@@ -6,6 +6,8 @@ CHANGES in VERSION 2.11.1

 * `anno_block()`: add `align_to` argument.

 * add `anno_text_box()` and `grid.text_box()`.

 * add `show_name` argument in `anno_empty()`.

+* the validation of annotations in `HeatmapAnnotation()` is simplified.

+* add `anno_numeric()`.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -1300,18 +1300,18 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 		data_scale = range(rowSums(x, na.rm = TRUE), na.rm = TRUE)

 	}

-	if(data_scale[1] == data_scale[2]) data_scale[2] = data_scale[1] + 1

+	if(data_scale[1] == data_scale[2]) data_scale[2] = data_scale[1] + .Machine$double.eps*1.1

 	if(!is.null(ylim)) data_scale = ylim

 	if(baseline == "min") {

 		data_scale = data_scale + c(0, extend)*(data_scale[2] - data_scale[1])

-		baseline = min(x)

+		baseline = min(x, na.rm = TRUE)

 	} else if(baseline == "max") {

 		data_scale = data_scale + c(-extend, 0)*(data_scale[2] - data_scale[1])

-		baseline = max(x)

+		baseline = max(x, na.rm = TRUE)

 	} else {

 		if(is.numeric(baseline)) {

-			if(baseline == 0 && all(abs(rowSums(x) - 1) < 1e-6) && !beside) {

+			if(baseline == 0 && all(abs(rowSums(x, na.rm = TRUE) - 1) < 1e-6) && !beside) {

 				data_scale = c(0, 1)

 			} else if(baseline <= data_scale[1]) {

 				data_scale = c(baseline, extend*(data_scale[2] - baseline) + data_scale[2])

@@ -4314,8 +4314,8 @@ anno_customize = function(x, graphics = list(), which = c("column", "row"),

 # == param

 # -x A vector of numeric values.

 # -rg Range. A numeric vector of length two.

-# -labels_gp. Graphics parameters for labels.

-# -x_convert. A function applied on ``x``. E.g. when ``x`` contains p-values, to map ``x`` to the heights of bars, a transformation of ``-log10(x)`` 

+# -labels_gp Graphics parameters for labels.

+# -x_convert A function applied on ``x``. E.g. when ``x`` contains p-values, to map ``x`` to the heights of bars, a transformation of ``-log10(x)`` 

 #      is normally applied.

 # -labels_format A function applied on ``x``. E.g., when ``x`` is a numeric, ``labels_format`` can be set to ``function(x) sprintf("\%.2f", x)``.

 # -labels_offset Offset of labels to the left or right of bars.

@@ -4330,7 +4330,7 @@ anno_customize = function(x, graphics = list(), which = c("column", "row"),

 #

 # == example

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

-# x = numeric(10)

+# x = rnorm(10)

 # Heatmap(m, right_annotation = rowAnnotation(numeric = anno_numeric(x)))

 anno_numeric = function(x, rg = range(x), labels_gp = gpar(), x_convert = NULL, 

 	labels_format = NULL, labels_offset = unit(4, "pt"),

@@ -4359,6 +4359,10 @@ anno_numeric = function(x, rg = range(x), labels_gp = gpar(), x_convert = NULL,

 		rg = range(x_convert(rg))

 	}

+	if(rg[1] == rg[2]) {

+		rg[2] = rg[2] + .Machine$double.eps*1.1

+	}

+

     x[x < rg[1]] = rg[1]

     x[x > rg[2]] = rg[2]

@@ -95,7 +95,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # Zuguang Gu <z.gu@dkfz.de>

 #

 HeatmapAnnotation = function(..., 

-	df, name, col, na_col = "grey",

+	df = NULL, name, col, na_col = "grey",

 	annotation_legend_param = list(), 

 	show_legend = TRUE, 

 	which = c("column", "row"), 

@@ -150,53 +150,8 @@ HeatmapAnnotation = function(...,

 	.Object@name = name

 	n_anno = 0

-	#### check system calls ####

-	# HeatmapAnnotation is either called by `HeatmapAnnotation()` or by `rowAnnotation()`/`columnAnnotation()`

-	sc = sys.calls()

-	nsc = length(sc)

-	if(nsc == 1) {  # HeatmapAnnotation(...)

-		scl = as.list(sc[[1]])

-		arg_list = scl[-1]

-	} else {

-		

-		scl = as.list(sc[[nsc-1]])

-		if(is.function(scl[[1]])) {

-			if(identical(scl[[1]], pheatmap)) {

-				scl = as.list(sc[[nsc]])

-				arg_list = scl[-1]

-			} else if(identical(scl[[1]], heatmap)) {

-				scl = as.list(sc[[nsc]])

-				arg_list = scl[-1]

-			} else if(identical(scl[[1]], heatmap.2)) {

-				scl = as.list(sc[[nsc]])

-				arg_list = scl[-1]

-			} else {

-				# do.call(rowAnnotation, list(...))

-				# do.call(columnAnnotation, list(...))

-				arg_list = scl[-1]

-			}

-		} else if(any(as.character(scl[[1]]) %in% c("HeatmapAnnotation", "rowAnnotation", "columnAnnotation"))) { 

-			# columnAnnotation(...), rowAnnotation(...)

-			# do.call("columnAnnotation", list(...))

-			# do.call("rowAnnotation", list(...))

-			arg_list = scl[-1]

-		} else {

-			# do.call("HeatmapAnnotation", list(...))

-			# do.call(HeatmapAnnotation, list(...))

-			scl = as.list(sc[[nsc]])

-			arg_list = scl[-1]

-		}

-	}

-

-    called_args = names(arg_list)

-    anno_args = setdiff(called_args, fun_args)

-    if(any(anno_args == "")) stop_wrap("annotations should have names.")

-    if(is.null(called_args)) {

-    	stop_wrap("It seems you are putting only one argument to the function. If it is a simple vector annotation or a function annotation (e.g. anno_*()), specify it as HeatmapAnnotation(name = value). If it is a data frame annotation, specify it as HeatmapAnnotation(df = value)")

-    }

-

     ##### pull all annotation to `anno_value_list`####

-    if("df" %in% called_args) {

+    if(!is.null(df)) {

     	if(is.matrix(df)) {

     		warning_wrap("`df` should be a data frame while not a matrix. Convert it to data frame.")

     		df = as.data.frame(df)

@@ -209,23 +164,35 @@ HeatmapAnnotation = function(...,

     }

     anno_arg_list = list(...)

-	if("df" %in% called_args && length(anno_arg_list)) {

-		if(any(duplicated(c(names(df), names(anno_arg_list))))) {

-			stop_wrap("Annotation names are duplicated. Check the column names of `df`.")

+    anno_arg_names = names(anno_arg_list)

+	if(any(anno_arg_names == "")) {

+		stop_wrap("Annotations should have names.")

+	}

+	if(is.null(anno_arg_names)) {

+		if(length(anno_arg_list) == 1) {

+			stop_wrap("The annotation should be specified as name-value pairs or via argument `df` with a data frame.")

+		}

+		if(length(anno_arg_list) > 1) {

+			stop_wrap("Annotations should have names.")

+		}

+	}

+

+	if(!is.null(df) && length(anno_arg_list)) {

+		if(any(duplicated(c(names(df), anno_arg_names)))) {

+			stop_wrap("Annotation names are duplicated to those in `df`. Check the column names of `df`.")

 		}

 	}

 	anno_value_list = list()

-	for(nm in called_args) {

-		if(nm %in% names(anno_arg_list)) {

-			anno_value_list[[nm]] = anno_arg_list[[nm]]

-		} else if(nm == "df") {

-			for(nm2 in colnames(df)) {

-				if(is.null(rownames(df))) {

-					anno_value_list[[nm2]] = df[, nm2]

-				} else {

-					anno_value_list[[nm2]] = structure(df[, nm2], names = rownames(df))

-				}

+	for(nm in anno_arg_names) {

+		anno_value_list[[nm]] = anno_arg_list[[nm]]

+	}

+	if(!is.null(df)) {

+		for(nm2 in colnames(df)) {

+			if(is.null(rownames(df))) {

+				anno_value_list[[nm2]] = df[, nm2]

+			} else {

+				anno_value_list[[nm2]] = structure(df[, nm2], names = rownames(df))

 			}

 		}

 	}

@@ -12,7 +12,7 @@

 # -round_corners Whether to draw round corners for the box.

 # -r Radius of the round corners.

 # -line_space Space between lines. The value can be a `grid::unit` object or a numeric scalar which is measured in mm.

-# -word_space Space between texts The value can be a `grid::unit` object or a numeric scalar which is measured in mm.

+# -text_space Space between texts The value can be a `grid::unit` object or a numeric scalar which is measured in mm.

 # -max_width The maximal width of the viewport to put the word cloud. The value can be a `grid::unit` object or a numeric scalar which is measured in mm.

 #        Note this might be larger than the final width of the returned grob object.

 # -padding Padding of the box, i.e. space between text and the four box borders. The value should be a `grid::unit` object with length 1, 2 or 4. If 

@@ -213,7 +213,7 @@ text_box_grob = function(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just

 # Width for text_box grob

 #

 # == param

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

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

 #

 # == value

 # A `grid::unit` object.

@@ -8,7 +8,7 @@ Constructor Method for HeatmapAnnotation class

 }

 \usage{

 HeatmapAnnotation(...,

-    df, name, col, na_col = "grey",

+    df = NULL, name, col, na_col = "grey",

     annotation_legend_param = list(),

     show_legend = TRUE,

     which = c("column", "row"),

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

 }

 }

 \examples{

@@ -18,8 +18,8 @@ anno_numeric(x, rg = range(x), labels_gp = gpar(), x_convert = NULL,

   \item{x}{A vector of numeric values.}

   \item{rg}{Range. A numeric vector of length two.}

-  \item{labels_gp.}{Graphics parameters for labels.}

-  \item{x_convert.}{A function applied on \code{x}. E.g. when \code{x} contains p-values, to map \code{x} to the heights of bars, a transformation of \code{-log10(x)}  is normally applied.}

+  \item{labels_gp}{Graphics parameters for labels.}

+  \item{x_convert}{A function applied on \code{x}. E.g. when \code{x} contains p-values, to map \code{x} to the heights of bars, a transformation of \code{-log10(x)}  is normally applied.}

   \item{labels_format}{A function applied on \code{x}. E.g., when \code{x} is a numeric, \code{labels_format} can be set to \code{function(x) sprintf("\%.2f", x)}.}

   \item{labels_offset}{Offset of labels to the left or right of bars.}

   \item{bg_gp}{Graphics parameters for the background bars.}

@@ -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{

@@ -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{

@@ -10,12 +10,12 @@ Method dispatch page for \code{draw}.

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

 \itemize{

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

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

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

 }

 }

 \examples{

@@ -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{

@@ -10,12 +10,12 @@ Method dispatch page for \code{show}.

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

 \itemize{

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

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

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

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

 }

 }

 \examples{

@@ -23,7 +23,7 @@ text_box_grob(text, x = unit(0.5, "npc"), y = unit(0.5, "npc"), just = "centre",

   \item{round_corners}{Whether to draw round corners for the box.}

   \item{r}{Radius of the round corners.}

   \item{line_space}{Space between lines. The value can be a \code{\link[grid]{unit}} object or a numeric scalar which is measured in mm.}

-  \item{word_space}{Space between texts The value can be a \code{\link[grid]{unit}} object or a numeric scalar which is measured in mm.}

+  \item{text_space}{Space between texts The value can be a \code{\link[grid]{unit}} object or a numeric scalar which is measured in mm.}

   \item{max_width}{The maximal width of the viewport to put the word cloud. The value can be a \code{\link[grid]{unit}} object or a numeric scalar which is measured in mm. Note this might be larger than the final width of the returned grob object.}

   \item{padding}{Padding of the box, i.e. space between text and the four box borders. The value should be a \code{\link[grid]{unit}} object with length 1, 2 or 4. If  length of the input unit is 2, the first value is the padding both to the top and to the bottom, and the second value is the padding to the left and right. If length of the input unit is 4, the four values correspond to paddings to the bottom, left, top and right of the box.}

   \item{first_text_from}{Should the texts be added from the top of the box or from the bottom? Value should be either "top" or "bottom".}

@@ -11,7 +11,7 @@ Width for text_box grob

 }

 \arguments{

-  \item{x}{The \code{text_box} grob returned by \code{\link{text_boxd_grob}}.}

+  \item{x}{The \code{text_box} grob returned by \code{\link{text_box_grob}}.}

 }

 \value{

@@ -270,3 +270,36 @@ ha = HeatmapAnnotation(foo = 1:10, bar = letters[1:10],

 		foo = gt_render("foo", gp = gpar(box_fill = "red")),

 		bar = gt_render("bar", gp = gpar(box_fill = "blue"))))

 draw(ha, test = TRUE)

+

+

+### test whether arguments can be captured

+HeatmapAnnotation(a = 1:10)

+rowAnnotation(a = 1:10)

+columnAnnotation(a = 1:10)

+do.call(HeatmapAnnotation, list(a = 1:10))

+do.call(rowAnnotation, list(a = 1:10))

+do.call(columnAnnotation, list(a = 1:10))

+do.call("HeatmapAnnotation", list(a = 1:10))

+do.call("rowAnnotation", list(a = 1:10))

+do.call("columnAnnotation", list(a = 1:10))

+

+f = function() HeatmapAnnotation(a = 1:10)

+f()

+f = function() rowAnnotation(a = 1:10)

+f()

+f = function() columnAnnotation(a = 1:10)

+f()

+

+sapply(1, function(x) HeatmapAnnotation(a = 1:10))

+sapply(1, function(x) rowAnnotation(a = 1:10))

+sapply(1, function(x) columnAnnotation(a = 1:10))

+

+mapply(function(x, y) HeatmapAnnotation(a = 1:10), list(1), list(1))

+mapply(function(x, y) rowAnnotation(a = 1:10), list(1), list(1))

+mapply(function(x, y) columnAnnotation(a = 1:10), list(1), list(1))

+

+

+try({

+	HeatmapAnnotation(1:10)

+	HeatmapAnnotation(df = data.frame(a = 1:10), a = 1:10)

+})