@@ -3,6 +3,7 @@ CHANGES in VERSION 1.7.1

 * `x` and `y` are `unit` object now in `cell_fun`

 * add an example to visualize GO game

 * transparency is kept when making discreate color mappings

+* `oncoPrint()`: barplots on top now are controlled by `top_annotation` argument

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

@@ -20,11 +20,10 @@

 # -axis_gp graphic paramters for axes

 # -show_row_barplot whether show barplot annotation on rows

 # -row_barplot_width width of barplot annotation on rows. It should be a `grid::unit` object

-# -show_column_barplot whether show barplot annotation on columns

-# -column_barplot_height height of barplot annotatioin on columns. it should be a `grid::unit` object.

 # -remove_empty_columns if there is no alteration in that sample, whether remove it on the heatmap

 # -heatmap_legend_param pass to `Heatmap`

-# -... pass to `Heatmap`

+# -top_annotation by default the top annotation contains barplots representing frequency of mutations in every sample.

+# -... pass to `Heatmap`, so can set ``bottom_annotation`` here.

 #

 # == details

 # The function returns a normal heatmap list and you can add more heatmaps/row annotations to it.

@@ -47,16 +46,20 @@ oncoPrint = function(mat, get_type = function(x) x,

 	alter_fun_list, col, 

 	row_order = oncoprint_row_order(),

 	column_order = oncoprint_column_order(),

-	show_column_names = FALSE, 

+	show_column_names = FALSE,

 	pct_gp = gpar(), 

 	axis_gp = gpar(fontsize = 8), 

 	show_row_barplot = TRUE, 

 	row_barplot_width = unit(2, "cm"),

-	show_column_barplot = TRUE, 

-	column_barplot_height = unit(2, "cm"),

 	remove_empty_columns = FALSE,

 	heatmap_legend_param = list(title = "Alterations"),

+	top_annotation = HeatmapAnnotation(column_bar = anno_column_bar, 

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

 	...) {

+

+	if(names(list(...)) %in% c("show_column_barplot", "column_barplot_height")) {

+		stop("`show_column_barplot` and `column_barplot_height` is deprecated, please configure `top_annotation` directly.")

+	}

 	# convert mat to mat_list

 	if(inherits(mat, "matrix")) {

@@ -221,7 +224,7 @@ oncoPrint = function(mat, get_type = function(x) x,

 		upViewport()

 	}

-	ha_column_bar = HeatmapAnnotation(column_bar = anno_column_bar, which = "column", height = column_barplot_height)

+	top_annotation = top_annotation

 	#####################################################################

 	# the main matrix

@@ -229,30 +232,17 @@ oncoPrint = function(mat, get_type = function(x) x,

 	dim(pheudo) = dim(arr)[1:2]

 	dimnames(pheudo) = dimnames(arr)[1:2]

-	if(show_column_barplot) {

-		ht = Heatmap(pheudo, col = col, rect_gp = gpar(type = "none"), 

-			cluster_rows = FALSE, cluster_columns = FALSE, row_order = row_order, column_order = column_order,

-			cell_fun = function(j, i, x, y, width, height, fill) {

-				z = arr[i, j, ]

-				add_oncoprint("background", x, y, width, height)

-				for(type in all_type[z]) {

-					add_oncoprint(type, x, y, width, height)

-				}

-			}, show_column_names = show_column_names,

-			top_annotation = ha_column_bar, 

-			heatmap_legend_param = heatmap_legend_param, ...)

-	} else {

-		ht = Heatmap(pheudo, col = col, rect_gp = gpar(type = "none"), 

-			cluster_rows = FALSE, cluster_columns = FALSE, row_order = row_order, column_order = column_order,

-			cell_fun = function(j, i, x, y, width, height, fill) {

-				z = arr[i, j, ]

-				add_oncoprint("background", x, y, width, height)

-				for(type in all_type[z]) {

-					add_oncoprint(type, x, y, width, height)

-				}

-			}, show_column_names = show_column_names, 

-			heatmap_legend_param = heatmap_legend_param, ...)

-	}

+	ht = Heatmap(pheudo, col = col, rect_gp = gpar(type = "none"), 

+		cluster_rows = FALSE, cluster_columns = FALSE, row_order = row_order, column_order = column_order,

+		cell_fun = function(j, i, x, y, width, height, fill) {

+			z = arr[i, j, ]

+			add_oncoprint("background", x, y, width, height)

+			for(type in all_type[z]) {

+				add_oncoprint(type, x, y, width, height)

+			}

+		}, show_column_names = show_column_names,

+		top_annotation = top_annotation, 

+		heatmap_legend_param = heatmap_legend_param, ...)

 	if(show_row_barplot) {

 		ht_list = ha_pct + ht + ha_row_bar

@@ -16,10 +16,10 @@ oncoPrint(mat, get_type = function(x) x,

     axis_gp = gpar(fontsize = 8),

     show_row_barplot = TRUE,

     row_barplot_width = unit(2, "cm"),

-    show_column_barplot = TRUE,

-    column_barplot_height = unit(2, "cm"),

     remove_empty_columns = FALSE,

     heatmap_legend_param = list(title = "Alterations"),

+    top_annotation = HeatmapAnnotation(column_bar = anno_column_bar,

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

     ...)

 }

 \arguments{

@@ -35,11 +35,10 @@ oncoPrint(mat, get_type = function(x) x,

   \item{axis_gp}{graphic paramters for axes}

   \item{show_row_barplot}{whether show barplot annotation on rows}

   \item{row_barplot_width}{width of barplot annotation on rows. It should be a \code{\link[grid]{unit}} object}

-  \item{show_column_barplot}{whether show barplot annotation on columns}

-  \item{column_barplot_height}{height of barplot annotatioin on columns. it should be a \code{\link[grid]{unit}} object.}

   \item{remove_empty_columns}{if there is no alteration in that sample, whether remove it on the heatmap}

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

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

+  \item{top_annotation}{by default the top annotation contains barplots representing frequency of mutations in every sample.}

+  \item{...}{pass to \code{\link{Heatmap}}, so can set \code{bottom_annotation} here.}

 }

 \details{