@@ -2,6 +2,8 @@ CHANGES in VERSION 1.4.4

 * NULL can be added to the heatmap list

 * give message if users mess up with row and column annotations

+* `oncoPrint`: columns are sorted by `memo sort` method to enhance

+  the mutual exclusivity.

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

@@ -25,10 +25,10 @@ setGeneric('prepare', function(object, ...) standardGeneric('prepare'))

 setGeneric('draw_annotation', function(object, ...) standardGeneric('draw_annotation'))

-setGeneric('get_color_mapping_param_list', function(object, ...) standardGeneric('get_color_mapping_param_list'))

-

 setGeneric('draw_dimnames', function(object, ...) standardGeneric('draw_dimnames'))

+setGeneric('get_color_mapping_param_list', function(object, ...) standardGeneric('get_color_mapping_param_list'))

+

 setGeneric('color_mapping_legend', function(object, ...) standardGeneric('color_mapping_legend'))

 setGeneric('draw', function(object, ...) standardGeneric('draw'))

@@ -10,6 +10,10 @@

 # -alter_fun_list a list of functions which define how to add graphics for different alterations.

 #                 The names of the list should cover all alteration types.

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

+# -row_order order of genes. By default it is sorted by frequency of alterations decreasingly.

+#                            Set it to ``NULL`` if you don't want to set the order

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

+#                                 the mutual exclusivity across genes.

 # -show_column_names whether show column names

 # -pct_gp graphic paramters for percent row annotation

 # -axis_gp graphic paramters for axes

@@ -23,6 +27,9 @@

 # == details

 # The function returns a normal heatmap list and you can add more heatmaps/row annotations to it.

 #

+# The 'memo sort' method is from https://gist.github.com/armish/564a65ab874a770e2c26 . Thanks to

+# B. Arman Aksoy for contributing the code.

+#

 # For more explanation, please go to the vignette.

 #

 # == value

@@ -33,6 +40,8 @@

 #

 oncoPrint = function(mat, get_type = function(x) x,

 	alter_fun_list, col, 

+	row_order = oncoprint_row_order(),

+	column_order = oncoprint_column_order(),

 	show_column_names = FALSE, 

 	pct_gp = gpar(), 

 	axis_gp = gpar(fontsize = 8), 

@@ -83,9 +92,39 @@ oncoPrint = function(mat, get_type = function(x) x,

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

 	}

+	oncoprint_row_order = function() {

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

+	}

+

+	oncoprint_column_order = function() {

+		scoreCol = function(x) {

+			score = 0

+			for(i in 1:length(x)) {

+				if(x[i]) {

+					score = score + 2^(length(x)-i)

+				}

+			}

+			return(score)

+		}

+		scores = apply(count_matrix[row_order, ], 2, scoreCol)

+		order(scores, decreasing=TRUE)

+	}

+

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

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

+	row_order = row_order

+	if(is.character(column_order)) {

+		column_order = structure(seq_len(dim(arr)[2]), names = dimnames(arr)[[2]])[column_order]

+	}

+

 	if(remove_empty_columns) {

 		l = rowSums(apply(arr, c(2, 3), sum)) > 0

 		arr = arr[, l, , drop = FALSE]

+		count_matrix = count_matrix[, l, drop = FALSE]

+		column_order = column_order

+		if(length(column_order) > ncol(count_matrix)) {

+			column_order = order(column_order[l])

+		}

 	}

 	# validate alter_fun_list

@@ -170,9 +209,10 @@ oncoPrint = function(mat, get_type = function(x) x,

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

 	dim(pheudo) = dim(arr[, , 1])

 	dimnames(pheudo) = dimnames(arr[, , 1])

+	

 	if(show_column_barplot) {

 		ht = Heatmap(pheudo, col = col, rect_gp = gpar(type = "none"), 

-			cluster_rows = FALSE, cluster_columns = FALSE,

+			cluster_rows = FALSE, cluster_columns = FALSE, row_order = row_order, column_order = column_order,

 			cell_fun = function(j, i, x, y, width, height, fill) {

 				z = arr[i, j, ]

 				add_oncoprint("background", x, y, width, height)

@@ -183,7 +223,7 @@ oncoPrint = function(mat, get_type = function(x) x,

 			top_annotation = ha_column_bar, ...)

 	} else {

 		ht = Heatmap(pheudo, rect_gp = gpar(type = "none"), 

-			cluster_rows = FALSE, cluster_columns = FALSE,

+			cluster_rows = FALSE, cluster_columns = FALSE, row_order = row_order, column_order = column_order,

 			cell_fun = function(j, i, x, y, width, height, fill) {

 				z = arr[i, j, ]

 				add_oncoprint("background", x, y, width, height)

@@ -9,6 +9,8 @@ Make oncoPrint

 \usage{

 oncoPrint(mat, get_type = function(x) x,

     alter_fun_list, col,

+    row_order = oncoprint_row_order(),

+    column_order = oncoprint_column_order(),

     show_column_names = FALSE,

     pct_gp = gpar(),

     axis_gp = gpar(fontsize = 8),

@@ -25,6 +27,8 @@ oncoPrint(mat, get_type = function(x) x,

   \item{get_type}{If different alterations are encoded in the matrix, this self-defined functiondetermines how to extract them. Only work when \code{mat} is a matrix.}

   \item{alter_fun_list}{a list of functions which define how to add graphics for different alterations.The names of the list should cover all alteration types.}

   \item{col}{a vector of color for which names correspond to alteration types.}

+  \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 visualizethe mutual exclusivity across genes.}

   \item{show_column_names}{whether show column names}

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

   \item{axis_gp}{graphic paramters for axes}

@@ -39,6 +43,9 @@ oncoPrint(mat, get_type = function(x) x,

 \details{

 The function returns a normal heatmap list and you can add more heatmaps/row annotations to it.

+The 'memo sort' method is from \url{https://gist.github.com/armish/564a65ab874a770e2c26} . Thanks to

+B. Arman Aksoy for contributing the code.

+

 For more explanation, please go to the vignette.

 }

 \value{

@@ -128,15 +128,7 @@ rownames(mat) = mat[, 1]

 mat = mat[, -1]

 mat=  mat[, -ncol(mat)]

 mat = t(as.matrix(mat))

-```

-

-We can adjust the order of the matrix. Here cbioPortal also provides sample orders:

-

-```{r}

-sample_order = scan(paste0(system.file("extdata", package = "ComplexHeatmap"), 

-    "/sample_order.txt"), what = "character")

-mat = mat[, sample_order]

-mat[1:4, 1:4]

+head(mat)

 ```

 There are three different alterations in `mat`: `HOMDEL`, `AMP` and `MUT`. We first 

@@ -175,6 +167,27 @@ oncoPrint(mat, get_type = function(x) strsplit(x, ";")[[1]],

 		labels = c("Amplification", "Deep deletion", "Mutation")))

 ```

+As you see, the genes and samples are sorted automatically. Rows are sorted based on the frequency

+of the alterations in all samples and columns are sorted to visualize the mutual exclusivity across genes

+based on the "memo sort" method which is

+kindly provided by [B. Arman Aksoy](https://gist.github.com/armish/564a65ab874a770e2c26). If you want

+to turn off the default sorting, set `row_order` or `column_order` to `NULL`.

+

+As the normal `Heatmap()` function, `row_order` or `column_order` can be assigned with a vector of 

+orders (either numeric or character). Following the order of samples are gathered from cBio as well.

+You can see the difference for the sample order between 'memo sort' and the method used by cBio.

+

+```{r, fig.width = 12, fig.height = 8}

+sample_order = scan(paste0(system.file("extdata", package = "ComplexHeatmap"), 

+    "/sample_order.txt"), what = "character")

+oncoPrint(mat, get_type = function(x) strsplit(x, ";")[[1]],

+	alter_fun_list = alter_fun_list, col = col, 

+	row_order = NULL, column_order = sample_order,

+	column_title = "OncoPrint for TCGA Lung Adenocarcinoma, genes in Ras Raf MEK JNK signalling",

+	heatmap_legend_param = list(title = "Alternations", at = c("AMP", "HOMDEL", "MUT"), 

+		labels = c("Amplification", "Deep deletion", "Mutation")))

+```

+

 By default, if one sample has no alteration, it will be removed from the heatmap, but you can set

 `remove_empty_columns` to `FALSE` to keep it: