@@ -256,8 +256,8 @@ import(grDevices)

 import(graphics)

 import(grid)

 import(methods)

-import(stats)

 import(png)

+import(stats)

 importFrom("GetoptLong", qq)

 importFrom("GetoptLong", qq.options)

 importFrom("GetoptLong", qqcat)

@@ -1,31 +1,31 @@

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -555,6 +555,9 @@ anno_image = function(image, which = c("column", "row"), border = TRUE,

 # -facing Whether the axis faces to the outside of the annotation region or inside. Sometimes when

 #         appending more than one heatmaps, the axes of column annotations of one heatmap might

 #         overlap to the neighbouring heatmap, setting ``facing`` to ``inside`` may invoild it.

+# -direction The direction of the axis. Value should be "normal" or "reverse".

+#

+# All the parameters are passed to `annotation_axis_grob` to construct an axis grob.

 #

 # == example

 # default_axis_param("column")

@@ -566,7 +569,8 @@ default_axis_param = function(which) {

 		labels_rot = ifelse(which == "column", 0, 90), 

 		gp = gpar(fontsize = 8), 

 		side = ifelse(which == "column", "left", "bottom"), 

-		facing = "outside"

+		facing = "outside",

+		direction = "normal"

 	)

 }

@@ -600,9 +604,12 @@ construct_axis_grob = function(axis_param, which, data_scale) {

 		axis_param$at = at

 		axis_param$labels = at

 	}

+

 	if(is.null(axis_param$labels)) {

 		axis_param$labels = axis_param$at

 	}

+

+	axis_param$scale = data_scale

 	axis_grob = do.call(annotation_axis_grob, axis_param)

 	return(axis_grob)

 }

@@ -709,6 +716,10 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()

 		n = length(index)

+		if(axis_param$direction == "reverse") {

+			value = data_scale[2] - value + data_scale[1]

+		}

+

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

 		if(is.matrix(value)) {

 			for(i in seq_len(ncol(value))) {

@@ -732,6 +743,10 @@ anno_points = function(x, which = c("column", "row"), border = TRUE, gp = gpar()

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

 		n = length(index)

+

+		if(axis_param$direction == "reverse") {

+			value = data_scale[2] - value + data_scale[1]

+		}

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

 		if(is.matrix(value)) {

@@ -903,6 +918,10 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),

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

 		n = length(index)

+		if(axis_param$direction == "reverse") {

+			value = data_scale[2] - value + data_scale[1]

+		}

+

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

 		if(is.matrix(value)) {

 			for(i in seq_len(ncol(value))) {

@@ -950,6 +969,10 @@ anno_lines = function(x, which = c("column", "row"), border = TRUE, gp = gpar(),

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

 		n = length(index)

+		if(axis_param$direction == "reverse") {

+			value = data_scale[2] - value + data_scale[1]

+		}

+

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

 		if(is.matrix(value)) {

 			for(i in seq_len(ncol(value))) {

@@ -1147,6 +1170,12 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

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

 		n = length(index)

+		if(axis_param$direction == "reverse") {

+			value_origin = value

+			value = data_scale[2] - value + data_scale[1]

+			baseline = data_scale[2] - baseline + data_scale[1]

+		}

+

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

 		if(ncol(value) == 1) {

 			width = value[index] - baseline

@@ -1154,9 +1183,16 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 			grid.rect(x = x_coor, y = n - seq_along(index) + 1, width = abs(width), height = 1*bar_width, default.units = "native", gp = subset_gp(gp, index))

 		} else {

 			for(i in seq_len(ncol(value))) {

-				width = value[index, i]

-				x_coor = rowSums(value[index, seq_len(i-1), drop = FALSE]) + width/2

-				grid.rect(x = x_coor, y = n - seq_along(index) + 1, width = abs(width), height = 1*bar_width, default.units = "native", gp = subset_gp(gp, i))

+				if(axis_param$direction == "normal") {

+					width = abs(value[index, i])

+					x_coor = rowSums(value[index, seq_len(i-1), drop = FALSE]) + width/2

+					grid.rect(x = x_coor, y = n - seq_along(index) + 1, width = abs(width), height = 1*bar_width, default.units = "native", gp = subset_gp(gp, i))

+				} else {

+					width = value_origin[index, i] # the original width

+					x_coor = rowSums(value_origin[index, seq_len(i-1), drop = FALSE]) + width/2 #distance to the right

+					x_coor = data_scale[2] - x_coor + data_scale[1]

+					grid.rect(x = x_coor, y = n - seq_along(index) + 1, width = abs(width), height = 1*bar_width, default.units = "native", gp = subset_gp(gp, i))

+				}

 			}

 		}

 		if(axis_param$side == "top") {

@@ -1170,7 +1206,13 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 	}

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

 		n = length(index)

-	

+		

+		if(axis_param$direction == "reverse") {

+			value_origin = value

+			value = data_scale[2] - value + data_scale[1]

+			baseline = data_scale[2] - baseline + data_scale[1]

+		}

+

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

 		if(ncol(value) == 1) {

 			height = value[index] - baseline

@@ -1178,9 +1220,16 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 			grid.rect(y = y_coor, x = seq_along(index), height = abs(height), width = 1*bar_width, default.units = "native", gp = subset_gp(gp, index))

 		} else {

 			for(i in seq_len(ncol(value))) {

-				height = value[index, i]

-				y_coor = rowSums(value[index, seq_len(i-1), drop = FALSE]) + height/2

-				grid.rect(y = y_coor, x = seq_along(index), height = abs(height), width = 1*bar_width, default.units = "native", gp = subset_gp(gp, i))

+				if(axis_param$direction == "normal") {

+					height = value[index, i]

+					y_coor = rowSums(value[index, seq_len(i-1), drop = FALSE]) + height/2

+					grid.rect(y = y_coor, x = seq_along(index), height = abs(height), width = 1*bar_width, default.units = "native", gp = subset_gp(gp, i))

+				} else {

+					height = value_origin[index, i]

+					y_coor = rowSums(value_origin[index, seq_len(i-1), drop = FALSE]) + height/2

+					y_coor = data_scale[2] - y_coor + data_scale[1]

+					grid.rect(y = y_coor, x = seq_along(index), height = abs(height), width = 1*bar_width, default.units = "native", gp = subset_gp(gp, i))

+				}

 			}

 		}

 		if(axis_param$side == "left") {

@@ -1321,6 +1370,10 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

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

+		if(axis_param$direction == "reverse") {

+			value = lapply(value, function(x) data_scale[2] - x + data_scale[1])

+		}

+

 		n_all = length(value)

 		value = value[index]

 		boxplot_stats = boxplot(value, plot = FALSE)$stats

@@ -1372,6 +1425,11 @@ anno_boxplot = function(x, which = c("column", "row"), border = TRUE,

 		popViewport()

 	}

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

+

+		if(axis_param$direction == "reverse") {

+			value = lapply(value, function(x) data_scale[2] - x + data_scale[1])

+		}

+

 		value = value[index]

 		boxplot_stats = boxplot(value, plot = FALSE)$stats

@@ -1524,6 +1582,10 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,

 	axis_grob = if(axis) construct_axis_grob(axis_param, which, xscale) else NULL

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

+

+		if(axis_param$direction == "reverse") {

+			value = lapply(value, function(x) data_scale[2] - x + data_scale[1])

+		}

 		n_all = length(value)

 		value = value[index]

@@ -1550,6 +1612,10 @@ anno_histogram = function(x, which = c("column", "row"), n_breaks = 11,

 		popViewport()

 	}

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

+

+		if(axis_param$direction == "reverse") {

+			value = lapply(value, function(x) data_scale[2] - x + data_scale[1])

+		}

 		n_all = length(value)

 		value = value[index]

@@ -1712,6 +1778,10 @@ anno_density = function(x, which = c("column", "row"),

 	axis_grob = if(axis) construct_axis_grob(axis_param, which, xscale) else NULL

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

+

+		if(axis_param$direction == "reverse") {

+			value = lapply(value, function(x) data_scale[2] - x + data_scale[1])

+		}

 		n = length(index)

 		value = value[index]

@@ -1766,6 +1836,10 @@ anno_density = function(x, which = c("column", "row"),

 		popViewport()

 	}

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

+		

+		if(axis_param$direction == "reverse") {

+			value = lapply(value, function(x) data_scale[2] - x + data_scale[1])

+		}

 		n_all = length(value)

 		value = value[index]

@@ -2145,6 +2219,10 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000

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

+		if(axis_param$direction == "reverse") {

+			value = lapply(value, function(x) data_scale[2] - x + data_scale[1])

+		}

+

 		n_all = length(value)

 		value = value[index]

@@ -2178,6 +2256,10 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000

 	}

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

+		if(axis_param$direction == "reverse") {

+			value = lapply(value, function(x) data_scale[2] - x + data_scale[1])

+		}

+

 		n_all = length(value)

 		value = value[index]

@@ -2362,6 +2444,10 @@ anno_horizon = function(x, which = c("column", "row"),

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

+		if(axis_param$direction == "reverse") {

+			value = lapply(value, function(x) data_scale[2] - x + data_scale[1])

+		}

+

 		n_all = length(value)

 		value = value[index]

@@ -8,7 +8,8 @@

 # -gp Graphic parameters.

 # -side side of the axis of the annotation viewport.

 # -facing Facing of the axis.

-# -direction direction of the axis. Value should be "normal" or "reverse".

+# -direction Direction of the axis. Value should be "normal" or "reverse".

+# -scale The data scale. If it is ``NULL``, it is inferred from current viewport.

 #

 # == value

 # A `grid::grob` object.

@@ -129,7 +130,7 @@

 # popViewport()

 #

 annotation_axis_grob = function(at = NULL, labels = at, labels_rot = 0, gp = gpar(), 

-	side = "left", facing = "outside", direction = "normal") {

+	side = "left", facing = "outside", direction = "normal", scale = NULL) {

 	if(!side %in% c("left", "right", "top", "bottom")) {

 		stop_wrap("`side` can only be in 'left', 'right', 'top' and 'bottom'.")

@@ -141,10 +142,12 @@ annotation_axis_grob = function(at = NULL, labels = at, labels_rot = 0, gp = gpa

 		stop_wrap("`direction` can only be in `normal` and `reverse`.")

 	}

-	if(side %in% c("top", "bottom")) {

-		scale = current.viewport()$xscale

-	} else {

-		scale = current.viewport()$yscale

+	if(is.null(scale)) {

+		if(side %in% c("top", "bottom")) {

+			scale = current.viewport()$xscale

+		} else {

+			scale = current.viewport()$yscale

+		}

 	}

 	if(is.null(at)) {

 		at = pretty_breaks(scale)

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

 \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

 }

 }

 \examples{

@@ -8,7 +8,7 @@ Grob for Annotation Axis

 }

 \usage{

 annotation_axis_grob(at = NULL, labels = at, labels_rot = 0, gp = gpar(),

-    side = "left", facing = "outside")

+    side = "left", facing = "outside", direction = "normal", scale = NULL)

 }

 \arguments{

@@ -18,6 +18,8 @@ annotation_axis_grob(at = NULL, labels = at, labels_rot = 0, gp = gpar(),

   \item{gp}{Graphic parameters.}

   \item{side}{side of the axis of the annotation viewport.}

   \item{facing}{Facing of the axis.}

+  \item{direction}{Direction of the axis. Value should be "normal" or "reverse".}

+  \item{scale}{The data scale. If it is \code{NULL}, it is inferred from current viewport.}

 }

 \value{

@@ -27,87 +29,114 @@ A \code{\link[grid:grid.grob]{grob}} object.

 gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

     side = "left", facing = "outside")

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+grid.rect()

+grid.text('side = "left", facing = "outside"')

 grid.draw(gb)

-grid.rect(x = unit(0, "npc"), width = grobWidth(gb), just = "right")

 popViewport()

 gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

     side = "left", facing = "inside")

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+grid.rect()

+grid.text('side = "left", facing = "inside"')

 grid.draw(gb)

-grid.rect(x = unit(0, "npc"), width = grobWidth(gb), just = "left")

 popViewport()

 gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

     side = "right", facing = "outside")

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+grid.rect()

+grid.text('side = "right", facing = "outside"')

 grid.draw(gb)

-grid.rect(x = unit(1, "npc"), width = grobWidth(gb), just = "left")

 popViewport()

 gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

     side = "right", facing = "inside")

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+grid.rect()

+grid.text('side = "right", facing = "inside"')

 grid.draw(gb)

-grid.rect(x = unit(1, "npc"), width = grobWidth(gb), just = "right")

 popViewport()

-gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, 

     side = "top", facing = "outside")

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+grid.rect()

+grid.text('side = "top", facing = "outside"')

 grid.draw(gb)

-grid.rect(y = unit(1, "npc"), height = grobHeight(gb), just = "bottom")

 popViewport()

-gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 90, 

+gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 90, 

     side = "top", facing = "outside")

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+grid.rect()

+grid.text('side = "top", facing = "outside"')

 grid.draw(gb)

-grid.rect(y = unit(1, "npc"), height = grobHeight(gb), just = "bottom")

 popViewport()

-gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 45, 

+gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 45, 

     side = "top", facing = "outside")

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+grid.rect()

+grid.text('side = "top", facing = "outside"')

 grid.draw(gb)

-grid.rect(y = unit(1, "npc"), height = grobHeight(gb), just = "bottom")

 popViewport()

-gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, 

     side = "top", facing = "inside")

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+grid.rect()

+grid.text('side = "top", facing = "inside"')

 grid.draw(gb)

-grid.rect(y = unit(1, "npc"), height = grobHeight(gb), just = "top")

 popViewport()

-gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, 

     side = "bottom", facing = "outside")

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+grid.rect()

+grid.text('side = "bottom", facing = "outside"')

 grid.draw(gb)

-grid.rect(y = unit(0, "npc"), height = grobHeight(gb), just = "top")

 popViewport()

-gb = annotation_axis_grob(at = 1:5, labels = month.name[1:5], labels_rot = 0, 

+gb = annotation_axis_grob(at = 1:3, labels = month.name[1:3], labels_rot = 0, 

     side = "bottom", facing = "inside")

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+grid.rect()

+grid.text('side = "bottom", facing = "inside"')

 grid.draw(gb)

-grid.rect(y = unit(0, "npc"), height = grobHeight(gb), just = "bottom")

 popViewport()

 grid.newpage()

-pushViewport(viewport(xscale = c(0, 6), yscale = c(0, 6), width = 0.6, height = 0.6))

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

 gb = annotation_axis_grob(labels_rot = 0, side = "left", facing = "outside")

+grid.rect()

+grid.text('side = "left", facing = "outside"')

+grid.draw(gb)

+popViewport()

+

+grid.newpage()

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+gb = annotation_axis_grob(side = "left", direction = "reverse")

+grid.rect()

+grid.text('side = "left", direction = "reverse')

+grid.draw(gb)

+popViewport()

+

+grid.newpage()

+pushViewport(viewport(xscale = c(0, 4), yscale = c(0, 6), width = 0.6, height = 0.6))

+gb = annotation_axis_grob(side = "bottom", direction = "reverse")

+grid.rect()

+grid.text('side = "bottom", directio = "reverse"')

 grid.draw(gb)

-grid.rect(x = unit(0, "npc"), width = grobWidth(gb), just = "right")

 popViewport()

 }

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

 \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

 }

 }

 \examples{

@@ -7,11 +7,12 @@ Sizes of the Combination sets

 Sizes of the Combination sets

 }

 \usage{

-comb_size(m)

+comb_size(m, degree = NULL)

 }

 \arguments{

   \item{m}{A combination matrix returned by \code{\link{make_comb_mat}}.}

+  \item{degree}{degree of the intersection. The value can be a vector.}

 }

 \value{

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

 \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

 }

 }

 \examples{

@@ -24,7 +24,10 @@ There are following parameters for the annotation axis:

   \item{gp}{Graphc parameters of axis labels. The value should be a \code{\link[grid]{unit}} object.}

   \item{side}{If it is for column annotation, the value should only be one of \code{left} and \code{right}. If it is for row annotation, the value should only be one of \code{top} and \code{bottom}.}

   \item{facing}{Whether the axis faces to the outside of the annotation region or inside. Sometimes when appending more than one heatmaps, the axes of column annotations of one heatmap might overlap to the neighbouring heatmap, setting \code{facing} to \code{inside} may invoild it.}

+  \item{direction}{The direction of the axis. Value should be "normal" or "reverse".}

 }

+

+All the parameters are passed to \code{\link{annotation_axis_grob}} to construct an axis grob.

 }

 \examples{

 default_axis_param("column")

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

 \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,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,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{

@@ -8,7 +8,7 @@ Draw Annotation Axis

 }

 \usage{

 grid.annotation_axis(at = NULL, labels = at, labels_rot = 0, gp = gpar(),

-    side = "left", facing = "outside")

+    side = "left", facing = "outside", direction = "normal")

 }

 \arguments{

@@ -18,6 +18,7 @@ grid.annotation_axis(at = NULL, labels = at, labels_rot = 0, gp = gpar(),

   \item{gp}{Graphic parameters.}

   \item{side}{side of the axis of the annotation viewport.}

   \item{facing}{Facing of the axis.}

+  \item{direction}{direction of the axis. Value should be "normal" or "reverse".}

 }

 \details{

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

 \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

 }

 }

 \examples{

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

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

 \itemize{

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

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

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

 }

 }

 \examples{

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

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

 }

 }

 \examples{

@@ -123,6 +123,12 @@ anno = anno_points(c(1:5, NA, 7:10))

 draw(anno, test = "anno_points")

+anno = anno_points(runif(10), axis_param = list(direction = "reverse"), ylim = c(0, 1))

+draw(anno, test = "anno_points")

+

+anno = anno_points(runif(10), axis_param = list(direction = "reverse"), ylim = c(0, 1), which = "row")

+draw(anno, test = "anno_points")

+

 ##### test anno_lines ###

 anno = anno_lines(runif(10))

 draw(anno, test = "anno_lines")

@@ -146,6 +152,8 @@ draw(anno, test = "anno_lines, smooth, matrix, by row")

 anno = anno_lines(c(1:5, NA, 7:10))

 draw(anno, test = "anno_lines")

+anno = anno_lines(runif(10), axis_param = list(direction = "reverse"))

+draw(anno, test = "anno_lines")

 ###### test anno_text #######

 anno = anno_text(month.name)

@@ -199,6 +207,16 @@ draw(anno, test = "proportion matrix")

 anno = anno_barplot(c(1:5, NA, 7:10))

 draw(anno, test = "a vector")

+anno = anno_barplot(1:10, which = "row", axis_param = list(direction = "reverse"))

+draw(anno, test = "a vector")

+

+anno = anno_barplot(1:10, baseline = 5, which = "row", axis_param = list(direction = "reverse"))

+draw(anno, test = "a vector")

+

+anno = anno_barplot(matrix(nc = 2, c(1:10, 10:1)), which = "row", axis_param = list(direction = "reverse"))

+draw(anno, test = "a vector")

+

+

 ##### test anno_boxplot #####

 set.seed(123)

 m = matrix(rnorm(100), 10)