@@ -6,6 +6,8 @@ CHANGES in VERSIONS 1.17.1

 * `grid.dendrogram()`: fix a bug that the dendrogram is wrong when row/column

   names have duplicated names.

 * `anno_boxplot()`: axis rescaled when outline = FALSE

+* `oncoPrint()`: rows are first ordered by total number of mutations and then

+  ordered by number of samples that have mutations

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

@@ -207,7 +207,7 @@ oncoPrint = function(mat, get_type = function(x) x,

 	}

 	oncoprint_row_order = function() {

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

+		order(rowSums(count_matrix), pct_num, decreasing = TRUE)

 	}

 	oncoprint_column_order = function() {

@@ -246,8 +246,8 @@ 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), "%")

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

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

 	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))

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