@@ -6,6 +6,7 @@ CHANGES in VERSION 1.9.3

 * when `gap` is set for the main heatmap, other heatmps also adjust their `gap` values to it

 * fixed a bug that when rownames/colnames are not complete, dendrograms are corrupted

 * `alter_fun` now supports adding graphics grid by grid

+* add `show_pct` option in `oncoPrint()`

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

@@ -17,6 +17,7 @@

 # -column_order order of samples. By default the order is calculated by the 'memo sort' method which can visualize

 #                                 the mutual exclusivity across genes. Set it to ``NULL`` if you don't want to set the order

 # -show_column_names whether show column names

+# -show_pct whether show percent values on the left of the oncoprint

 # -pct_gp graphic paramters for percent row annotation

 # -pct_digits digits for percent values

 # -axis_gp graphic paramters for axes

@@ -50,7 +51,7 @@ oncoPrint = function(mat, get_type = function(x) x,

 	row_order = oncoprint_row_order(),

 	column_order = oncoprint_column_order(),

 	show_column_names = FALSE,

-	pct_gp = gpar(), pct_digits = 0,

+	show_pct = TRUE, pct_gp = gpar(), pct_digits = 0,

 	axis_gp = gpar(fontsize = 8), 

 	show_row_barplot = TRUE, 

 	row_barplot_width = unit(2, "cm"),

@@ -72,6 +73,9 @@ oncoPrint = function(mat, get_type = function(x) x,

 	}

 	# convert mat to mat_list

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

+		mat = as.matrix(mat)

+	}

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

 		all_type = unique(unlist(lapply(mat, get_type)))

@@ -84,6 +88,7 @@ oncoPrint = function(mat, get_type = function(x) x,

 			dimnames(m) = dimnames(mat)

 			m

 		})

+		names(mat_list) = all_type

 	} else if(inherits(mat, "list")) {

 		mat_list = mat

@@ -195,7 +200,7 @@ oncoPrint = function(mat, get_type = function(x) x,

 	# for each gene, percent of samples that have alterations

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

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

-	ha_pct = rowAnnotation(pct = row_anno_text(pct, just = "right", offset = unit(1, "npc"), gp = pct_gp), width = grobWidth(textGrob("100%", gp = pct_gp)))

+	ha_pct = rowAnnotation(pct = row_anno_text(pct, just = "right", offset = unit(1, "npc"), gp = pct_gp), width = max_text_width(pct, gp = pct_gp))

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

 	# row annotation which is a barplot

@@ -272,10 +277,14 @@ oncoPrint = function(mat, get_type = function(x) x,

 		top_annotation = top_annotation,

 		heatmap_legend_param = heatmap_legend_param, ...)

-	if(show_row_barplot) {

-		ht_list = ha_pct + ht + ha_row_bar

-	} else {

+	if(show_pct) {

 		ht_list = ha_pct + ht

+	} else {

+		ht_list = ht

+	}

+

+	if(show_row_barplot) {

+		ht_list = ht_list + ha_row_bar

 	}

 	return(ht_list)

@@ -12,7 +12,7 @@ oncoPrint(mat, get_type = function(x) x,

     row_order = oncoprint_row_order(),

     column_order = oncoprint_column_order(),

     show_column_names = FALSE,

-    pct_gp = gpar(), pct_digits = 0,

+    show_pct = TRUE, pct_gp = gpar(), pct_digits = 0,

     axis_gp = gpar(fontsize = 8),

     show_row_barplot = TRUE,

     row_barplot_width = unit(2, "cm"),

@@ -33,6 +33,7 @@ oncoPrint(mat, get_type = function(x) x,

   \item{row_order}{order of genes. By default it is sorted by frequency of alterations decreasingly. Set it to \code{NULL} if you don't want to set the order}

   \item{column_order}{order of samples. By default the order is calculated by the 'memo sort' method which can visualize the mutual exclusivity across genes. Set it to \code{NULL} if you don't want to set the order}

   \item{show_column_names}{whether show column names}

+  \item{show_pct}{whether show percent values on the left of the oncoprint}

   \item{pct_gp}{graphic paramters for percent row annotation}

   \item{pct_digits}{digits for percent values}

   \item{axis_gp}{graphic paramters for axes}

@@ -140,7 +140,9 @@ oncoPrint(mat_list,

     alter_fun = function(x, y, w, h, v) {

 		n = sum(v)

 		h = h*0.9

-		if(n) grid.rect(x, y - h*0.5 + 1:n/n*h, w*0.9, 1/n*h, gp = gpar(fill = col[which(v)], col = NA), just = "top")

+		# use `names(which(v))` to correctly map between `v` and `col`

+		if(n) grid.rect(x, y - h*0.5 + 1:n/n*h, w*0.9, 1/n*h, 

+			gp = gpar(fill = col[names(which(v))], col = NA), just = "top")

     }, col = col)

 ```