@@ -567,9 +567,11 @@ oncoPrint = function(mat, name,

 			# adjust order of alter_fun3 with at

 			if(!is.null(heatmap_legend_param$at)) {

-				if(length(setdiff(heatmap_legend_param$at, names(alter_fun3))) == 0) {

-					alter_fun3 = alter_fun3[heatmap_legend_param$at]

-				}

+				ind = which(heatmap_legend_param$at %in% names(alter_fun3))

+				heatmap_legend_param$at = heatmap_legend_param$at[ind]

+				heatmap_legend_param$labels = heatmap_legend_param$labels[ind]

+

+				alter_fun3 = alter_fun3[heatmap_legend_param$at]

 			}

 			heatmap_legend_param$graphics = alter_fun3

@@ -23,6 +23,7 @@

 # -pct_gp Graphic paramters for percent values

 # -pct_digits Digits for the percent values.

 # -pct_side Side of the percent values to the oncoPrint. This argument is currently disabled.

+# -pct_include Alteration types that are included for the calculation of percent values.

 # -row_labels Labels as the row names of the oncoPrint.

 # -show_row_names Whether show row names?

 # -row_names_side Side of the row names to the oncoPrint. This argument is currently disabled.

@@ -69,6 +70,7 @@ oncoPrint = function(mat, name,

 	pct_gp = gpar(fontsize = 10), 

 	pct_digits = 0,

 	pct_side = "left",

+	pct_include = NULL,

 	row_labels = NULL,

 	show_row_names = TRUE,

@@ -368,7 +370,10 @@ oncoPrint = function(mat, name,

 	}

 	# for each gene, percent of samples that have alterations

-	pct_num = rowSums(apply(arr, 1:2, any)) / ncol(mat_list[[1]])

+	if(is.null(pct_include)) {

+		pct_include = dimnames(arr)[[3]]

+	}

+	pct_num = rowSums(apply(arr[, , dimnames(arr)[[3]] %in% pct_include, drop = FALSE], 1:2, any)) / ncol(mat_list[[1]])

 	pct = paste0(round(pct_num * 100, digits = pct_digits), "%")

 	### now the annotations

@@ -593,6 +593,7 @@ oncoPrint = function(mat, name,

 		...

 	)

 	ht@heatmap_param$oncoprint_env = environment()

+	ht@heatmap_param$type = "oncoPrint"

 	return(ht)

 }

@@ -809,7 +809,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		var_import = list(border, type, bar_width, beside, axis, axis_param, anno_size, ylim, show_fraction)

 	)

-	anno@subsetable = TRUE

+	anno@subsettable = TRUE

 	anno@show_name = FALSE

 	if(exists("arr", envir = parent.frame(1))) {

@@ -135,7 +135,7 @@ oncoPrint = function(mat, name,

 		## check whether there are NA values in the matrix

 		if(any(is.na(mat))) {

-			message_wrap("Found NA values in the matrix and treat as no alteration. If `NA` means no alteration, you can explicitly set it to empty strings like ''. If `NA` is an alteration type, you should format it to a string like `'NA'` and define a graphic for it.")

+			message_wrap("Found NA values in the matrix and treat as no alteration. If `NA` means no alteration, you can explicitly set it to empty strings like ''. If `NA` is an alteration type, you should format it to a string like `'NA'` and define graphics for it.")

 		}

 		mat_list = lapply(all_type, function(type) {

@@ -711,6 +711,7 @@ unify_mat_list = function(mat_list, default = 0) {

 # -type A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.

 # -which Is it a row annotation or a column annotation?

 # -bar_width Width of the bars.

+# -beside Will bars be stacked or be positioned beside each other?

 # -ylim Data range.

 # -show_fraction Whether to show the numbers or the fractions?

 # -axis Whether draw axis?

@@ -726,7 +727,7 @@ unify_mat_list = function(mat_list, default = 0) {

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

 #

 anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

-	bar_width = 0.6, ylim = NULL, show_fraction = FALSE, axis = TRUE,

+	bar_width = 0.6, beside = FALSE, ylim = NULL, show_fraction = FALSE, axis = TRUE,

 	axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),

 	width = NULL, height = NULL, border = FALSE) {

@@ -761,7 +762,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		v = v[, !is.na(col), drop = FALSE]

 		col = col[!is.na(col)]

 		fun = anno_barplot(v, gp = gpar(fill = col, col = NA), which = "column", ylim = ylim,

-			baseline = 0, height = anno_size$height, border = border, bar_width = bar_width,

+			baseline = 0, height = anno_size$height, border = border, bar_width = bar_width, beside = beside,

 			axis = axis, axis_param = axis_param)@fun

 		fun(index, k, n)

 	}

@@ -788,7 +789,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		v = v[, !is.na(col), drop = FALSE]

 		col = col[!is.na(col)]

 		fun = anno_barplot(v, gp = gpar(fill = col, col = NA), which = "row", ylim = ylim,

-			baseline = 0, width = anno_size$width, border = border, bar_width = bar_width,

+			baseline = 0, width = anno_size$width, border = border, bar_width = bar_width, beside = beside,

 			axis = axis, axis_param = axis_param)@fun

 		fun(index, k, n)

 	}

@@ -805,7 +806,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		which = which,

 		width = anno_size$width,

 		height = anno_size$height,

-		var_import = list(border, type, bar_width, axis, axis_param, anno_size, ylim, show_fraction)

+		var_import = list(border, type, bar_width, beside, axis, axis_param, anno_size, ylim, show_fraction)

 	)

 	anno@subsetable = TRUE

@@ -299,6 +299,8 @@ oncoPrint = function(mat, name,

 		if(alter_fun_is_vectorized) {

 			layer_fun = function(j, i, x, y, w, h, fill) {

 				v = pindex(arr, i, j)

+				v = as.vector(v)

+				names(v) = dimnames[[3]]

 				af(x, y, w, h, v, j, i)

 			}

 			cell_fun = NULL

@@ -306,6 +308,7 @@ oncoPrint = function(mat, name,

 			layer_fun = NULL

 			cell_fun = function(j, i, x, y, w, h, fill) {

 				v = arr[i, j, ]

+				names(v) = dimnames[[3]]

 				af(x, y, w, h, v, j, i)

 			}

 		}

@@ -184,10 +184,10 @@ oncoPrint = function(mat, name,

 	}

 	if(missing(name)) {

-        name = paste0("matrix_", get_oncoprint_index() + 1)

+        name = paste0("oncoPrint_", get_oncoprint_index() + 1)

         increase_oncoprint_index()

     } else if(is.null(name)) {

-        name = paste0("matrix_", get_oncoprint_index() + 1)

+        name = paste0("oncnPrint_", get_oncoprint_index() + 1)

         increase_oncoprint_index()

     }

@@ -8,6 +8,7 @@

 #      value representing whether the alteration is present or absent. 

 #      When the value is a list, the names of the list represent alteration types.

 #      You can use `unify_mat_list` to make all matrix having same row names and column names.

+# -name Name of the oncoPrint. Not necessary to specify.

 # -get_type If different alterations are encoded in the matrix as complex strings, this self-defined function

 #           determines how to extract them. It only works when ``mat`` is a matrix. The default value is `default_get_type`.

 # -alter_fun A single function or a list of functions which defines how to add graphics for different alterations.

@@ -53,7 +54,7 @@

 # == author

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

 #

-oncoPrint = function(mat, 

+oncoPrint = function(mat, name,

 	get_type = default_get_type,

 	alter_fun, 

 	alter_fun_is_vectorized = NULL,

@@ -182,6 +183,14 @@ oncoPrint = function(mat,

 		arr[, , i] = mat_list[[i]]

 	}

+	if(missing(name)) {

+        name = paste0("matrix_", get_oncoprint_index() + 1)

+        increase_oncoprint_index()

+    } else if(is.null(name)) {

+        name = paste0("matrix_", get_oncoprint_index() + 1)

+        increase_oncoprint_index()

+    }

+

 	oncoprint_row_order = function() {

 		order(rowSums(count_matrix), n_mut, decreasing = TRUE)

 	}

@@ -468,13 +477,17 @@ oncoPrint = function(mat,

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

 	# the main matrix

-	if(length(col)) {

-		pheudo = c(names(col), rep(NA, nrow(arr)*ncol(arr) - length(col)))

-	} else {

-		pheudo = c("mutation", rep(NA, nrow(arr)*ncol(arr) - 1))

+	if(length(col) == 0) {

 		col = c("mutation" = "black")

 	}

+	pheudo = apply(arr, 1:2, function(x) {

+		if(all(!x)) {

+			return("")

+		} else {

+			paste(all_type[x], collapse = ";")

+		}

+	})

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

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

@@ -558,7 +571,7 @@ oncoPrint = function(mat,

 		}

 	}

-	ht = Heatmap(pheudo, col = col, 

+	ht = Heatmap(pheudo, name = name, col = col, 

 		rect_gp = gpar(type = "none"), 

 		cluster_rows = cluster_rows, cluster_columns = cluster_columns, 

 		row_order = row_order, column_order = column_order,

@@ -172,7 +172,12 @@ oncoPrint = function(mat,

 	message_wrap(paste0("All mutation types: ", paste(all_type, collapse = ", "), "."))

 	# type as the third dimension

-	arr = array(FALSE, dim = c(dim(mat_list[[1]]), length(all_type)), dimnames = c(dimnames(mat_list[[1]]), list(all_type)))

+	if(is.null(dimnames(mat_list[[1]]))) {

+		dimnames = c(list(NULL), list(NULL), list(all_type))

+	} else {

+		dimnames = c(dimnames(mat_list[[1]]), list(all_type))

+	}

+	arr = array(FALSE, dim = c(dim(mat_list[[1]]), length(all_type)), dimnames = dimnames)

 	for(i in seq_along(all_type)) {

 		arr[, , i] = mat_list[[i]]

 	}

@@ -392,6 +392,28 @@ oncoPrint = function(mat,

 	} else {

 		rn_ha = NULL

 	}

+

+	

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

+		if(inherits(top_annotation, "AnnotationFunction")) {

+	        stop_wrap("The annotation function `anno_*()` should be put inside `HeatmapAnnotation()`.")

+	    }

+	}

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

+	    if(inherits(bottom_annotation, "AnnotationFunction")) {

+	        stop_wrap("The annotation function `anno_*()` should be put inside `HeatmapAnnotation()`.")

+	    }

+	}

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

+		if(inherits(left_annotation, "AnnotationFunction")) {

+	        stop_wrap("The annotation function `anno_*()` should be put inside `rowAnnotation()`.")

+	    }

+	}

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

+	    if(inherits(right_annotation, "AnnotationFunction")) {

+	        stop_wrap("The annotation function `anno_*()` should be put inside `rowAnnotation()`.")

+	    }

+	}

 	if(is.null(left_annotation)) {

 		if(pct_side == "left") {

@@ -715,6 +715,8 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		} else {

 			v = apply(arr, c(2, 3), sum)

 		}

+		v = v[, !is.na(col), drop = FALSE]

+		col = col[!is.na(col)]

 		fun = anno_barplot(v, gp = gpar(fill = col, col = NA), which = "column", ylim = ylim,

 			baseline = 0, height = anno_size$height, border = border, bar_width = bar_width,

 			axis = axis, axis_param = axis_param)@fun

@@ -740,6 +742,8 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		} else {

 			v = apply(arr, c(1, 3), sum)

 		}

+		v = v[, !is.na(col), drop = FALSE]

+		col = col[!is.na(col)]

 		fun = anno_barplot(v, gp = gpar(fill = col, col = NA), which = "row", ylim = ylim,

 			baseline = 0, width = anno_size$width, border = border, bar_width = bar_width,

 			axis = axis, axis_param = axis_param)@fun

@@ -87,7 +87,7 @@ oncoPrint = function(mat,

 	remove_empty_columns = FALSE,

 	remove_empty_rows = FALSE,

 	show_column_names = FALSE,

-	heatmap_legend_param = list(title = "Alterations"),

+	heatmap_legend_param = NULL,

 	...) {

 	dev.null()

@@ -169,7 +169,7 @@ oncoPrint = function(mat,

 		stop_wrap("Incorrect type of 'mat'")

 	}

-	message_wrap(paste0("All mutation types: ", paste(all_type, collapse = ", ")))

+	message_wrap(paste0("All mutation types: ", paste(all_type, collapse = ", "), "."))

 	# type as the third dimension

 	arr = array(FALSE, dim = c(dim(mat_list[[1]]), length(all_type)), dimnames = c(dimnames(mat_list[[1]]), list(all_type)))

@@ -347,7 +347,7 @@ oncoPrint = function(mat,

 	# validate col

 	sdf = setdiff(all_type, names(col))

 	if(length(sdf) > 0) {

-		message_wrap(paste0("Colors are not defined for: ", paste(sdf, collapse = ", ")))

+		message_wrap(paste0("Colors are not defined for: ", paste(sdf, collapse = ", "), ". They won't be shown in the barplots."))

 	}

 	# for each gene, percent of samples that have alterations

@@ -468,6 +468,69 @@ oncoPrint = function(mat,

 		}

 	}

+	if(is.list(alter_fun)) {

+		if(is.null(alter_fun$background)) {

+			background_fun = function(x, y, w, h) NULL

+		} else {

+			background_fun = alter_fun$background

+		}

+

+		alter_fun2 = alter_fun[names(alter_fun) != "background"]

+		alter_fun3 = alter_fun2

+		for(i in seq_along(alter_fun2)) {

+			alter_fun3[[i]] = local({

+				i = i

+				function(x, y, w, h) {

+					background_fun(x, y, w, h)

+					alter_fun2[[i]](x, y, w, h)

+				}

+			})

+		}

+	} else {

+		all_type_binary = structure(rep(FALSE, length(all_type)), names = all_type)

+		background_fun = function(x, y, w, h) {

+			alter_fun(x, y, w, h, all_type_binary)

+		}

+		alter_fun3 = list()

+		for(nm in all_type) {

+			alter_fun3[[nm]] = local({

+				all_type_binary2 = all_type_binary

+				all_type_binary2[nm] = TRUE

+				function(x, y, w, h) {

+					alter_fun(x, y, w, h, all_type_binary2)

+				}

+			})

+		}

+	}

+

+	if(is.null(heatmap_legend_param)) {

+		heatmap_legend_param = list(

+			title = "Alterations",

+			at = names(alter_fun3),

+			graphics = alter_fun3

+		)

+		col2 = structure(rep(NA, length(alter_fun3)), names = names(alter_fun3))

+		col2[names(col)] = col

+		col = col2

+	} else {

+		if(! "graphics" %in% names(heatmap_legend_param)) {

+			if(is.null(heatmap_legend_param$at)) heatmap_legend_param$at = names(alter_fun3)

+			if(is.null(heatmap_legend_param$labels)) heatmap_legend_param$labels = heatmap_legend_param$at

+

+			# adjust order of alter_fun3 with at

+			if(!is.null(heatmap_legend_param$at)) {

+				if(length(setdiff(heatmap_legend_param$at, names(alter_fun3))) == 0) {

+					alter_fun3 = alter_fun3[heatmap_legend_param$at]

+				}

+			}

+

+			heatmap_legend_param$graphics = alter_fun3

+			col2 = structure(rep(NA, length(alter_fun3)), names = names(alter_fun3))

+			col2[names(col)] = col

+			col = col2

+		}

+	}

+

 	ht = Heatmap(pheudo, col = col, 

 		rect_gp = gpar(type = "none"), 

 		cluster_rows = cluster_rows, cluster_columns = cluster_columns, 

@@ -722,6 +785,12 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 guess_alter_fun_is_vectorized = function(alter_fun) {

 	n = 50

 	if(is.list(alter_fun)) {

+

+		# check whether grid.polygon is called

+		if(any(sapply(alter_fun, function(f) any(grepl("grid\\.polygon\\(", as.character(body(f))))))) {

+			return(FALSE)

+		}

+

 		x = unit(1:n/n, "npc")

 		y = unit(1:n/n, "npc")

 		w = unit(1:n, "mm")

@@ -736,6 +805,7 @@ guess_alter_fun_is_vectorized = function(alter_fun) {

 		if(inherits(oe, "try-error")) {

 			return(FALSE)

 		} else {

+			message_wrap("`alter_fun` is assumed vectorizable. If it does not generate correct plot, please set `alter_fun_is_vectorized = FALSE` in `oncoPrint()`.")

 			return(TRUE)

 		}

 	} else {

@@ -722,8 +722,8 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 guess_alter_fun_is_vectorized = function(alter_fun) {

 	n = 50

 	if(is.list(alter_fun)) {

-		x = 1:n

-		y = 1:n

+		x = unit(1:n/n, "npc")

+		y = unit(1:n/n, "npc")

 		w = unit(1:n, "mm")

 		h = unit(1:n, "mm")

 		dev.null()

@@ -754,7 +754,8 @@ guess_alter_fun_is_vectorized = function(alter_fun) {

 #

 default_get_type = function(x) {

 	x = strsplit(x, "\\s*[;:,|]\\s*")[[1]]

-	x[!x %in% c("na", "NA")]

+	# x[!x %in% c("na", "NA")]

+	x

 }

 # == title

@@ -606,6 +606,7 @@ unify_mat_list = function(mat_list, default = 0) {

 # -which Is it a row annotation or a column annotation?

 # -bar_width Width of the bars.

 # -ylim Data range.

+# -show_fraction Whether to show the numbers or the fractions?

 # -axis Whether draw axis?

 # -axis_param Parameters for controlling axis.

 # -width Width of the annotation.

@@ -619,7 +620,7 @@ unify_mat_list = function(mat_list, default = 0) {

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

 #

 anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

-	bar_width = 0.6, ylim = NULL, axis = TRUE, 

+	bar_width = 0.6, ylim = NULL, show_fraction = FALSE, axis = TRUE,

 	axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),

 	width = NULL, height = NULL, border = FALSE) {

@@ -646,8 +647,12 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		arr = arr[, , all_type, drop = FALSE]

 		col = col[all_type]

-		count = apply(arr, c(2, 3), sum)

-		fun = anno_barplot(count, gp = gpar(fill = col, col = NA), which = "column", ylim = ylim,

+		if(show_fraction) {

+			v = apply(arr, c(2, 3), sum)/dim(arr)[1]

+		} else {

+			v = apply(arr, c(2, 3), sum)

+		}

+		fun = anno_barplot(v, gp = gpar(fill = col, col = NA), which = "column", ylim = ylim,

 			baseline = 0, height = anno_size$height, border = border, bar_width = bar_width,

 			axis = axis, axis_param = axis_param)@fun

 		fun(index, k, n)

@@ -667,8 +672,12 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		arr = arr[, , all_type, drop = FALSE]

 		col = col[all_type]

-		count = apply(arr, c(1, 3), sum)

-		fun = anno_barplot(count, gp = gpar(fill = col, col = NA), which = "row", ylim = ylim,

+		if(show_fraction) {

+			v = apply(arr, c(1, 3), sum)/dim(arr)[2]

+		} else {

+			v = apply(arr, c(1, 3), sum)

+		}

+		fun = anno_barplot(v, gp = gpar(fill = col, col = NA), which = "row", ylim = ylim,

 			baseline = 0, width = anno_size$width, border = border, bar_width = bar_width,

 			axis = axis, axis_param = axis_param)@fun

 		fun(index, k, n)

@@ -686,7 +695,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		which = which,

 		width = anno_size$width,

 		height = anno_size$height,

-		var_import = list(border, type, bar_width, axis, axis_param, anno_size, ylim)

+		var_import = list(border, type, bar_width, axis, axis_param, anno_size, ylim, show_fraction)

 	)

 	anno@subsetable = TRUE

@@ -499,7 +499,7 @@ oncoPrint = function(mat,

 # -width Relative width of the rectangle.

 # -height Relative height of the rectangle.

 # -horiz_margin Horizontal margin. E.g. if you want 1mm margin on top and 1mm margin

-#        at bottom of the rectangle, set this value to ``unit(1, 'mm')`.

+#        at bottom of the rectangle, set this value to ``unit(1, 'mm')``.

 # -vertical_margin Vertical margin.

 # -fill Filled color.

 # -col Border color.

@@ -527,7 +527,7 @@ oncoPrint = function(mat,

 #

 alter_graphic = function(graphic = c("rect", "point"),

 	width = 1, height = 1, 

-	vertical_margin = unit(0, "mm"), horiz_margin = unit(0, "mm"),

+	horiz_margin = unit(1, "pt"), vertical_margin = unit(1, "pt"),

 	fill = "red", col = NA, pch = 16, ...) {

 	graphic = match.arg(graphic)[1]

@@ -539,13 +539,23 @@ alter_graphic = function(graphic = c("rect", "point"),

 		if(!is.numeric(height)) {

 			stop_wrap("`height` should be nummeric.")

 		}

+		if(width != 1) {

+			if(missing(horiz_margin)) {

+				horiz_margin = unit(0, "pt")

+			}

+		}

+		if(height != 1) {

+			if(missing(vertical_margin)) {

+				vertical_margin = unit(0, "pt")

+			}

+		}

 		fun = function(x, y, w, h) {

 			w = w*width

 			h = h*height

-			grid.rect(x, y, w*width - horiz_margin*2, h*height - vertical_margin*2,

+			grid.rect(x, y, w - horiz_margin*2, h - vertical_margin*2,

 				gp = gpar(fill = fill, col = col, ...))

 		}

-	} else if(graphc == "point") {

+	} else if(graphic == "point") {

 		fun = function(x, y, w, h) {

 			grid.points(x, y, pch = pch, gp = gpar(fill = fill, col = col, ...))

 		}

@@ -11,6 +11,7 @@

 # -get_type If different alterations are encoded in the matrix as complex strings, this self-defined function

 #           determines how to extract them. It only works when ``mat`` is a matrix. The default value is `default_get_type`.

 # -alter_fun A single function or a list of functions which defines how to add graphics for different alterations.

+#      You can use `alter_graphic` to automatically generate for rectangles and points.

 # -alter_fun_is_vectorized Whether ``alter_fun`` is implemented vectorized. Internally the function will guess.

 # -col A vector of color for which names correspond to alteration types.

 # -top_annotation Annotation put on top of the oncoPrint. By default it is barplot which shows the number of genes with a certain alteration in each sample.

@@ -490,6 +491,68 @@ oncoPrint = function(mat,

 	return(ht)

 }

+# == title

+# Automatically generate alter_fun

+#

+# == param

+# -graphic Graphic to draw.

+# -width Relative width of the rectangle.

+# -height Relative height of the rectangle.

+# -horiz_margin Horizontal margin. E.g. if you want 1mm margin on top and 1mm margin

+#        at bottom of the rectangle, set this value to ``unit(1, 'mm')`.

+# -vertical_margin Vertical margin.

+# -fill Filled color.

+# -col Border color.

+# -pch Pch for points

+# -... Pass to `grid::gpar`

+#

+# == details

+# This function aims to simplify the definition of functions in ``alter_fun``. Now it only

+# supports rectangles and points.

+#

+# == example

+# 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 = ",", stringsAsFactors = FALSE)

+# mat = as.matrix(mat)

+# col = c(snv = "red", indel = "blue")

+#

+# oncoPrint(mat, 

+# 	alter_fun = list(

+# 		snv = alter_graphic("rect", width = 0.9, height = 0.9, fill = col["snv"]),

+# 		indel = alter_graphic("rect", width = 0.9, height = 0.9, fill = col["indel"])

+# 	), col = col)

+#

+alter_graphic = function(graphic = c("rect", "point"),

+	width = 1, height = 1, 

+	vertical_margin = unit(0, "mm"), horiz_margin = unit(0, "mm"),

+	fill = "red", col = NA, pch = 16, ...) {

+

+	graphic = match.arg(graphic)[1]

+

+	if(graphic == "rect") {

+		if(!is.numeric(width)) {

+			stop_wrap("`width` should be nummeric.")

+		}

+		if(!is.numeric(height)) {

+			stop_wrap("`height` should be nummeric.")

+		}

+		fun = function(x, y, w, h) {

+			w = w*width

+			h = h*height

+			grid.rect(x, y, w*width - horiz_margin*2, h*height - vertical_margin*2,

+				gp = gpar(fill = fill, col = col, ...))

+		}

+	} else if(graphc == "point") {

+		fun = function(x, y, w, h) {

+			grid.points(x, y, pch = pch, gp = gpar(fill = fill, col = col, ...))

+		}

+	}

+	return(fun)

+}

+

 ONCOPRINT_ENV = new.env()

 ONCOPRINT_ENV$fun_env = NULL

@@ -89,6 +89,9 @@ oncoPrint = function(mat,

 	heatmap_legend_param = list(title = "Alterations"),

 	...) {

+	dev.null()

+    on.exit(dev.off2())

+

 	arg_list = as.list(match.call())[-1]

 	arg_names = names(arg_list)

@@ -128,6 +128,11 @@ oncoPrint = function(mat,

 		all_type = all_type[!is.na(all_type)]

 		all_type = all_type[grepl("\\S", all_type)]

+		## check whether there are NA values in the matrix

+		if(any(is.na(mat))) {

+			message_wrap("Found NA values in the matrix and treat as no alteration. If `NA` means no alteration, you can explicitly set it to empty strings like ''. If `NA` is an alteration type, you should format it to a string like `'NA'` and define a graphic for it.")

+		}

+

 		mat_list = lapply(all_type, function(type) {

 			m = sapply(mat, function(x) type %in% get_type2(x))

 			dim(m) = dim(mat)

@@ -30,6 +30,8 @@

 # -column_names_gp Pass to `Heatmap`.

 # -column_split Pass to `Heatmap`.

 # -row_order Order of rows. By default rows are sorted by the number of occurence of the alterations.

+# -cluster_rows If it is set, it must be a dendrogram/hclust object.

+# -cluster_columns If it is set, it must be a dendrogram/hclust object.

 # -column_order Order of columns. By default the columns are sorted to show the mutual exclusivity of alterations.

 # -remove_empty_columns If there is no alteration in some samples, whether remove them on the oncoPrint?

 # -remove_empty_rows If there is no alteration in some samples, whether remove them on the oncoPrint?

@@ -78,6 +80,8 @@ oncoPrint = function(mat,

 	row_order = NULL,

 	column_order = NULL,

+	cluster_rows = FALSE,

+	cluster_columns = FALSE,

 	remove_empty_columns = FALSE,

 	remove_empty_rows = FALSE,

@@ -439,14 +443,25 @@ oncoPrint = function(mat,

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

 	if(length(arg_list)) {

-		if(any(arg_names %in% c("rect_gp", "cluster_rows", "cluster_columns", "cell_fun"))) {

-			stop_wrap("'rect_gp', 'cluster_rows', 'cluster_columns', 'cell_fun' are not allowed to use in `oncoPrint()`.")

+		if(any(arg_names %in% c("rect_gp", "cell_fun"))) {

+			stop_wrap("'rect_gp', 'cell_fun' are not allowed to use in `oncoPrint()`.")

+		}

+

+		if("cluster_rows" %in% arg_names) {

+			if(!inherits(cluster_rows, c("dendrogram", "hclust"))) {

+				stop_wrap("`cluster_rows` can only be a dendrogram/hclust object if it is set.")

+			}

+		}

+		if("cluster_columns" %in% arg_names) {

+			if(!inherits(cluster_columns, c("dendrogram", "hclust"))) {

+				stop_wrap("`cluster_columns` can only be a dendrogram/hclust object if it is set.")

+			}

 		}

 	}

 	ht = Heatmap(pheudo, col = col, 

 		rect_gp = gpar(type = "none"), 

-		cluster_rows = FALSE, cluster_columns = FALSE, 

+		cluster_rows = cluster_rows, cluster_columns = cluster_columns, 

 		row_order = row_order, column_order = column_order,

 		row_split = row_split, 

 		column_labels = column_labels,

@@ -509,9 +509,10 @@ unify_mat_list = function(mat_list, default = 0) {

 # -type A vector of the alteration types in the data. It can be a subset of all alteration types if you don't want to show them all.

 # -which Is it a row annotation or a column annotation?

 # -bar_width Width of the bars.

+# -ylim Data range.

 # -axis Whether draw axis?

 # -axis_param Parameters for controlling axis.

-# -width Wisth of the annotation.

+# -width Width of the annotation.

 # -height Height of the annotation.

 # -border Whether draw the border?

 #

@@ -522,7 +523,7 @@ unify_mat_list = function(mat_list, default = 0) {

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

 #

 anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

-	bar_width = 0.6, axis = TRUE, 

+	bar_width = 0.6, ylim = NULL, axis = TRUE, 

 	axis_param = if(which == "column") default_axis_param("column") else list(side = "top", labels_rot = 0),

 	width = NULL, height = NULL, border = FALSE) {

@@ -550,7 +551,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		col = col[all_type]

 		count = apply(arr, c(2, 3), sum)

-		fun = anno_barplot(count, gp = gpar(fill = col, col = NA), which = "column",

+		fun = anno_barplot(count, gp = gpar(fill = col, col = NA), which = "column", ylim = ylim,

 			baseline = 0, height = anno_size$height, border = border, bar_width = bar_width,

 			axis = axis, axis_param = axis_param)@fun

 		fun(index, k, n)

@@ -571,7 +572,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		col = col[all_type]

 		count = apply(arr, c(1, 3), sum)

-		fun = anno_barplot(count, gp = gpar(fill = col, col = NA), which = "row",

+		fun = anno_barplot(count, gp = gpar(fill = col, col = NA), which = "row", ylim = ylim,

 			baseline = 0, width = anno_size$width, border = border, bar_width = bar_width,

 			axis = axis, axis_param = axis_param)@fun

 		fun(index, k, n)

@@ -589,7 +590,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		which = which,

 		width = anno_size$width,

 		height = anno_size$height,

-		var_import = list(border, type, bar_width, axis, axis_param, anno_size)

+		var_import = list(border, type, bar_width, axis, axis_param, anno_size, ylim)

 	)

 	anno@subsetable = TRUE

@@ -94,8 +94,8 @@ oncoPrint = function(mat,

 	if("axis_gp" %in% arg_names) {

 		stop_wrap("`axis_gp` is removed from the arguments. Please set `axis_param(gp = ...)` in `anno_oncoprint_barplot()` when you define the `top_annotation` or `right_annotation`.")

 	}

-	if("show_row_names" %in% arg_names) {

-		stop_wrap("`show_row_names` is removed from the arguments. Please directly remove `anno_oncoprint_barplot()` in `right_annotation` to remove barplots on the left of the oncoPrint.")

+	if("show_row_barplot" %in% arg_names) {

+		stop_wrap("`show_row_barplot` is removed from the arguments. Please directly remove `anno_oncoprint_barplot()` in `right_annotation` to remove barplots on the right of the oncoPrint.")

 	}

 	if("row_barplot_width" %in% arg_names) {

 		stop_wrap("`row_barplot_width` is removed from the arguments. Please directly set `width` in `anno_oncoprint_barplot()` in `right_annotation`.")

@@ -110,6 +110,10 @@ oncoPrint = function(mat,

 		stop_wrap("`barplot_ignore` is removed from the arguments. The subset of alterations now can be controlled in `anno_oncoprint_barplot()`.")

 	}

+	if(inherits(col, "function")) {

+		stop_wrap("`col` should be specified as a vector.")

+	}

+

 	# convert mat to mat_list

 	if(inherits(mat, "data.frame")) {

 		mat = as.matrix(mat)

@@ -152,8 +156,7 @@ oncoPrint = function(mat,

 		stop_wrap("Incorrect type of 'mat'")

 	}

-	cat("All mutation types:", paste(all_type, collapse = ", "), "\n")

-

+	message_wrap(paste0("All mutation types: ", paste(all_type, collapse = ", ")))

 	# type as the third dimension

 	arr = array(FALSE, dim = c(dim(mat_list[[1]]), length(all_type)), dimnames = c(dimnames(mat_list[[1]]), list(all_type)))

@@ -573,7 +576,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 			axis = axis, axis_param = axis_param)@fun

 		fun(index, k, n)

 	}

-	

+

 	if(which == "row") {

 		fun = row_fun

 	} else if(which == "column") {

@@ -592,8 +595,19 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 	anno@subsetable = TRUE

 	anno@show_name = FALSE

+	if(exists("arr", envir = parent.frame(1))) {

+		arr = get("arr", envir = parent.frame(1))

+		if(which == "row") {

+			data_scale = c(0, max(apply(arr, 1, sum)))

+		} else {

+			data_scale = c(0, max(apply(arr, 2, sum)))

+		}

+	} else {

+		data_scale = c(0, 100)

+	}

+

 	axis_param = validate_axis_param(axis_param, which)

-	axis_grob = if(axis) construct_axis_grob(axis_param, which, c(0, 100)) else NULL

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

 	anno@extended = update_anno_extend(anno, axis_grob, axis_param)

 	return(anno) 

@@ -445,9 +445,13 @@ oncoPrint = function(mat,

 		rect_gp = gpar(type = "none"), 

 		cluster_rows = FALSE, cluster_columns = FALSE, 

 		row_order = row_order, column_order = column_order,

-		row_split = row_split, column_split = column_split,

+		row_split = row_split, 

+		column_labels = column_labels,

+		column_names_gp = column_names_gp,

+		column_split = column_split,

 		cell_fun = cell_fun, layer_fun = layer_fun,

 		top_annotation = top_annotation,

+		bottom_annotation = bottom_annotation,

 		left_annotation = left_annotation,

 		right_annotation = right_annotation,

 		show_row_names = FALSE,

@@ -54,7 +54,7 @@ oncoPrint = function(mat,

 	get_type = default_get_type,

 	alter_fun, 

 	alter_fun_is_vectorized = NULL,

-	col, 

+	col = NULL, 

 	top_annotation = HeatmapAnnotation(cbar = anno_oncoprint_barplot()),

 	right_annotation = rowAnnotation(rbar = anno_oncoprint_barplot()),

@@ -331,7 +331,7 @@ oncoPrint = function(mat,

 	# validate col

 	sdf = setdiff(all_type, names(col))

 	if(length(sdf) > 0) {

-		stop_wrap(paste0("You should define colors for:", paste(sdf, collapse = ", ")))

+		message_wrap(paste0("Colors are not defined for: ", paste(sdf, collapse = ", ")))

 	}

 	# for each gene, percent of samples that have alterations

@@ -339,6 +339,10 @@ oncoPrint = function(mat,

 	pct = paste0(round(pct_num * 100, digits = pct_digits), "%")

 	### now the annotations

+	if(length(col) == 0) {

+		if(missing(top_annotation)) top_annotation = NULL

+		if(missing(right_annotation)) right_annotation = NULL

+	}

 	top_annotation = top_annotation

 	right_annotation = right_annotation

@@ -421,7 +425,13 @@ oncoPrint = function(mat,

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

 	# the main matrix

-	pheudo = c(all_type, rep(NA, nrow(arr)*ncol(arr) - length(all_type)))

+	if(length(col)) {

+		pheudo = c(names(col), rep(NA, nrow(arr)*ncol(arr) - length(col)))

+	} else {

+		pheudo = c("mutation", rep(NA, nrow(arr)*ncol(arr) - 1))

+		col = c("mutation" = "black")

+	}

+

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

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

@@ -523,7 +533,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		all_type = pf$all_type

 		col = pf$col

-		if(is.null(type)) type = all_type

+		if(is.null(type)) type = names(col)

 		all_type = intersect(all_type, type)

 		if(length(all_type) == 0) {

@@ -544,7 +554,7 @@ anno_oncoprint_barplot = function(type = NULL, which = c("column", "row"),

 		all_type = pf$all_type

 		col = pf$col

-		if(is.null(type)) type = all_type

+		if(is.null(type)) type = names(col)

 		all_type = intersect(all_type, type)

 		if(length(all_type) == 0) {

@@ -615,7 +615,133 @@ guess_alter_fun_is_vectorized = function(alter_fun) {

 # == param

 # -x A strings which encode multiple altertations.

 #

+# == details

+# It recognizes following separators: ``;:,|``.