@@ -11,6 +11,7 @@ export(anno_boxplot)

 export(anno_density)

 export(anno_histogram)

 export(anno_link)

+export(anno_oncoprint_barplot)

 export(anno_points)

 export(anno_text)

 export(columnAnnotation)

@@ -3,6 +3,7 @@ CHANGES in VERSION 1.11.5

 * `gap` in `HeatmapAnnotation` has been adjusted

 * annotations support drawing names of either sides

 * `densityHeatmap()`: quantile lines are also reordered

+* export `anno_oncoprint_barplot`

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

@@ -58,7 +58,7 @@ oncoPrint = function(mat, get_type = function(x) x,

 	row_barplot_width = unit(2, "cm"),

 	remove_empty_columns = FALSE,

 	heatmap_legend_param = list(title = "Alterations"),

-	top_annotation = HeatmapAnnotation(column_bar = anno_column_bar, 

+	top_annotation = HeatmapAnnotation(column_bar = anno_oncoprint_barplot(), 

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

 	barplot_ignore = NULL,

 	...) {

@@ -286,6 +286,13 @@ oncoPrint = function(mat, get_type = function(x) x,

 		top_annotation = top_annotation,

 		heatmap_legend_param = heatmap_legend_param, ...)

+	ht@matrix_param$oncoprint = list()

+	ht@matrix_param$oncoprint$arr = arr

+	ht@matrix_param$oncoprint$barplot_ignore = barplot_ignore

+	ht@matrix_param$oncoprint$all_type = all_type

+	ht@matrix_param$oncoprint$axis_gp = axis_gp

+	ht@matrix_param$oncoprint$col = col

+

 	if(show_pct) {

 		ht_list = ha_pct + ht

 	} else {

@@ -331,3 +338,45 @@ unify_mat_list = function(mat_list, default = 0) {

 }

+

+# == title

+# Column barplot annotaiton for oncoPrint

+#

+# == details

+# This function is only used for column annotation

+#

+# == author

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

+#

+anno_oncoprint_barplot = function() {

+

+	function(index) {

+		object = get("object", envir = parent.frame(n = 5))

+		arr = object@matrix_param$oncoprint$arr

+		barplot_ignore = object@matrix_param$oncoprint$barplot_ignore

+		all_type = object@matrix_param$oncoprint$all_type

+		axis_gp = object@matrix_param$oncoprint$axis_gp

+		col = object@matrix_param$oncoprint$col

+

+		n = length(index)

+		count = apply(arr, c(2, 3), sum)[index, , drop = FALSE]

+		all_type = all_type[!(colnames(count) %in% barplot_ignore)]

+		count = count[, setdiff(colnames(count), barplot_ignore), drop = FALSE]

+		max_count = max(rowSums(count))

+		pushViewport(viewport(yscale = c(0, max_count*1.1), xscale = c(0.5, n + 0.5)))

+		for(i in seq_len(nrow(count))) {

+			if(any(count[i, ] > 0)) {

+				y = count[i, ]

+				y = y[y > 0]

+				y2 = cumsum(y)

+				type = all_type[count[i, ] > 0]

+				grid.rect(i, y2, height = y, width = 0.8, default.units = "native", just = "top", gp = gpar(col = NA, fill = col[type]))

+			}

+		}

+		breaks = grid.pretty(c(0, max_count))

+		grid.yaxis(at = breaks, label = breaks, gp = axis_gp)

+		upViewport()

+	}

+}

+

+

new file mode 100644

@@ -0,0 +1,21 @@

+\name{anno_oncoprint_barplot}

+\alias{anno_oncoprint_barplot}

+\title{

+Column barplot annotaiton for oncoPrint

+}

+\description{

+Column barplot annotaiton for oncoPrint

+}

+\usage{

+anno_oncoprint_barplot()

+}

+\details{

+This function is only used for column annotation

+}

+\author{

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

+}

+\examples{

+# There is no example

+NULL

+}

@@ -18,7 +18,7 @@ oncoPrint(mat, get_type = function(x) x,

     row_barplot_width = unit(2, "cm"),

     remove_empty_columns = FALSE,

     heatmap_legend_param = list(title = "Alterations"),

-    top_annotation = HeatmapAnnotation(column_bar = anno_column_bar,

+    top_annotation = HeatmapAnnotation(column_bar = anno_oncoprint_barplot(),

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

     barplot_ignore = NULL,

     ...)

@@ -45,10 +45,10 @@ element would include multiple alterations in a form of a complex string. In fol

 ```{r}

 mat = read.table(textConnection(

-"	s1	s2	s3

-g1	snv;indel	snv	indel

-g2		snv;indel	snv

-g3	snv		indel;snv"), row.names = 1, header = TRUE, sep = "\t", stringsAsFactors = FALSE)

+",s1,s2,s3

+g1,snv;indel,snv,indel

+g2,,snv;indel,snv

+g3,snv,,indel;snv"), row.names = 1, header = TRUE, sep = ",", stringsAsFactors = FALSE)

 mat = as.matrix(mat)

 mat

 ```

@@ -99,10 +99,11 @@ mat_list

 to adjust the matrix list.

 ```{r}

-mat_list$indel = mat_list$indel[1:2, 1:2]

-mat_list

-mat_list = unify_mat_list(mat_list)

-mat_list

+mat_list2 = mat_list

+mat_list2$indel = mat_list2$indel[1:2, 1:2]

+mat_list2

+mat_list2 = unify_mat_list(mat_list2)

+mat_list2

 ```

 Pass `mat_list` to `oncoPrint()`: