add a new add_points argument in anno_boxplot()

NEWS

@@ -1,6 +1,7 @@
 CHANGES in VERSION 2.13.4
 
 * `anno_barplot()`: fixed a bug when split is set, the bars are wrongly plotted under besides = TRUE.
+* `anno_boxplot()`: add two new argumetn: `add_points` and `pt_gp`.
 
 ========================
 

R/00_S4_generic_methods.R

@@ -1,32 +1,32 @@
-setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
-setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
 setGeneric('prepare', function(object, ...) standardGeneric('prepare'))
-setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
-setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
+setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
+setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
+setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
 setGeneric('adjust_heatmap_list', function(object, ...) standardGeneric('adjust_heatmap_list'))
 setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))
-setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
-setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
-setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
-setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))
-setGeneric('make_row_cluster', function(object, ...) standardGeneric('make_row_cluster'))
-setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
 setGeneric('copy_all', function(object, ...) standardGeneric('copy_all'))
-setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
-setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
-setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
-setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
-setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
-setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
-setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
 setGeneric('draw_title', function(object, ...) standardGeneric('draw_title'))
+setGeneric('draw_annotation_legend', function(object, ...) standardGeneric('draw_annotation_legend'))
 setGeneric('column_order', function(object, ...) standardGeneric('column_order'))
-setGeneric('make_column_cluster', function(object, ...) standardGeneric('make_column_cluster'))
-setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
-setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
-setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
-setGeneric('draw', function(object, ...) standardGeneric('draw'))
-setGeneric('set_component_height', function(object, ...) standardGeneric('set_component_height'))
+setGeneric('get_legend_param_list', function(object, ...) standardGeneric('get_legend_param_list'))
+setGeneric('draw_heatmap_legend', function(object, ...) standardGeneric('draw_heatmap_legend'))
 setGeneric('add_heatmap', function(object, ...) standardGeneric('add_heatmap'))
+setGeneric('draw_heatmap_body', function(object, ...) standardGeneric('draw_heatmap_body'))
 setGeneric('draw_dend', function(object, ...) standardGeneric('draw_dend'))
+setGeneric('annotation_legend_size', function(object, ...) standardGeneric('annotation_legend_size'))
+setGeneric('get_color_mapping_list', function(object, ...) standardGeneric('get_color_mapping_list'))
+setGeneric('column_dend', function(object, ...) standardGeneric('column_dend'))
+setGeneric('draw', function(object, ...) standardGeneric('draw'))
+setGeneric('draw_heatmap_list', function(object, ...) standardGeneric('draw_heatmap_list'))
+setGeneric('row_order', function(object, ...) standardGeneric('row_order'))
+setGeneric('heatmap_legend_size', function(object, ...) standardGeneric('heatmap_legend_size'))
+setGeneric('attach_annotation', function(object, ...) standardGeneric('attach_annotation'))
+setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))
+setGeneric('make_layout', function(object, ...) standardGeneric('make_layout'))
+setGeneric('row_dend', function(object, ...) standardGeneric('row_dend'))
+setGeneric('map_to_colors', function(object, ...) standardGeneric('map_to_colors'))
 setGeneric('set_component_width', function(object, ...) standardGeneric('set_component_width'))
+setGeneric('component_width', function(object, ...) standardGeneric('component_width'))
+setGeneric('re_size', function(object, ...) standardGeneric('re_size'))
+setGeneric('component_height', function(object, ...) standardGeneric('component_height'))
+setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

R/AnnotationFunction-function.R

@@ -1561,8 +1561,10 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
 # -extend The extension to both side of ``ylim``. The value is a percent value corresponding to ``ylim[2] - ylim[1]``.
 # -outline Whether draw outline of boxplots?
 # -box_width Relative width of boxes. The value should be smaller than one.
+# -add_points Whether add points on top of the boxes?
 # -pch Point style.
 # -size Point size.
+# -pt_gp Graphics parameters for points.
 # -axis Whether to add axis?
 # -axis_param parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters.
 # -width Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.
@@ -1584,8 +1586,8 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR
 # draw(anno, test = "anno_boxplot with gp")
 anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
 	gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6,
-	pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which),
-	width = NULL, height = NULL, ...) {
+	add_points = FALSE, pch = 16, size = unit(4, "pt"), pt_gp = gpar(), axis = TRUE, 
+	axis_param = default_axis_param(which), width = NULL, height = NULL, ...) {
 
 	other_args = list(...)
 	if(length(other_args)) {
@@ -1639,6 +1641,7 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
 
 	n = length(value)
 	gp = recycle_gp(gp, n)
+	pt_gp = recycle_gp(pt_gp, n)
 	if(length(pch) == 1) pch = rep(pch, n)
 	if(length(size) == 1) size = rep(size, n)
 
@@ -1657,6 +1660,7 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
 
 		n = length(index)
 		gp = subset_gp(gp, index)
+		pt_gp = subset_gp(pt_gp, index)
 		pch = pch[index]
 		size = size[index]
 		pushViewport(viewport(xscale = data_scale, yscale = c(0.5, n+0.5)))
@@ -1680,18 +1684,25 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
 		grid.segments(boxplot_stats[3, ], n - seq_along(index) + 1 - 0.5*box_width, 
 			          boxplot_stats[3, ], n - seq_along(index) + 1 + 0.5*box_width, 
 			          default.units = "native", gp = gp)
-		if(outline) {
+		if(!add_points && outline) {
 			for(i in seq_along(value)) {
 				l1 = value[[i]] > boxplot_stats[5,i]
 				l1[is.na(l1)] = FALSE
 				if(sum(l1)) grid.points(y = rep(n - i + 1, sum(l1)), x = value[[i]][l1], 
-					default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i])
+					default.units = "native", gp = subset_gp(pt_gp, i), pch = pch[i], size = size[i])
 				l2 = value[[i]] < boxplot_stats[1,i]
 				l2[is.na(l2)] = FALSE
 				if(sum(l2)) grid.points(y = rep(n - i + 1, sum(l2)), x = value[[i]][l2], 
-					default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i])
+					default.units = "native", gp = subset_gp(pt_gp, i), pch = pch[i], size = size[i])
+			}
+		}
+		if(add_points && outline) {
+			for(i in seq_along(value)) {
+				grid.points(y = n - runif(length(value[[i]]), min = i - 0.5*0.5*box_width, max = i + 0.5*0.5*box_width) + 1,
+					        x = value[[i]], default.units = "native", gp = subset_gp(pt_gp, i), pch = pch[i], size = size[i])
 			}
 		}
+
 		if(axis_param$side == "top") {
 			if(k > 1) axis = FALSE
 		} else if(axis_param$side == "bottom") {
@@ -1712,6 +1723,7 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
 
 		n = length(index)
 		gp = subset_gp(gp, index)
+		pt_gp = subset_gp(pt_gp, index)
 		pch = pch[index]
 		size = size[index]
 		pushViewport(viewport(xscale = c(0.5, n+0.5), yscale = data_scale))
@@ -1734,16 +1746,24 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
 		grid.segments(seq_along(index) - 0.5*box_width, boxplot_stats[3, ],
 			          seq_along(index) + 0.5*box_width, boxplot_stats[3, ], 
 			          default.units = "native", gp = gp)
-		if(outline) {	
+
+		if(!add_points && outline) {	
 			for(i in seq_along(value)) {
 				l1 = value[[i]] > boxplot_stats[5,i]
 				l1[is.na(l1)] = FALSE
 				if(sum(l1)) grid.points(x = rep(i, sum(l1)), y = value[[i]][l1], 
-					default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i])
+					default.units = "native", gp = subset_gp(pt_gp, i), pch = pch[i], size = size[i])
 				l2 = value[[i]] < boxplot_stats[1,i]
 				l2[is.na(l2)] = FALSE
 				if(sum(l2)) grid.points(x = rep(i, sum(l2)), y = value[[i]][l2], 
-					default.units = "native", gp = subset_gp(gp, i), pch = pch[i], size = size[i])
+					default.units = "native", gp = subset_gp(pt_gp, i), pch = pch[i], size = size[i])
+			}
+		}
+
+		if(add_points && outline) {
+			for(i in seq_along(value)) {
+				grid.points(x = runif(length(value[[i]]), min = i - 0.5*0.5*box_width, max = i + 0.5*0.5*box_width),
+					        y = value[[i]], default.units = "native", gp = subset_gp(pt_gp, i), pch = pch[i], size = size[i])
 			}
 		}
 		if(axis_param$side == "left") {
@@ -1770,11 +1790,12 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,
 		width = anno_size$width,
 		height = anno_size$height,
 		data_scale = data_scale,
-		var_import = list(value, gp, border, box_width, axis, axis_param, axis_grob, data_scale, pch, size, outline)
+		var_import = list(value, gp, border, box_width, axis, axis_param, axis_grob, data_scale, add_points, pch, pt_gp, size, outline)
 	)
 
 	anno@subset_rule$value = subset_vector
 	anno@subset_rule$gp = subset_gp
+	anno@subset_rule$pt_gp = subset_gp
 	anno@subset_rule$pch = subset_vector
 	anno@subset_rule$size = subset_vector
 

man/add_heatmap-dispatch.Rd

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

man/anno_boxplot.Rd

@@ -9,8 +9,8 @@ Boxplot Annotation
 \usage{
 anno_boxplot(x, which = c("column", "row"), border = TRUE,
     gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, outline = TRUE, box_width = 0.6,
-    pch = 1, size = unit(2, "mm"), axis = TRUE, axis_param = default_axis_param(which),
-    width = NULL, height = NULL, ...)
+    add_points = FALSE, pch = 16, size = unit(4, "pt"), pt_gp = gpar(), axis = TRUE,
+    axis_param = default_axis_param(which), width = NULL, height = NULL, ...)
 }
 \arguments{
 
@@ -22,8 +22,10 @@ anno_boxplot(x, which = c("column", "row"), border = TRUE,
   \item{extend}{The extension to both side of \code{ylim}. The value is a percent value corresponding to \code{ylim[2] - ylim[1]}.}
   \item{outline}{Whether draw outline of boxplots?}
   \item{box_width}{Relative width of boxes. The value should be smaller than one.}
+  \item{add_points}{Whether add points on top of the boxes?}
   \item{pch}{Point style.}
   \item{size}{Point size.}
+  \item{pt_gp}{Graphics parameters for points.}
   \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.}
   \item{width}{Width of the annotation. The value should be an absolute unit. Width is not allowed to be set for column annotation.}

man/column_dend-dispatch.Rd

@@ -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{

man/component_height-dispatch.Rd

@@ -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{

man/copy_all-dispatch.Rd

@@ -10,8 +10,8 @@ Method dispatch page for \code{copy_all}.
 \code{copy_all} can be dispatched on following classes:
 
 \itemize{
-\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
 \item \code{\link{copy_all,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
+\item \code{\link{copy_all,SingleAnnotation-method}}, \code{\link{SingleAnnotation-class}} class method
 }
 }
 \examples{

man/draw-dispatch.Rd

@@ -10,12 +10,12 @@ 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,SingleAnnotation-method}}, \code{\link{SingleAnnotation-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
+\item \code{\link{draw,AnnotationFunction-method}}, \code{\link{AnnotationFunction-class}} class method
 \item \code{\link{draw,HeatmapAnnotation-method}}, \code{\link{HeatmapAnnotation-class}} class method
-\item \code{\link{draw,Legends-method}}, \code{\link{Legends-class}} class method
+\item \code{\link{draw,HeatmapList-method}}, \code{\link{HeatmapList-class}} class method
 }
 }
 \examples{

man/draw_title-dispatch.Rd

@@ -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{

man/make_layout-dispatch.Rd

@@ -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{

man/show-dispatch.Rd

@@ -10,12 +10,12 @@ Method dispatch page for \code{show}.
 \code{show} can be dispatched on following classes:
 
 \itemize{
-\item \code{\link{show,HeatmapList-method}}, \code{\link{HeatmapList-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,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
 }
 }
 \examples{

tests/test-AnnotationFunction.R

@@ -271,7 +271,6 @@ anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), beside = TRUE, gp = gpar(fill
 draw(anno, test = "a matrix with fill")
 
 
-
 ##### test anno_boxplot #####
 set.seed(123)
 m = matrix(rnorm(100), 10)