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

 ^\..*

 README.*

-tests/

+tests_not_run/

 check.bat

 ^.*\.Rproj$

 ^\.Rproj\.user$

@@ -1,14 +1,14 @@

 Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

-Version: 1.99.5

-Date: 2019-02-12

+Version: 1.99.6

+Date: 2019-03-15

 Author: Zuguang Gu

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

 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

 Imports: circlize (>= 0.4.5), GetoptLong, colorspace,

     RColorBrewer, GlobalOptions (>= 0.1.0), parallel

-Suggests: testthat (>= 0.3), knitr, markdown, dendsort, 

+Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, 

     Cairo, png, jpeg, tiff, fastcluster,

     dendextend (>= 1.0.1), grImport, grImport2, glue

 VignetteBuilder: knitr

@@ -265,8 +265,9 @@ importFrom("circlize", rand_color)

 importFrom("circlize", smartAlign)

 importFrom("colorspace", diverge_hcl)

 importFrom("colorspace", rainbow_hcl)

+importFrom("parallel", "mclapply")

 importFrom("utils", "combn")

 importFrom("utils", "getFromNamespace")

 importFrom("utils", "packageDescription")

 importFrom("utils", "str")

-importFrom("parallel", "mclapply")

+

@@ -1,3 +1,9 @@

+CHANGES in VERSION 1.99.6

+

+* adjust the size of heatmap annotations and add testing scripts

+

+========================

+

 CHANGES in VERSION 1.99.5

 * add `UpSet()` and some related functions to make Upset plots

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -126,7 +126,7 @@ subset_vector = function(x, i) x[i]

 #          only be a single value.

 # -pt_gp Graphic parameters for points/symbols. The length setting is same as ``pt_size``.

 #     If ``pch`` is set as letters, the fontsize should be set as ``pt_gp = gpar(fontsize = ...)``.

-# -anno_simple_size size of the simple annotation.

+# -simple_anno_size size of the simple 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.

 #

@@ -162,7 +162,7 @@ subset_vector = function(x, i) x[i]

 anno_simple = function(x, col, na_col = "grey", 

 	which = c("column", "row"), border = FALSE, gp = gpar(col = NA),

 	pch = NULL, pt_size = unit(1, "snpc")*0.8, pt_gp = gpar(), 

-	anno_simple_size = ht_opt$anno_simple_size,

+	simple_anno_size = ht_opt$simple_anno_size,

 	width = NULL, height = NULL) {

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

@@ -180,7 +180,7 @@ anno_simple = function(x, col, na_col = "grey",

 	input_is_matrix = is.matrix(x)

 	anno_size = anno_width_and_height(which, width, height, 

-		anno_simple_size*ifelse(input_is_matrix, ncol(x), 1))

+		simple_anno_size*ifelse(input_is_matrix, ncol(x), 1))

 	if(missing(col)) {

 		col = default_col(x)

@@ -26,14 +26,16 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 		height = "ANY",  

 		gap = "ANY",

 		subsetable = "logical",

-		extended = "ANY"

+		extended = "ANY",

+		param = "list"

 	),

 	prototype = list(

 		anno_list = list(),

 		which = "column",

 		gap = unit(0, "mm"),

 		subsetable = FALSE,

-		extended = unit(c(0, 0, 0, 0), "mm")

+		extended = unit(c(0, 0, 0, 0), "mm"),

+		param = list()

 	),

     contains = "AdditiveUnit"

 )

@@ -65,7 +67,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # -annotation_width Width of each annotation if annotations are row annotations.

 # -height Height of the whole column annotations.

 # -width Width of the whole heatmap annotations.

-# -anno_simple_size Size of the simple annotation.

+# -simple_anno_size Size of the simple annotation.

 # -simple_anno_size_adjust Whether also adjust the size of simple annotations when adjusting the whole heatmap annotation.

 #

 # == details

@@ -109,12 +111,17 @@ HeatmapAnnotation = function(...,

 	annotation_width = NULL, 

 	height = NULL,

 	width = NULL,

-	anno_simple_size = ht_opt$anno_simple_size,

+	simple_anno_size = ht_opt$simple_anno_size,

 	simple_anno_size_adjust = FALSE

 	) {

 	dev.null()

+	is_height_set = !missing(height)

+	is_width_set = !missing(width)

+	is_annotation_height_set = !missing(annotation_height)

+	is_annotation_width_set = !missing(annotation_width)

+

 	.ENV$current_annotation_which = NULL

 	which = match.arg(which)[1]

 	.ENV$current_annotation_which = which

@@ -198,6 +205,10 @@ HeatmapAnnotation = function(...,

     n_simple_anno = sum(l_simple_anno)

     simple_anno_name = names(anno_value_list[l_simple_anno])

+    if("anno_simple_size" %in% names(anno_value_list)) {

+    	stop_wrap("Please use `simple_anno_size` as the argument.")

+    }

+

     if(verbose) qqcat("in total there are @{length(anno_value_list)} annotations (@{n_simple_anno} simple annotations)\n")

     # normalize `show_legend`

@@ -318,7 +329,7 @@ HeatmapAnnotation = function(...,

 			arg_list$legend_param = annotation_legend_param[[i_simple + 1]]

 			arg_list$value = anno_value_list[[ag]]

 			arg_list$na_col = na_col

-			# arg_list$anno_simple_size = anno_simple_size

+			arg_list$simple_anno_size = simple_anno_size

 			if(missing(col)) {

 				anno_list[[ag]] = do.call(SingleAnnotation, arg_list)

 		    } else {

@@ -361,6 +372,8 @@ HeatmapAnnotation = function(...,

 	if(is.null(gap)) gap = unit(0, "mm")

+	if(identical(gap, 0)) gap = unit(0, "mm")

+	if(!inherits(gap, "unit")) stop_wrap("`gap` needs to be a unit object.")

 	# the nth gap does not really matter

     if(length(gap) == 1) {

@@ -428,14 +441,20 @@ HeatmapAnnotation = function(...,

     	}))

     }

     .Object@extended = extended

+    .Object@param = list(

+    	simple_anno_size = simple_anno_size, 

+    	simple_anno_size_adjust = simple_anno_size_adjust,

+    	is_height_set = is_height_set,

+    	is_width_set = is_width_set,

+    	is_annotation_height_set = is_annotation_height_set,

+    	is_annotation_width_set = is_annotation_width_set

+    )

     ## adjust height/width if `width`/`annotation_width` is set

     if(which == "column") {

-	    .Object = re_size(.Object, height = height, annotation_height = annotation_height,

-	    	anno_simple_size = anno_simple_size, simple_anno_size_adjust = simple_anno_size_adjust)

+	    .Object = re_size(.Object, height = height, annotation_height = annotation_height)

 	} else {

-		.Object = re_size(.Object, width = width, annotation_width = annotation_width, 

-			anno_simple_size = anno_simple_size, simple_anno_size_adjust = simple_anno_size_adjust)

+		.Object = re_size(.Object, width = width, annotation_width = annotation_width)

 	}

     return(.Object)

@@ -1015,7 +1034,7 @@ length.HeatmapAnnotation = function(x) {

 # -annotation_width A vector of of annotation widths in `grid::unit` class.

 # -height The height of the complete heatmap annotation.

 # -width The width of the complete heatmap annotation.

-# -anno_simple_size The size of one line of the simple annotation.

+# -simple_anno_size The size of one line of the simple annotation.

 # -simple_anno_size_adjust Whether adjust the size of the simple annotation?

 #

 # == details

@@ -1027,10 +1046,10 @@ length.HeatmapAnnotation = function(x) {

 #    ``annotation_height`` are absolute units, ``height`` is ignored.

 # 2. If ``annotation_height`` contains non-absolute units, ``height`` also need to be set and the

 #    non-absolute units should be set in a simple form such as 1:10 or ``unit(1, "null")``.

-# 3. ``anno_simple_size`` is only used when ``annotation_height`` is NULL.

+# 3. ``simple_anno_size`` is only used when ``annotation_height`` is NULL.

 # 4. If only ``height`` is set, non-simple annotation is adjusted while keeps simple anntation unchanged.

 # 5. If only ``height`` is set and all annotations are simple annotations, all anntations are adjusted,

-#      and ``anno_simple_size`` is disabled.

+#      and ``simple_anno_size`` is disabled.

 # 6. If ``simple_anno_size_adjust`` is ``FALSE``, the size of the simple annotations will not change.

 #

 setMethod(f = "re_size",

@@ -1040,17 +1059,17 @@ setMethod(f = "re_size",

 	annotation_width = NULL,

 	height = NULL, 

 	width = NULL, 

-	anno_simple_size = ht_opt$anno_simple_size,

-	simple_anno_size_adjust = NULL) {

+	simple_anno_size = object@param$simple_anno_size,

+	simple_anno_size_adjust = object@param$simple_anno_size_adjust) {

 	if(object@which == "column") {

 		if(!missing(width) || !missing(annotation_width)) {

-			stop_wrap("Please use ComplexHeatmap:::width() directly")

+			stop_wrap("You cannot set the width of the column annotations.")

 		}

 	}

 	if(object@which == "colrowumn") {

 		if(!missing(height) || !missing(annotation_height)) {

-			stop_wrap("Please use ComplexHeatmap:::height() directly")

+			stop_wrap("You cannot set the height of the row annotations.")

 		}

 	}

@@ -1078,7 +1097,6 @@ setMethod(f = "re_size",

 			return(object)

 		}

 	}

-

 	if(which == "column") {

 		if(is.null(height)) {

 			is_size_set = FALSE

@@ -1106,7 +1124,7 @@ setMethod(f = "re_size",

 				if(length(object@anno_list) == 1 && !inherits(annotation_height, "unit")) {

 					stop_wrap("When there is only one annotation, `annotation_height` should be set as a unit object.")

 				}

-				if(!inherits(height, "unit")) {

+				if(!inherits(height, "unit") || !object@param$is_height_set) {

 					height = annotation_height[1]

 				}

 				if(!inherits(height, "unit")) {

@@ -1151,7 +1169,7 @@ setMethod(f = "re_size",

 				if(length(object@anno_list) == 1 && !inherits(annotation_width, "unit")) {

 					stop_wrap("When there is only one annotation, `annotation_width` should be set as a unit object.")

 				}

-				if(!inherits(width, "unit")) {

+				if(!inherits(width, "unit") || !object@param$is_width_set) {

 					width = annotation_width[1]

 				}

 				if(!inherits(width, "unit")) {

@@ -1260,10 +1278,14 @@ setMethod(f = "re_size",

 	} else {

 		size = convertUnitFun(size, "mm", valueOnly = TRUE)

 		anno_size = convertUnitFun(anno_size, "mm", valueOnly = TRUE)

-	

-		l_simple_anno = sapply(seq_len(n), function(i) {

-			!is.null(object@anno_list[[i]]@color_mapping)

-		})

+		

+		if(simple_anno_size_adjust) {

+			l_simple_anno = rep(FALSE, n)

+		} else {

+			l_simple_anno = sapply(seq_len(n), function(i) {

+				!is.null(object@anno_list[[i]]@color_mapping)

+			})

+		}

 		if(all(l_simple_anno)) {

 			anno_size2 = anno_size/sum(anno_size) * (size_adjusted - sum(gap))

@@ -1273,22 +1295,21 @@ setMethod(f = "re_size",

 			anno_size2 = anno_size

 			# size_adjusted = convertUnitFun(size_adjusted, "mm", valueOnly = TRUE)

-			if(is.null(anno_simple_size)) {

-				anno_simple_size = 5

+			if(is.null(simple_anno_size)) {

+				simple_anno_size = 5

 			} else {

-				anno_simple_size = convertUnitFun(anno_simple_size, "mm", valueOnly = TRUE)

+				simple_anno_size = convertUnitFun(simple_anno_size, "mm", valueOnly = TRUE)

 			}

 			if(size_adjusted <= sum(gap)) {

 				stop_wrap(paste0(size_name, " you set is smaller than sum of gaps."))

 			}

 			## fix the size of simple annotation and zoom function annotations

-			ts = size_adjusted - sum(gap) - sum(anno_size[l_simple_anno]*anno_simple_size/5)

+			ts = size_adjusted - sum(gap) - sum(anno_size[l_simple_anno]) # total size excluding simple annotations and gap

 			if(ts < 0) {

 				stop_wrap(paste0(size_name, " you set is too small."))

 			}

 			anno_size2[!l_simple_anno] = anno_size[!l_simple_anno]/sum(anno_size[!l_simple_anno]) * ts

-			anno_size2[l_simple_anno] = anno_size[l_simple_anno]*anno_simple_size/5

 			size_adjusted = unit(size_adjusted, "mm")

 			anno_size2 = unit(anno_size2, "mm")

@@ -235,7 +235,7 @@ setMethod(f = "add_heatmap",

 # -heatmap_border this set the value in `ht_opt` and reset back after the plot is done

 # -annotation_border  this set the value in `ht_opt` and reset back after the plot is done

 # -fastcluster this set the value in `ht_opt` and reset back after the plot is done

-# -anno_simple_size  this set the value in `ht_opt` and reset back after the plot is done

+# -simple_anno_size  this set the value in `ht_opt` and reset back after the plot is done

 # -show_parent_dend_line this set the value in `ht_opt` and reset back after the plot is done

 #

 # == detail

@@ -330,7 +330,7 @@ setMethod(f = "draw",

     heatmap_border = NULL,

     annotation_border = NULL,

     fastcluster = NULL,

-    anno_simple_size = NULL,

+    simple_anno_size = NULL,

     show_parent_dend_line = NULL

     ) {

@@ -350,7 +350,7 @@ setMethod(f = "draw",

                     "heatmap_border",

                     "annotation_border",

                     "fastcluster",

-                    "anno_simple_size",

+                    "simple_anno_size",

                     "show_parent_dend_line")) {

         v = get(opt_nm, inherits = FALSE)

         if(!is.null(v)) {

@@ -73,7 +73,7 @@ SingleAnnotation = setClass("SingleAnnotation",

 # -name_offset Offset to the annotation, a `grid::unit` object.

 # -name_side 'right' and 'left' for column annotations and 'top' and 'bottom' for row annotations

 # -name_rot Rotation of the annotation name, it can only take values in ``c(0, 90, 180, 270)``.

-# -anno_simple_size size of the simple annotation.

+# -simple_anno_size size of the simple annotation.

 # -width The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation,

 #        the width must be an absolute unit.

 # -height The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation,

@@ -152,7 +152,7 @@ SingleAnnotation = function(name, value, col, fun,

 	name_offset = NULL,

 	name_side = ifelse(which == "column", "right", "bottom"),

     name_rot = NULL,

-    anno_simple_size = ht_opt$anno_simple_size,

+    simple_anno_size = ht_opt$simple_anno_size,

     width = NULL, height = NULL) {

     .ENV$current_annotation_which = NULL

@@ -471,7 +471,7 @@ SingleAnnotation = function(name, value, col, fun,

         value = value

         if(verbose) qqcat("@{name}: generate AnnotationFunction for simple annotation values by anno_simple()\n")

-        .Object@fun = anno_simple(value, col = color_mapping, which = which, na_col = na_col, gp = gp, border = border, anno_simple_size = anno_simple_size)

+        .Object@fun = anno_simple(value, col = color_mapping, which = which, na_col = na_col, gp = gp, border = border, simple_anno_size = simple_anno_size)

         if(missing(width)) {

             .Object@width = .Object@fun@width

         } else {

@@ -35,7 +35,7 @@

 # Following parameters control heatmap annotations:

 #

 # -annotation_border ``border`` in all `HeatmapAnnotation`.

-# -anno_simple_size size for the simple annotation.

+# -simple_anno_size size for the simple annotation.

 #

 # Following parameters control the space between heatmap components:

 #

@@ -126,7 +126,7 @@ ht_opt = setGlobalOptions(

 		},

 		.length = 1),

 	show_vp = FALSE,

-	anno_simple_size = list(

+	simple_anno_size = list(

 		.value = unit(5, "mm"),

 		.class = "unit"

 	),

@@ -26,7 +26,7 @@ HeatmapAnnotation(...,

     annotation_width = NULL,

     height = NULL,

     width = NULL,

-    anno_simple_size = ht_opt$anno_simple_size,

+    simple_anno_size = ht_opt$simple_anno_size,

     simple_anno_size_adjust = FALSE)

 }

 \arguments{

@@ -51,7 +51,7 @@ HeatmapAnnotation(...,

   \item{annotation_width}{Width of each annotation if annotations are row annotations.}

   \item{height}{Height of the whole column annotations.}

   \item{width}{Width of the whole heatmap annotations.}

-  \item{anno_simple_size}{Size of the simple annotation.}

+  \item{simple_anno_size}{Size of the simple annotation.}

   \item{simple_anno_size_adjust}{Whether also adjust the size of simple annotations when adjusting the whole heatmap annotation.}

 }

@@ -19,7 +19,7 @@ SingleAnnotation(name, value, col, fun,

     name_offset = NULL,

     name_side = ifelse(which == "column", "right", "bottom"),

     name_rot = NULL,

-    anno_simple_size = ht_opt$anno_simple_size,

+    simple_anno_size = ht_opt$simple_anno_size,

     width = NULL, height = NULL)

 }

 \arguments{

@@ -39,7 +39,7 @@ SingleAnnotation(name, value, col, fun,

   \item{name_offset}{Offset to the annotation, a \code{\link[grid]{unit}} object.}

   \item{name_side}{'right' and 'left' for column annotations and 'top' and 'bottom' for row annotations}

   \item{name_rot}{Rotation of the annotation name, it can only take values in \code{c(0, 90, 180, 270)}.}

-  \item{anno_simple_size}{size of the simple annotation.}

+  \item{simple_anno_size}{size of the simple annotation.}

   \item{width}{The width of the plotting region (the viewport) that the annotation is drawn. If it is a row annotation, the width must be an absolute unit.}

   \item{height}{The height of the plotting region (the viewport) that the annotation is drawn. If it is a column annotation, the width must be an absolute unit.}

@@ -10,8 +10,8 @@ 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,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method

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

 }

 }

@@ -10,7 +10,7 @@ Simple Annotation

 anno_simple(x, col, na_col = "grey",

     which = c("column", "row"), border = FALSE, gp = gpar(col = NA),

     pch = NULL, pt_size = unit(1, "snpc")*0.8, pt_gp = gpar(),

-    anno_simple_size = ht_opt$anno_simple_size,

+    simple_anno_size = ht_opt$simple_anno_size,

     width = NULL, height = NULL)

 }

 \arguments{

@@ -24,7 +24,7 @@ anno_simple(x, col, na_col = "grey",

   \item{pch}{Points/symbols that are added on top of the annotation grids. The value can be numeric or single letters. It can be a vector if \code{x} is a vector and a matrix if \code{x} is a matrix. No points are drawn if the corresponding values are NA.}

   \item{pt_size}{Size of the points/symbols. It should be a \code{\link[grid]{unit}} object. If \code{x} is a vector, the value of \code{pt_size} can be a vector, while if \code{x} is a matrix, \code{pt_size} can only be a single value.}

   \item{pt_gp}{Graphic parameters for points/symbols. The length setting is same as \code{pt_size}. If \code{pch} is set as letters, the fontsize should be set as \code{pt_gp = gpar(fontsize = ...)}.}

-  \item{anno_simple_size}{size of the simple annotation.}

+  \item{simple_anno_size}{size of the simple 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.}

@@ -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{

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

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

 \itemize{

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

 \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

 }

 }

 \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{

@@ -82,7 +82,7 @@ Draw a list of heatmaps

     heatmap_border = NULL,

     annotation_border = NULL,

     fastcluster = NULL,

-    anno_simple_size = NULL,

+    simple_anno_size = NULL,

     show_parent_dend_line = NULL)

 }

 \arguments{

@@ -153,7 +153,7 @@ Draw a list of heatmaps

   \item{heatmap_border}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

   \item{annotation_border}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

   \item{fastcluster}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

-  \item{anno_simple_size}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

+  \item{simple_anno_size}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

   \item{show_parent_dend_line}{this set the value in \code{\link{ht_opt}} and reset back after the plot is done}

 }

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

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

@@ -48,7 +48,7 @@ Following parameters control heatmap annotations:

 \describe{

   \item{annotation_border}{\code{border} in all \code{\link{HeatmapAnnotation}}.}

-  \item{anno_simple_size}{size for the simple annotation.}

+  \item{simple_anno_size}{size for the simple annotation.}

 }

 Following parameters control the space between heatmap components:

@@ -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{

@@ -13,8 +13,8 @@ Resize the Width or Height of Heatmap Annotations

     annotation_width = NULL,

     height = NULL,

     width = NULL,

-    anno_simple_size = ht_opt$anno_simple_size,

-    simple_anno_size_adjust = NULL)

+    simple_anno_size = object@param$simple_anno_size,

+    simple_anno_size_adjust = object@param$simple_anno_size_adjust)

 }

 \arguments{

@@ -23,7 +23,7 @@ Resize the Width or Height of Heatmap Annotations

   \item{annotation_width}{A vector of of annotation widths in \code{\link[grid]{unit}} class.}

   \item{height}{The height of the complete heatmap annotation.}

   \item{width}{The width of the complete heatmap annotation.}

-  \item{anno_simple_size}{The size of one line of the simple annotation.}

+  \item{simple_anno_size}{The size of one line of the simple annotation.}

   \item{simple_anno_size_adjust}{Whether adjust the size of the simple annotation?}

 }

@@ -36,10 +36,10 @@ The basic rules are (take \code{height} and \code{annotation_height} for example

    \code{annotation_height} are absolute units, \code{height} is ignored.

 2. If \code{annotation_height} contains non-absolute units, \code{height} also need to be set and the

    non-absolute units should be set in a simple form such as 1:10 or \code{unit(1, "null")}.

-3. \code{anno_simple_size} is only used when \code{annotation_height} is NULL.

+3. \code{simple_anno_size} is only used when \code{annotation_height} is NULL.

 4. If only \code{height} is set, non-simple annotation is adjusted while keeps simple anntation unchanged.

 5. If only \code{height} is set and all annotations are simple annotations, all anntations are adjusted,

-     and \code{anno_simple_size} is disabled.

+     and \code{simple_anno_size} is disabled.

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

 }

 \examples{

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

 \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

 }

 }

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

 \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

 }

 }

 \examples{

@@ -10,12 +10,12 @@ 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,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method

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

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

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

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

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

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

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

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

 }

 }

 \examples{

new file mode 100644

@@ -0,0 +1,377 @@

+

+context("test annotation size for a single HeatmapAnntoation object with only one annotation.")

+ComplexHeatmap:::dev.null()

+

+size_num = function(ha) {

+	s = sapply(ha@anno_list, function(anno) {

+		convertHeight(size(anno), "mm", valueOnly = TRUE)

+	})

+	unname(s)

+}

+

+test_that("a single simple annotation", {

+	ha = HeatmapAnnotation(foo = 1:10)

+	expect_that(size_num(ha), equals(5))

+

+	ha = HeatmapAnnotation(foo = cbind(1:10, 10:1))

+	expect_that(size_num(ha), equals(10))

+

+	ha = HeatmapAnnotation(foo = 1:10)

+	expect_that(size_num(ha), equals(5))

+

+	ha = HeatmapAnnotation(foo1 = 1:10, 

+		simple_anno_size = unit(1, "cm")

+	)

+	expect_that(size_num(ha), equals(10))

+

+	ha = HeatmapAnnotation(foo1 = 1:10, 

+		annotation_height = unit(1, "cm"),

+		simple_anno_size_adjust = TRUE

+	)

+	expect_that(size_num(ha), equals(10))

+

+	ha = HeatmapAnnotation(foo1 = 1:10, 

+		height = unit(1, "cm"),

+		simple_anno_size_adjust = TRUE

+	)

+	expect_that(size_num(ha), equals(10))

+

+	ha = HeatmapAnnotation(foo1 = 1:10, 

+		annotation_height = unit(1, "cm")

+	)

+	expect_that(size_num(ha), equals(5))

+	

+	ha = HeatmapAnnotation(foo1 = 1:10, 

+		height = unit(1, "cm")

+	)

+	expect_that(size_num(ha), equals(5))

+

+	ht_opt$simple_anno_size = unit(1, "cm")

+	ha = HeatmapAnnotation(foo1 = 1:10)

+	expect_that(size_num(ha), equals(10))

+	ht_opt$simple_anno_size = unit(5, "mm")

+

+})

+

+test_that("a single complex annotation", {

+	ha = HeatmapAnnotation(foo = anno_points(1:10))

+	expect_that(size_num(ha), equals(10))

+

+	ha = HeatmapAnnotation(foo = anno_points(1:10),

+		annotation_height = unit(2, "cm"))

+	expect_that(size_num(ha), equals(20))

+

+	ha = HeatmapAnnotation(foo = anno_points(1:10),

+		height = unit(2, "cm"))

+	expect_that(size_num(ha), equals(20))

+})

+

+test_that("multiple simple annotations", {

+	ha = HeatmapAnnotation(foo = 1:10, bar = 10:1)

+	expect_that(size_num(ha), equals(c(5, 5)))

+

+	ha = HeatmapAnnotation(foo = cbind(1:10, 10:1), bar = 10:1)

+	expect_that(size_num(ha), equals(c(10, 5)))

+

+	ha = HeatmapAnnotation(foo = cbind(1:10, 10:1), bar = 10:1, 

+		simple_anno_size = unit(1, "cm")

+	)

+	expect_that(size_num(ha), equals(c(20, 10)))

+

+	ha = HeatmapAnnotation(foo = cbind(1:10, 10:1), bar = 10:1, 

+		annotation_height = unit(c(2, 1), "cm"),

+		simple_anno_size_adjust = TRUE

+	)

+	expect_that(size_num(ha), equals(c(20, 10)))

+

+	ha = HeatmapAnnotation(foo = cbind(1:10, 10:1), bar = 10:1, gap = unit(0, "mm"),

+		height = unit(3, "cm"),

+		simple_anno_size_adjust = TRUE

+	)

+	expect_that(size_num(ha), equals(c(20, 10)))

+

+	ha = HeatmapAnnotation(foo = cbind(1:10, 10:1), bar = 10:1, 

+		annotation_height = unit(c(2, 1), "cm")

+	)

+	expect_that(size_num(ha), equals(c(10, 5)))

+

+	ha = HeatmapAnnotation(foo = cbind(1:10, 10:1), bar = 10:1, gap = unit(0, "mm"),

+		height = unit(3, "cm")

+	)

+	expect_that(size_num(ha), equals(c(10, 5)))

+

+})

+

+test_that("multiple complex annotations", {

+	ha = HeatmapAnnotation(foo = anno_points(1:10), bar = anno_barplot(10:1))

+	expect_that(size_num(ha), equals(c(10, 10)))

+

+	ha = HeatmapAnnotation(

+		foo = anno_points(1:10, height = unit(2, "cm")), 

+		bar = anno_barplot(10:1, height =unit(3, "cm")))

+	expect_that(size_num(ha), equals(c(20, 30)))

+

+	ha = HeatmapAnnotation(

+		foo = anno_points(1:10, height = unit(2, "cm")), 

+		bar = anno_barplot(10:1, height =unit(3, "cm")),

+		annotation_height = unit(c(1, 2), "cm"))

+	expect_that(size_num(ha), equals(c(10, 20)))

+

+	ha = HeatmapAnnotation(

+		foo = anno_points(1:10, height = unit(2, "cm")), 

+		bar = anno_barplot(10:1, height =unit(3, "cm")),

+		gap = unit(0, "mm"),

+		height = unit(10, "cm"))

+	expect_that(size_num(ha), equals(c(40, 60)))

+})

+

+test_that("mix of simple and complex annotations", {

+	ha = HeatmapAnnotation(

+		foo = 1:10, 

+		bar = anno_barplot(10:1))

+	expect_that(size_num(ha), equals(c(5, 10)))

+

+	ha = HeatmapAnnotation(

+		foo = 1:10, 

+		bar = anno_barplot(10:1),

+		simple_anno_size = unit(1, "cm"))

+	expect_that(size_num(ha), equals(c(10, 10)))

+

+	ha = HeatmapAnnotation(

+		foo = 1:10, 

+		bar = anno_barplot(10:1),

+		annotation_height = unit(c(1, 2), "cm"))

+	expect_that(size_num(ha), equals(c(10, 20)))

+

+	ha = HeatmapAnnotation(

+		foo = 1:10, 

+		bar = anno_barplot(10:1),

+		gap = unit(0, "mm"),

+		height = unit(3, "cm"))

+	expect_that(size_num(ha), equals(c(5, 25)))

+

+	ha = HeatmapAnnotation(

+		foo = 1:10, 

+		bar = anno_barplot(10:1),

+		gap = unit(0, "mm"),

+		height = unit(3, "cm"),

+		simple_anno_size_adjust = TRUE)

+	expect_that(size_num(ha), equals(c(10, 20)))

+

+	ha = HeatmapAnnotation(

+		foo = 1:10, 

+		bar = anno_barplot(10:1),

+		gap = unit(0, "mm"),

+		height = unit(3, "cm"),

+		simple_anno_size_adjust = FALSE)

+	expect_that(size_num(ha), equals(c(5, 25)))

+

+})

+

+

+test_that("annotation_height as fractions", {

+	ha = HeatmapAnnotation(foo = 1:10, 

+		bar = cbind(1:10, 10:1),

+		pt = anno_points(1:10),

+		gap = unit(0, "mm"),

+		annotation_height = 1,

+		height = unit(6, "cm"))

+	expect_that(size_num(ha), equals(c(20, 20, 20)))

+

+	ha = HeatmapAnnotation(foo = 1:10, 

+		bar = cbind(1:10, 10:1),

+		pt = anno_points(1:10),

+		gap = unit(0, "mm"),

+		annotation_height = 1:3,

+		height = unit(6, "cm"))

+	expect_that(size_num(ha), equals(c(10, 20, 30)))

+

+	ha = HeatmapAnnotation(foo = 1:10, 

+		bar = cbind(1:10, 10:1),

+		pt = anno_points(1:10),

+		gap = unit(0, "mm"),

+		annotation_height = unit(c(1, 2, 3), c("null", "null", "cm")),

+		height = unit(6, "cm"))

+	expect_that(size_num(ha), equals(c(10, 20, 30)))

+

+	ha = HeatmapAnnotation(foo = 1:10, 

+		bar = cbind(1:10, 10:1),

+		pt = anno_points(1:10),

+		gap = unit(0, "mm"),

+		annotation_height = unit(c(2, 2, 3), c("cm", "null", "cm")),

+		height = unit(6, "cm"))

+	expect_that(size_num(ha), equals(c(20, 10, 30)))

+

+})

+

+context("test heatmap annotations on multiple heatmaps")