@@ -1016,7 +1016,7 @@ anno_barplot = function(x, baseline = 0, which = c("column", "row"), border = TR

 		baseline = max(x)

 	} else {

 		if(is.numeric(baseline)) {

-			if(baseline == 0 && all(rowSums(x) == 1)) {

+			if(baseline == 0 && all(abs(rowSums(x) - 1) < 1e-6)) {

 				data_scale = c(0, 1)

 			} else if(baseline <= min(x)) {

 				data_scale = c(baseline, extend*(data_scale[2] - baseline) + data_scale[2])

@@ -2074,7 +2074,7 @@ anno_joyplot = function(x, which = c("column", "row"), gp = gpar(fill = "#000000

 # -n_slice Number of slices on y-axis.

 # -slice_size Height of the slice. If the value is not ``NULL``, ``n_slice`` will be recalculated. 

 # -negative_from_top Whether the areas for negative values start from the top or the bottom of the plotting region?

-# -normalize Whether normalize ``x`` to let data range of each observation in (0, 1)?

+# -normalize Whether normalize ``x`` by max(abs(x)).

 # -gap Gap size of neighbouring horizon chart.

 # -axis Whether to add axis?

 # -axis_param parameters for controlling axis. See `default_axis_param` for all possible settings and default parameters.

@@ -649,7 +649,7 @@ setMethod(f = "show",

 	cat("  items:", ifelse(length(len), len[1], "unknown"), "\n")

 	cat("  width:", as.character(object@width), "\n")

 	cat("  height:", as.character(object@height), "\n")

-    cat("  this object is", ifelse(object@subsetable, "\b", "not"), "subsetable\n")

+    cat("  this object is", ifelse(object@subsetable, "", "not"), "subsetable\n")

     dirt = c("bottom", "left", "top", "right")

     for(i in 1:4) {

         if(!identical(unit(0, "mm"), object@extended[i])) {

@@ -47,11 +47,10 @@ oncoPrint = function(mat,

 	alter_fun_is_vectorized = NULL,

 	col, 

-	top_annotation = HeatmapAnnotation(column_barplot = anno_oncoprint_barplot(),

-		show_annotation_name = FALSE),

+	top_annotation = HeatmapAnnotation(column_barplot = anno_oncoprint_barplot()),

 	right_annotation = rowAnnotation(row_barplot = anno_oncoprint_barplot(

-			axis_param = list(side = "top", labels_rot = 0)),

-		show_annotation_name = FALSE),

+			axis_param = list(side = "top", labels_rot = 0))),

+	bottom_annotation = NULL,

 	show_pct = TRUE, 

 	pct_gp = gpar(fontsize = 10), 

@@ -70,11 +69,13 @@ oncoPrint = function(mat,

 	heatmap_legend_param = list(title = "Alterations"),

 	...) {

-	.in_oncoprint = TRUE

-

 	arg_list = list(...)

 	arg_names = names(arg_list)

+	oe = environment(anno_oncoprint_barplot)

+	environment(anno_oncoprint_barplot) = environment()

+	on.exit(environment(anno_oncoprint_barplot) <- oe)

+

 	# convert mat to mat_list

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

 		mat = as.matrix(mat)

@@ -247,17 +248,16 @@ oncoPrint = function(mat,

 	col = col[intersect(names(col), all_type)]

-

 	count_matrix = apply(arr, c(1, 2), sum)

 	n_mut = rowSums(apply(arr, 1:2, any))

-	if(!"row_order" %in% arg_names) {

+	if(is.null(row_order)) {

 		row_order = oncoprint_row_order()

 	}

-	if(!"column_order" %in% arg_names) {

+	if(is.null(column_order)) {

 		column_order = oncoprint_column_order()

 	}

-	

+

 	if(is.null(row_order)) row_order = seq_len(nrow(count_matrix))

 	if(is.null(column_order)) column_order = seq_len(ncol(count_matrix))

 	if(is.character(column_order)) {

@@ -286,6 +286,12 @@ oncoPrint = function(mat,

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

 	### now the annotations

+	err = try(top_annotation <- eval(substitute(top_annotation)), silent = TRUE)

+	if(inherits(err, "try-error")) {

+		stop_wrap("find an error when executing top_annotation. ")

+	}

+	right_annotation = eval(substitute(right_annotation))

+

 	if("left_annotation" %in% arg_names) {

 		stop("'left_annotation' are not allowed to specify, you can add...")

 	}

@@ -297,7 +303,7 @@ oncoPrint = function(mat,

 	if(show_row_names) {

 		ha_row_names = rowAnnotation(rownames = anno_text(dimnames(arr)[[1]], gp = pct_gp, just = "left", location = unit(0, "npc")),

 			show_annotation_name = FALSE)

-		right_annotation = c(ha_row_names, right_annotation)

+		right_annotation = c(ha_row_names, right_annotation, gap = unit(2, "mm"))

 	}

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

@@ -388,18 +394,17 @@ anno_oncoprint_barplot = function(type = all_type, which = c("column", "row"),

 	}

 	anno_size = anno_width_and_height(which, width, height, unit(2, "cm"))

-

 	# get variables fron oncoPrint() function

-	pf = parent.frame()

-	if(!exists(".in_oncoprint", envir = pf, inherits = FALSE)) {

-		stop_wrap("`anno_oncoprint_barplot()` should only be used with `oncoPrint()`.")

-	}

-	arr = get("arr", envir = pf, inherits = FALSE)

-	all_type = get("all_type", envir = pf, inherits = FALSE)

-	col = get("col", envir = pf, inherits = FALSE)

+	pf = parent.env(environment())

+	arr = pf$arr

+	all_type = pf$all_type

+	col = pf$col

 	type = type

 	all_type = intersect(all_type, type)

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

+		stop_wrap("find no overlap, check your `type` argument.")

+	}

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

 	col = col[all_type]

@@ -417,6 +422,7 @@ anno_oncoprint_barplot = function(type = all_type, which = c("column", "row"),

 	return(fun)

 }

+

 guess_alter_fun_is_vectorized = function(alter_fun) {

 	n = 50

 	if(is.list(alter_fun)) {

new file mode 100644

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