@@ -159,8 +159,6 @@ export("decorate_row_title")

 export("decorate_title")

 export("default_axis_param")

 export("default_get_type")

-export("default_upset_right_annotation")

-export("default_upset_top_annotation")

 export("dend_heights")

 export("dend_xy")

 export("dendrogramGrob")

@@ -180,7 +178,9 @@ export("make_comb_mat")

 export("max_text_height")

 export("max_text_width")

 export("merge_dendrogram")

+export("normalize_comb_mat")

 export("oncoPrint")

+export("order.comb_mat")

 export("packLegend")

 export("pindex")

 export("rowAnnotation")

@@ -198,6 +198,8 @@ export("subset_gp")

 export("subset_matrix_by_row")

 export("subset_vector")

 export("unify_mat_list")

+export("upset_right_annotation")

+export("upset_top_annotation")

 exportClasses("AdditiveUnit")

 export("AdditiveUnit")

 exportClasses("AnnotationFunction")

@@ -58,7 +58,7 @@ HeatmapAnnotation = setClass("HeatmapAnnotation",

 # -show_annotation_name Whether show annotation names? For column annotation, annotation names are drawn either on the left

 #   or the right, and for row annotations, names are draw either on top or at the bottom. The value can be a vector.

 # -annotation_name_gp Graphic parameters for anntation names. Graphic paramters can be vectors.

-# -annotation_name_offset Offset to the annotations, `grid::unit` object. The value can be a vector.

+# -annotation_name_offset Offset to the annotation names, a `grid::unit` object. The value can be a vector.

 # -annotation_name_side Side of the annotation names.

 # -annotation_name_rot Rotation of the annotation names, it can only take values in ``c(00, 90, 180, 270)``. The value can be a vector.

 # -annotation_height Height of each annotation if annotations are column annotations.

@@ -110,6 +110,16 @@ make_comb_mat_from_list = function(lt, mode, value_fun = length, top_n_sets = In

     	stop_wrap("The list must have names.")

     }

+    if(inherits(lt[[1]], "GRanges")) {

+    	union = getFromNamespace("union", ns = "BiocGenerics")

+    	intersect = getFromNamespace("intersect", ns = "BiocGenerics")

+    	setdiff = getFromNamespace("setdiff", ns = "BiocGenerics")

+    } else if(inherits(lt[[1]], "IRanges")) {

+    	union = getFromNamespace("union", ns = "BiocGenerics")

+    	intersect = getFromNamespace("intersect", ns = "BiocGenerics")

+    	setdiff = getFromNamespace("setdiff", ns = "BiocGenerics")

+    }

+

     if(inherits(lt[[1]], "GRanges")) {

     	set_size = sapply(lt, function(x) {

 	    	value_fun(union(x, x[NULL]))

@@ -195,8 +205,8 @@ make_comb_mat_from_list = function(lt, mode, value_fun = length, top_n_sets = In

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # list_to_matrix(lt)

 list_to_matrix = function(lt) {

 	cn = unique(unlist(lt))

@@ -210,7 +220,7 @@ list_to_matrix = function(lt) {

 }

 # == title

-# Make a Combination matrix for UpSet Plot

+# Make a Combination Matrix for UpSet Plot

 #

 # == param

 # -... The input sets. If it is represented as a single variable, it should be a matrix/data frame

@@ -218,7 +228,7 @@ list_to_matrix = function(lt) {

 # -mode The mode for forming the combination set, see Mode section.

 # -top_n_sets Number of sets with largest size.

 # -min_set_size Ths minimal set size that is used for generating the combination matrix.

-# -value_fun For each combination set, how to calculate the size. If it is a scalar set, 

+# -value_fun For each combination set, how to calculate the size? If it is a scalar set, 

 #      the length of the vector is the size of the set, while if it is a region-based set,

 #      (i.e. ``GRanges`` or ``IRanges`` object), the sum of widths of regions in the set is

 #      calculated as the size of the set.

@@ -240,6 +250,7 @@ list_to_matrix = function(lt) {

 #     j 1 0 0

 #     u 1 0 1

 #     w 1 0 0

+#     ...

 #

 # If the variable is a data frame, the binary columns (only contain 0 and 1) and the logical

 # columns are only kept.

@@ -266,26 +277,29 @@ list_to_matrix = function(lt) {

 # we need to define how to calculate the size of that combination set. There are three modes:

 #

 # 1. ``distinct`` mode: 1 means in that set and 0 means not in that set, then "1 1 0" means a

-# set of elements also in set A and B, while not in C (``setdiff(intersect(A, B), C)``). Under

+# set of elements also in set A and B, while not in C (i.e. ``setdiff(intersect(A, B), C)``). Under

 # this mode, the seven combination sets are the seven partitions in the Venn diagram and they

 # are mutually exclusive.

 #

 # 2. ``intersect`` mode: 1 means in that set and 0 is not taken into account, then, "1 1 0" means

-# a set of elements in set A and B, and they can also in C or not in C (``intersect(A, B)``).

-# Under this mode, the seven combinatio sets can overlap.

+# a set of elements in set A and B, and they can also in C or not in C (i.e. ``intersect(A, B)``).

+# Under this mode, the seven combination sets can overlap.

 #

 # 3. ``union`` mode: 1 means in that set and 0 is not taken into account. When there are multiple

-# 1, the relationship is OR. Then, "1 1 0" means a set of elements in set A or B, and they can also in C or not in C (``union(A, B)``).

-# Under this mode, the seven combinatio sets can overlap.

+# 1, the relationship is OR. Then, "1 1 0" means a set of elements in set A or B, and they can also in C or not in C (i.e. ``union(A, B)``).

+# Under this mode, the seven combination sets can overlap.

 #

 # == value

 # A matrix also in a class of ``comb_mat``.

 #

+# Following functions can be applied to it: `set_name`, `comb_name`, `set_size`, `comb_size`, `comb_degree`,

+# `extract_comb` and `t.comb_mat`.

+#

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # m = make_comb_mat(lt)

 #

 # mat = list_to_matrix(lt)

@@ -297,7 +311,7 @@ list_to_matrix = function(lt) {

 # library(GenomicRanges)

 # lt = lapply(1:4, function(i) generateRandomBed())

 # lt = lapply(lt, function(df) GRanges(seqnames = df[, 1], 

-# 	ranges = IRanges(df[, 2], df[, 3])))

+#     ranges = IRanges(df[, 2], df[, 3])))

 # names(lt) = letters[1:4]

 # m = make_comb_mat(lt)

 # }

@@ -316,9 +330,9 @@ make_comb_mat = function(..., mode = c("distinct", "intersect", "union"),

 	if(missing(value_fun)) {

 		if(inherits(lt[[1]], "GRanges")) {

-			value_fun = function(x) sum(as.numeric(end(x) - start(x) + 1))

+			value_fun = function(x) sum(as.numeric(getFromNamespace("width", ns = "BiocGenerics")(x)))

 		} else if(inherits(lt[[1]], "IRanges")) {

-			value_fun = function(x) sum(as.numeric(end(x) - start(x) + 1))

+			value_fun = function(x) sum(as.numeric(getFromNamespace("width", ns = "BiocGenerics")(x)))

 		} else {

 			value_fun = length

 		}

@@ -331,6 +345,10 @@ binaryToInt = function(x) {

 	sum(x * 2^(rev(seq_along(x)) - 1))

 }

+intToBinary = function(x, len) {

+	rev(as.integer(intToBits(x))[1:len])

+}

+

 # == title

 # Set Names

 #

@@ -343,8 +361,8 @@ binaryToInt = function(x) {

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # m = make_comb_mat(lt)

 # set_name(m)

 set_name = function(m) {

@@ -368,8 +386,8 @@ set_name = function(m) {

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # m = make_comb_mat(lt)

 # set_size(m)

 set_size = function(m) {

@@ -388,8 +406,8 @@ set_size = function(m) {

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # m = make_comb_mat(lt)

 # comb_size(m)

 comb_size = function(m) {

@@ -415,8 +433,8 @@ comb_size = function(m) {

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # m = make_comb_mat(lt)

 # comb_name(m)

 comb_name = function(m) {

@@ -443,8 +461,8 @@ comb_name = function(m) {

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # m = make_comb_mat(lt)

 # comb_degree(m)

 comb_degree = function(m) {

@@ -469,9 +487,8 @@ comb_degree = function(m) {

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

-#

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # m = make_comb_mat(lt)

 # extract_comb(m, "110")

 extract_comb = function(m, comb_name) {

@@ -510,6 +527,17 @@ extract_comb = function(m, comb_name) {

 		}

 	}

 	if(!is.null(lt)) {

+

+		if(inherits(lt[[1]], "GRanges")) {

+	    	union = getFromNamespace("union", ns = "BiocGenerics")

+	    	intersect = getFromNamespace("intersect", ns = "BiocGenerics")

+	    	setdiff = getFromNamespace("setdiff", ns = "BiocGenerics")

+	    } else if(inherits(lt[[1]], "IRanges")) {

+	    	union = getFromNamespace("union", ns = "BiocGenerics")

+	    	intersect = getFromNamespace("intersect", ns = "BiocGenerics")

+	    	setdiff = getFromNamespace("setdiff", ns = "BiocGenerics")

+	    }

+

 		do_comb = function(lt, mode, do = rep(TRUE, length(lt))) {

 	        set1_index = which(do)

 	        set2_index = which(!do)

@@ -550,8 +578,8 @@ extract_comb = function(m, comb_name) {

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # m = make_comb_mat(lt)

 # t(m)

 t.comb_mat = function(x) {

@@ -566,16 +594,18 @@ t.comb_mat = function(x) {

 # == param

 # -x A combination matrix returned by `make_comb_mat`.

 # -i Indices on rows.

-# -j Indices on columns

+# -j Indices on columns.

 # -drop It is always reset to ``FALSE`` internally.

 #

 # == details

 # If sets are on rows of the combination matrix, the row indices correspond

-# to sets and column indices correspond to combination sets and if sets are

+# to sets and column indices correspond to combination sets, and if sets are

 # on columns of the combination matrix, rows correspond to the combination sets.

 #

-# You should not subset by the sets. It will give you wrong set size. The subsetting

-# on rows are only used internally.

+# If the index is one-dimension, e.g. ``x[i]``, the index always corresponds to the combination sets.

+#

+# You should not subset by the sets. It will give you wrong combination set size. The subsetting

+# on sets are only used internally.

 #

 # This subsetting method is mainly for subsetting combination sets, i.e., users

 # can first use `comb_size` to get the size of each combination set, and filter them

@@ -584,11 +614,12 @@ t.comb_mat = function(x) {

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # m = make_comb_mat(lt)

 # m2 = m[, comb_size(m) >= 3]

 # comb_size(m2)

+# m[comb_size(m) >= 3]

 "[.comb_mat" = function(x, i, j, drop = FALSE) {

 	set_size = attr(x, "set_size")

 	comb_size = attr(x, "comb_size")

@@ -596,12 +627,11 @@ t.comb_mat = function(x) {

 	mode = attr(x, "mode")

 	class(x) = "matrix"

-

 	if(set_on_rows) {

 		if(nargs() == 2) {

-			return(x[i])

-		}

-		if(missing(i)) {

+			x2 = x[, i, drop = FALSE]

+			comb_size = comb_size[i]

+		} else if(missing(i)) {

 			x2 = x[, j, drop = FALSE]

 			comb_size = comb_size[j]

 		} else if(missing(j)) {

@@ -614,9 +644,9 @@ t.comb_mat = function(x) {

 		}

 	} else {

 		if(nargs() == 2) {

-			return(x[i])

-		}

-		if(missing(i)) {

+			x2 = x[i, , drop = FALSE]

+			comb_size = comb_size[i]

+		} else if(missing(i)) {

 			x2 = x[, j, drop = FALSE]

 			set_size = set_size[j]

 		} else if(missing(j)) {

@@ -633,6 +663,8 @@ t.comb_mat = function(x) {

 	attr(x2, "comb_size") = comb_size

 	attr(x2, "mode") = mode

 	attr(x2, "set_on_rows") = set_on_rows

+	attr(x2, "x") = attr(x, "x")

+	attr(x2, "lt") = attr(x, "lt")

 	class(x2) = c("comb_mat", "matrix")

 	return(x2)

 }

@@ -666,21 +698,25 @@ print.comb_mat = function(x, ...) {

 # == param

 # -m A combination matrix returned by `make_comb_mat`. The matrix can be transposed to switch

 #    the position of sets and combination sets.

+# -comb_col The color for the dots representing combination sets.

+# -pt_size The point size for the dots representing combination sets.

+# -lwd The line width for the combination sets.

 # -set_order The order of sets.

 # -comb_order The order of combination sets.

 # -top_annotation A `HeatmapAnnotation` object on top of the combination matrix.

 # -right_annotation A `HeatmapAnnotation` object on the right of the combination matrix.

+# -row_names_side The side of row names.

 # -... Other arguments passed to `Heatmap`.

 #

 # == details

-# BY default, the sets are on rows and combination sets are on columns. The positions of the

+# By default, the sets are on rows and combination sets are on columns. The positions of the

 # two types of sets can be switched by transposing the matrix.

 #

 # When sets are on rows, the default top annotation is the barplot showing the size of each

 # combination sets and the default right annotation is the barplot showing the size of the sets.

 # The annotations are simply constructed by `HeatmapAnnotation` and `anno_barplot` with some

-# parameters pre-set. Users can check the source code of `default_upset_top_annotation` and

-# `default_upset_right_annotation` to find out how the annotations are defined.

+# parameters pre-set. Users can check the source code of `upset_top_annotation` and

+# `upset_right_annotation` to find out how the annotations are defined.

 #

 # To change or to add annotations, users just need to define a new `HeatmapAnnotation` object.

 # E.g. if we want to change the side of the axis and name on top annotation:

@@ -723,19 +759,51 @@ print.comb_mat = function(x, ...) {

 # == example

 # set.seed(123)

 # lt = list(a = sample(letters, 10),

-# 	      b = sample(letters, 15),

-# 	      c = sample(letters, 20))

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

 # m = make_comb_mat(lt)

 # UpSet(m)

 # UpSet(t(m))

 # 

 # m = make_comb_mat(lt, mode = "union")

 # UpSet(m)

+# UpSet(m, comb_col = c(rep(2, 3), rep(3, 3), 1))

 #

-UpSet = function(m, set_order = order(set_size(m), decreasing = TRUE), 

-	comb_order = order(comb_size(m), decreasing = TRUE), 

-	top_annotation = default_upset_top_annotation(m),

-	right_annotation = default_upset_right_annotation(m),

+#

+# # compare two UpSet plots

+# set.seed(123)

+# lt1 = list(a = sample(letters, 10),

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

+# m1 = make_comb_mat(lt1)

+# set.seed(456)

+# lt2 = list(a = sample(letters, 10),

+#           b = sample(letters, 15),

+#           c = sample(letters, 20))

+# m2 = make_comb_mat(lt2)

+#

+# max1 = max(c(set_size(m1), set_size(m2)))

+# max2 = max(c(comb_size(m1), comb_size(m2)))

+#

+# UpSet(m1, top_annotation = upset_top_annotation(m1, ylim = c(0, max2)),

+#     right_annotation = upset_right_annotation(m1, ylim = c(0, max1)),

+#     column_title = "UpSet1") +

+# UpSet(m2, top_annotation = upset_top_annotation(m2, ylim = c(0, max2)),

+#     right_annotation = upset_right_annotation(m2, ylim = c(0, max1)),

+#     column_title = "UpSet2")

+#

+UpSet = function(m, 

+	comb_col = "black",

+	pt_size = unit(3, "mm"), lwd = 2,

+	set_order = order(set_size(m), decreasing = TRUE), 

+	comb_order = if(attr(m, "set_on_rows")) {

+			order.comb_mat(m[set_order, ], decreasing = TRUE)

+		} else {

+			order.comb_mat(m[, set_order], decreasing = TRUE)

+		},

+	top_annotation = upset_top_annotation(m),

+	right_annotation = upset_right_annotation(m),

+	row_names_side = "left",

 	...) {

 	set_on_rows = attr(m, "set_on_rows")

@@ -745,7 +813,13 @@ UpSet = function(m, set_order = order(set_size(m), decreasing = TRUE),

 	class(m2) = "matrix"

+	pt_size = pt_size

+	lwd = lwd

+

 	if(set_on_rows) {

+		n_comb = ncol(m)

+		if(length(comb_col == 1)) comb_col = rep(comb_col, n_comb)

+

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

 			nr = round(1/as.numeric(h[1]))

 			nc = round(1/as.numeric(w[1]))

@@ -755,22 +829,41 @@ UpSet = function(m, set_order = order(set_size(m), decreasing = TRUE),

 					grid.rect(y = k/nr, height = 1/nr, just = "top", gp = gpar(fill = "#F0F0F0", col = NA))

 				}

 			}

-			grid.points(x, y, size = unit(3, "mm"), pch = 16, gp = gpar(col = ifelse(pindex(m2, i, j), "black", "#CCCCCC")))

+			grid.points(x, y, size = pt_size, pch = 16, gp = gpar(col = ifelse(pindex(m2, i, j), comb_col[j], "#CCCCCC")))

+			jj = unique(j)

 			for(k in seq_len(nc)) {

 		        if(sum(subm[, k]) >= 2) {

 		            i_min = min(which(subm[, k] > 0))

 		            i_max = max(which(subm[, k] > 0))

-		            grid.lines(c(k - 0.5, k - 0.5)/nc, (nr - c(i_min, i_max) + 0.5)/nr, gp = gpar(col = "black", lwd = 2))

+		            grid.lines(c(k - 0.5, k - 0.5)/nc, (nr - c(i_min, i_max) + 0.5)/nr, gp = gpar(col = comb_col[jj[k]], lwd = lwd))

 		        }

 		    }

 		}

+

+		# check top annotation

+		# if it is specified by upset_top_annotation and gp(col) is not set

+		ra = top_annotation

+		if(length(ra) == 1) {

+			ta_call = substitute(top_annotation)

+			ta_call = as.list(ta_call)

+			if(as.character(ta_call[[1]]) == "upset_top_annotation") {

+				if(!"gp" %in% names(as.list(ta_call))) {

+					ra@anno_list[[1]]@fun@var_env$gp$fill = comb_col

+					ra@anno_list[[1]]@fun@var_env$gp$col = comb_col

+				}

+			}

+		}

+

 		ht = Heatmap(m2, cluster_rows = FALSE, cluster_columns = FALSE, rect_gp = gpar(type = "none"),

 			layer_fun = layer_fun, show_heatmap_legend = FALSE,

-			top_annotation = top_annotation,

+			top_annotation = ra,

 			right_annotation = right_annotation,

-			row_names_side = "left",

+			row_names_side = row_names_side,

 			row_order = set_order, column_order = comb_order, ...)

 	} else {

+		n_comb = nrow(m)

+		if(length(comb_col == 1)) comb_col = rep(comb_col, n_comb)

+

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

 			nr = round(1/as.numeric(h[1]))

 			nc = round(1/as.numeric(w[1]))

@@ -780,53 +873,121 @@ UpSet = function(m, set_order = order(set_size(m), decreasing = TRUE),

 					grid.rect(x = k/nc, width = 1/nc, just = "right", gp = gpar(fill = "#F0F0F0", col = NA))

 				}

 			}

-			grid.points(x, y, size = unit(3, "mm"), pch = 16, gp = gpar(col = ifelse(pindex(m2, i, j), "black", "#CCCCCC")))

+			grid.points(x, y, size = pt_size, pch = 16, gp = gpar(col = ifelse(pindex(m2, i, j), comb_col[i], "#CCCCCC")))

+			ii = unique(i)

 			for(k in seq_len(nr)) {

 		        if(sum(subm[k, ]) >= 2) {

 		            i_min = min(which(subm[k, ] > 0))

 		            i_max = max(which(subm[k, ] > 0))

-		            grid.lines((c(i_min, i_max) - 0.5)/nc, (nr - c(k ,k) + 0.5)/nr, gp = gpar(col = "black", lwd = 2))

+		            grid.lines((c(i_min, i_max) - 0.5)/nc, (nr - c(k ,k) + 0.5)/nr, gp = gpar(col = comb_col[ii[k]], lwd = lwd))

 		        }

 		    }

 		}

+

+		ra = right_annotation

+		if(length(ra) == 1) {

+			ta_call = substitute(top_annotation)

+			ta_call = as.list(ta_call)

+			if(as.character(ta_call[[1]]) == "upset_right_annotation") {

+				if(!"gp" %in% names(as.list(ta_call))) {

+					ra@anno_list[[1]]@fun@var_env$gp$fill = comb_col

+					ra@anno_list[[1]]@fun@var_env$gp$col = comb_col

+				}

+			}

+		}

 		ht = Heatmap(m2, cluster_rows = FALSE, cluster_columns = FALSE, rect_gp = gpar(type = "none"),

 			layer_fun = layer_fun, show_heatmap_legend = FALSE,

 			top_annotation = top_annotation,

-			right_annotation = right_annotation,

+			right_annotation = ra,

 			row_order = comb_order, column_order = set_order, ...)

 	}

 	ht

 }

+# == title

+# Order of the Combination Sets

+#

+# == param

+# -m A combination matrix returned by `make_comb_mat`.

+# -on On sets or on combination sets?

+# -decreasing Whether the ordering is applied decreasingly.

+#

+# == details

+# It first sorts by the degree of the combination sets then

+# by the combination matrix.

+#

+order.comb_mat = function(m, decreasing = TRUE, on = "comb_set") {

+	if(on == "set") {

+		return(order(set_size(m), decreasing = decreasing))

+	} else {

+		set_on_rows = attr(m, "set_on_rows")

+		if(set_on_rows) {

+			lt = list(comb_degree(m))

+			lt = c(lt, as.list(as.data.frame(t(m))))

+			lt$decreasing = decreasing

+			do.call(order, lt)

+		} else {

+			lt = list(comb_degree(m))

+			lt = c(lt, as.list(as.data.frame(m)))

+			lt$decreasing = decreasing

+			do.call(order, lt)

+		}

+	}

+}

+

 # == title

 # Default UpSet Top Annotation

 #

 # == param

 # -m A combination matrix which is as same as the one for `UpSet`.

+# -gp Graphic parameters for bars.

+# -height The height of the top annotation.

+# -show_annotation_name Whether show annotation names?

+# -annotation_name_gp Graphic parameters for anntation names.

+# -annotation_name_offset Offset to the annotation name, a `grid::unit` object.

+# -annotation_name_side Side of the annotation name.

+# -annotation_name_rot Rotation of the annotation name, it can only take values in ``c(00, 90, 180, 270)``.

+# -... Passed to `anno_barplot`.

 #

 # == details

 # The default top annotation is actually barplot implemented by `anno_barplot`. For

 # how to set the top annotation or bottom annotation in `UpSet`, please refer to `UpSet`.

 #

-default_upset_top_annotation = function(m) {

+upset_top_annotation = function(m, 

+	gp = gpar(fill = "black"), 

+	height = unit(ifelse(set_on_rows, 2, 3), "cm"),

+	show_annotation_name = TRUE,

+	annotation_name_gp = gpar(),

+	annotation_name_offset = NULL,

+	annotation_name_side = "left",

+	annotation_name_rot = 0,

+	...) {

 	set_on_rows = attr(m, "set_on_rows")

 	if(set_on_rows) {

-		ha = HeatmapAnnotation("Intersection size" = anno_barplot(comb_size(m), 

-				border = FALSE, gp = gpar(fill = "black"), height = unit(2, "cm")), 

-			annotation_name_side = "left", annotation_name_rot = 0)

+		ha = HeatmapAnnotation("Intersection\nsize" = anno_barplot(comb_size(m), 

+					border = FALSE, gp = gp, height = height, ...), 

+				show_annotation_name = show_annotation_name,

+				annotation_name_gp = annotation_name_gp,

+				annotation_name_offset = annotation_name_offset,

+				annotation_name_side = annotation_name_side,

+				annotation_name_rot = annotation_name_rot)

 	} else {

-		ha = HeatmapAnnotation("Set size" = anno_barplot(set_size(m), border = FALSE, 

-				gp = gpar(fill = "black"), height = unit(3, "cm")),

-			annotation_name_side = "left", annotation_name_rot = 0)

+		ha = HeatmapAnnotation("Set\nsize" = anno_barplot(set_size(m), border = FALSE, 

+					gp = gp, height = height, ...),

+				show_annotation_name = show_annotation_name,

+				annotation_name_gp = annotation_name_gp,

+				annotation_name_offset = annotation_name_offset,

+				annotation_name_side = annotation_name_side,

+				annotation_name_rot = annotation_name_rot)

 	}

 	mode = attr(m, "mode")

 	if(set_on_rows) {

 		if(mode %in% c("distinct", "intersect")) {

-			names(ha) = "Intersection size"

+			names(ha) = "Intersection\nsize"

 		} else {

-			names(ha) = "Union size"

+			names(ha) = "Union\nsize"

 		}

 	}

 	return(ha)

@@ -837,29 +998,131 @@ default_upset_top_annotation = function(m) {

 #

 # == param

 # -m A combination matrix which is as same as the one for `UpSet`.

+# -gp Graphic parameters for bars.

+# -width Width of the right annotation.

+# -show_annotation_name Whether show annotation names?

+# -annotation_name_gp Graphic parameters for anntation names.

+# -annotation_name_offset Offset to the annotation name, a `grid::unit` object.

+# -annotation_name_side Side of the annotation name.

+# -annotation_name_rot Rotation of the annotation name, it can only take values in ``c(00, 90, 180, 270)``.

+# -... Passed to `anno_barplot`.

 #

 # == details

 # The default right annotation is actually barplot implemented by `anno_barplot`. For

 # how to set the right annotation or left annotation in `UpSet`, please refer to `UpSet`.

 #

-default_upset_right_annotation = function(m) {

+upset_right_annotation = function(m,

+	gp = gpar(fill = "black"),  

+	width = unit(ifelse(set_on_rows, 3, 2), "cm"),

+	show_annotation_name = TRUE,

+	annotation_name_gp = gpar(),

+	annotation_name_offset = NULL,

+	annotation_name_side = "bottom",

+	annotation_name_rot = NULL,

+	...) {

 	set_on_rows = attr(m, "set_on_rows")

 	if(set_on_rows) {

 		ha = rowAnnotation("Set size" = anno_barplot(set_size(m), border = FALSE, 

-					gp = gpar(fill = "black"), width = unit(3, "cm")))

+					gp = gp, width = width, ...),

+				show_annotation_name = show_annotation_name,

+				annotation_name_gp = annotation_name_gp,

+				annotation_name_offset = annotation_name_offset,

+				annotation_name_side = annotation_name_side,

+				annotation_name_rot = annotation_name_rot)

 	} else {

-		ha = rowAnnotation("Intersection size" = anno_barplot(comb_size(m), 

-				border = FALSE, gp = gpar(fill = "black"), width = unit(2, "cm")))

+		ha = rowAnnotation("Intersection\nsize" = anno_barplot(comb_size(m), 

+					border = FALSE, gp = gp, width = width, ...),

+				show_annotation_name = show_annotation_name,

+				annotation_name_gp = annotation_name_gp,

+				annotation_name_offset = annotation_name_offset,

+				annotation_name_side = annotation_name_side,

+				annotation_name_rot = annotation_name_rot)

 	}

 	mode = attr(m, "mode")

 	if(!set_on_rows) {

 		if(mode %in% c("distinct", "intersect")) {

-			names(ha) = "Intersection size"

+			names(ha) = "Intersection\nsize"

 		} else {

 			names(ha) = "Union size"

 		}

 	}

 	return(ha)

 }

+

+# == title

+# Normalize a list of combination matrice

+#

+# == param

+# -... If it is a single argument, the value should be a list of combination matrices.

+#

+# == details

+# It normalizes a list of combination matrice to make them have same number and order of sets and combination sets.

+#

+# The sets (by `set_name`) from all combination matrice should be the same.

+#

+normalize_comb_mat = function(...) {

+	lt = list(...)

+	if(length(lt) == 1) {

+		if(!is.list(lt)) {

+			stop_wrap("If you only specify one argument, it must be a list of comb_mat objects.")

+		}

+		lt = lt[[1]]

+	}

+

+	n = length(lt)

+	if(n == 1) {

+		stop_wrap("There should be at least two combination matrices.")

+	}

+

+	set1 = set_name(lt[[1]])

+	for(i in 2:n) {

+		if(!setequal(set1, set_name(lt[[i]]))) {

+			stop_wrap("The sets of all combination matrices should be identical.")

+		}

+	}

+	all_set_name = set_name(lt[[1]])

+	n_set = length(all_set_name)

+

+	all_comb_size = lapply(lt, function(x) {

+		set_on_rows = attr(x, "set_on_rows")

+		if(set_on_rows) {

+			code = apply(x, 2, binaryToInt)

+		} else {

+			code = apply(x, 1, binaryToInt)

+		}

+		structure(comb_size(x), names = code)

+	})

+

+	all_code = unique(unlist(lapply(all_comb_size, names)))

+	comb_mat = do.call(cbind, lapply(as.numeric(all_code), intToBinary, len = n_set))

+	rownames(comb_mat) = all_set_name

+

+	all_comb_size = lapply(all_comb_size, function(x) {

+		x2 = structure(rep(0, length(all_code)), names = all_code)

+		x2[names(x)] = x

+		x2

+	})

+

+	for(i in seq_along(lt)) {

+		x = lt[[i]]

+		set_on_rows = attr(x, "set_on_rows")

+		attr = attributes(x)

+		attr = attr[!names(attr) %in% c("dim", "dimname")]

+

+		if(set_on_rows) {

+			x2 = comb_mat

+		} else {

+			x2 = t(comb_mat)

+		}

+		for(nm in names(attr)) {

+			attr(x2, nm) = attr[[nm]]

+		}

+		attr(x2, "set_size") = attr$set_size[all_set_name]

+		attr(x2, "comb_size") = all_comb_size[[i]]

+		

+		lt[[i]] = x2

+	}

+	return(lt)

+}

@@ -14,17 +14,19 @@ Subset the Combination Matrix

   \item{x}{A combination matrix returned by \code{\link{make_comb_mat}}.}

   \item{i}{Indices on rows.}

-  \item{j}{Indices on columns}

+  \item{j}{Indices on columns.}

   \item{drop}{It is always reset to \code{FALSE} internally.}

 }

 \details{

 If sets are on rows of the combination matrix, the row indices correspond

-to sets and column indices correspond to combination sets and if sets are

+to sets and column indices correspond to combination sets, and if sets are

 on columns of the combination matrix, rows correspond to the combination sets.

-You should not subset by the sets. It will give you wrong set size. The subsetting

-on rows are only used internally.

+If the index is one-dimension, e.g. \code{x[i]}, the index always corresponds to the combination sets.

+

+You should not subset by the sets. It will give you wrong combination set size. The subsetting

+on sets are only used internally.

 This subsetting method is mainly for subsetting combination sets, i.e., users

 can first use \code{\link{comb_size}} to get the size of each combination set, and filter them

@@ -33,9 +35,10 @@ by the size.

 \examples{

 set.seed(123)

 lt = list(a = sample(letters, 10),

-	      b = sample(letters, 15),

-	      c = sample(letters, 20))

+          b = sample(letters, 15),

+          c = sample(letters, 20))

 m = make_comb_mat(lt)

 m2 = m[, comb_size(m) >= 3]

 comb_size(m2)

+m[comb_size(m) >= 3]

 }

@@ -44,7 +44,7 @@ HeatmapAnnotation(...,

   \item{gap}{Gap between annotations. It can be a single value or a vector of \code{\link[grid]{unit}} objects.}

   \item{show_annotation_name}{Whether show annotation names? For column annotation, annotation names are drawn either on the left or the right, and for row annotations, names are draw either on top or at the bottom. The value can be a vector.}

   \item{annotation_name_gp}{Graphic parameters for anntation names. Graphic paramters can be vectors.}

-  \item{annotation_name_offset}{Offset to the annotations, \code{\link[grid]{unit}} object. The value can be a vector.}

+  \item{annotation_name_offset}{Offset to the annotation names, a \code{\link[grid]{unit}} object. The value can be a vector.}

   \item{annotation_name_side}{Side of the annotation names.}

   \item{annotation_name_rot}{Rotation of the annotation names, it can only take values in \code{c(00, 90, 180, 270)}. The value can be a vector.}

   \item{annotation_height}{Height of each annotation if annotations are column annotations.}

@@ -7,31 +7,43 @@ Make the UpSet plot

 Make the UpSet plot

 }

 \usage{

-UpSet(m, set_order = order(set_size(m), decreasing = TRUE),

-    comb_order = order(comb_size(m), decreasing = TRUE),

-    top_annotation = default_upset_top_annotation(m),

-    right_annotation = default_upset_right_annotation(m),

+UpSet(m,

+    comb_col = "black",

+    pt_size = unit(3, "mm"), lwd = 2,

+    set_order = order(set_size(m), decreasing = TRUE),

+    comb_order = if(attr(m, "set_on_rows")) {

+    order.comb_mat(m[set_order, ], decreasing = TRUE)

+    } else {

+    order.comb_mat(m[, set_order], decreasing = TRUE)

+    },

+    top_annotation = upset_top_annotation(m),

+    right_annotation = upset_right_annotation(m),

+    row_names_side = "left",

     ...)

 }

 \arguments{

   \item{m}{A combination matrix returned by \code{\link{make_comb_mat}}. The matrix can be transposed to switch the position of sets and combination sets.}

+  \item{comb_col}{The color for the dots representing combination sets.}

+  \item{pt_size}{The point size for the dots representing combination sets.}

+  \item{lwd}{The line width for the combination sets.}

   \item{set_order}{The order of sets.}

   \item{comb_order}{The order of combination sets.}

   \item{top_annotation}{A \code{\link{HeatmapAnnotation}} object on top of the combination matrix.}

   \item{right_annotation}{A \code{\link{HeatmapAnnotation}} object on the right of the combination matrix.}

+  \item{row_names_side}{The side of row names.}

   \item{...}{Other arguments passed to \code{\link{Heatmap}}.}

 }

 \details{

-BY default, the sets are on rows and combination sets are on columns. The positions of the

+By default, the sets are on rows and combination sets are on columns. The positions of the

 two types of sets can be switched by transposing the matrix.

 When sets are on rows, the default top annotation is the barplot showing the size of each

 combination sets and the default right annotation is the barplot showing the size of the sets.

 The annotations are simply constructed by \code{\link{HeatmapAnnotation}} and \code{\link{anno_barplot}} with some

-parameters pre-set. Users can check the source code of \code{\link{default_upset_top_annotation}} and

-\code{\link{default_upset_right_annotation}} to find out how the annotations are defined.

+parameters pre-set. Users can check the source code of \code{\link{upset_top_annotation}} and

+\code{\link{upset_right_annotation}} to find out how the annotations are defined.

 To change or to add annotations, users just need to define a new \code{\link{HeatmapAnnotation}} object.

 E.g. if we want to change the side of the axis and name on top annotation:

@@ -76,12 +88,35 @@ by \code{+} or \code{\link[=pct_v_pct]{\%v\%}}.

 \examples{

 set.seed(123)

 lt = list(a = sample(letters, 10),

-	      b = sample(letters, 15),

-	      c = sample(letters, 20))

+          b = sample(letters, 15),

+          c = sample(letters, 20))

 m = make_comb_mat(lt)

 UpSet(m)

 UpSet(t(m))

 m = make_comb_mat(lt, mode = "union")

 UpSet(m)

+UpSet(m, comb_col = c(rep(2, 3), rep(3, 3), 1))

+

+# compare two UpSet plots

+set.seed(123)

+lt1 = list(a = sample(letters, 10),

+          b = sample(letters, 15),

+          c = sample(letters, 20))

+m1 = make_comb_mat(lt1)

+set.seed(456)

+lt2 = list(a = sample(letters, 10),

+          b = sample(letters, 15),

+          c = sample(letters, 20))

+m2 = make_comb_mat(lt2)

+

+max1 = max(c(set_size(m1), set_size(m2)))

+max2 = max(c(comb_size(m1), comb_size(m2)))

+

+UpSet(m1, top_annotation = upset_top_annotation(m1, ylim = c(0, max2)),

+    right_annotation = upset_right_annotation(m1, ylim = c(0, max1)),

+    column_title = "UpSet1") +

+UpSet(m2, top_annotation = upset_top_annotation(m2, ylim = c(0, max2)),