeatmapList-method}

+\alias{heatmap_legend_size}

 \title{

 Size of the heatmap legend viewport

 }

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

 \author{

 Zuguang Gu <z.gu@dkfz.de>

 }

-\alias{heatmap_legend_size}

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+

 }

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

 \examples{

 # There is no example

 NULL

+