@@ -1,3 +1,9 @@

+CHANGES in VERSION 1.99.7

+

+* `UpSet()` supports adding complement sets.

+

+========================

+

 CHANGES in VERSION 1.99.6

 * adjust the size of heatmap annotations and add testing scripts.

@@ -1,5 +1,5 @@

-make_comb_mat_from_matrix = function(x, mode, top_n_sets = Inf, min_set_size = -Inf) {

+make_comb_mat_from_matrix = function(x, mode, top_n_sets = Inf, min_set_size = -Inf, complement_size = NULL) {

 	# check whether x is a binary matrix

 	if(is.data.frame(x)) {

 		lc = sapply(x, function(x) {

@@ -93,6 +93,11 @@ make_comb_mat_from_matrix = function(x, mode, top_n_sets = Inf, min_set_size = -

 		})

 	}

+	if(!is.null(complement_size)) {

+		comb_mat = cbind(rep(0, nrow(comb_mat)), comb_mat)

+		comb_size = c(complement_size, comb_size)

+	}

+

 	attr(comb_mat, "set_size") = set_size

 	attr(comb_mat, "comb_size") = comb_size

 	attr(comb_mat, "mode") = mode

@@ -103,7 +108,7 @@ make_comb_mat_from_matrix = function(x, mode, top_n_sets = Inf, min_set_size = -

 }

-make_comb_mat_from_list = function(lt, mode, value_fun = length, top_n_sets = Inf, min_set_size = -Inf) {

+make_comb_mat_from_list = function(lt, mode, value_fun = length, top_n_sets = Inf, min_set_size = -Inf, complement_size = NULL) {

 	n = length(lt)

     nm = names(lt)

     if(is.null(nm)) {

@@ -183,6 +188,12 @@ make_comb_mat_from_list = function(lt, mode, value_fun = length, top_n_sets = In

     }

     comb_mat = comb_mat + 0

+

+    if(!is.null(complement_size)) {

+		comb_mat = cbind(rep(0, nrow(comb_mat)), comb_mat)

+		comb_size = c(complement_size, comb_size)

+	}

+

     attr(comb_mat, "set_size") = set_size

 	attr(comb_mat, "comb_size") = comb_size

 	attr(comb_mat, "mode") = mode

@@ -228,6 +239,8 @@ 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.

+# -complement_size The size for the complement of all sets. If it is specified, the combination

+#                  set name will be like "00...".

 # -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

@@ -316,7 +329,7 @@ list_to_matrix = function(lt) {

 # m = make_comb_mat(lt)

 # }

 make_comb_mat = function(..., mode = c("distinct", "intersect", "union"),

-	top_n_sets = Inf, min_set_size = -Inf, value_fun) {

+	top_n_sets = Inf, min_set_size = -Inf, complement_size = NULL, value_fun) {

 	lt = list(...)

@@ -324,7 +337,7 @@ make_comb_mat = function(..., mode = c("distinct", "intersect", "union"),

 	if(length(lt) == 1) {

 		lt = lt[[1]]

 		if(!is.null(dim(lt))) {

-			return(make_comb_mat_from_matrix(lt, mode = mode, top_n_sets = top_n_sets, min_set_size = min_set_size))

+			return(make_comb_mat_from_matrix(lt, mode = mode, top_n_sets = top_n_sets, min_set_size = min_set_size, complement_size = complement_size))

 		}

 	}

@@ -337,7 +350,7 @@ make_comb_mat = function(..., mode = c("distinct", "intersect", "union"),

 			value_fun = length

 		}

 	}

-	make_comb_mat_from_list(lt, value_fun, mode = mode, top_n_sets = top_n_sets, min_set_size = min_set_size)

+	make_comb_mat_from_list(lt, value_fun, mode = mode, top_n_sets = top_n_sets, min_set_size = min_set_size, complement_size = complement_size)

 }

@@ -492,6 +505,11 @@ comb_degree = function(m) {

 # m = make_comb_mat(lt)

 # extract_comb(m, "110")

 extract_comb = function(m, comb_name) {

+

+	if(grepl("^0+$", comb_name)) {

+		stop_wrap(qq("Cannot extract elements for the complement set '@{comb_name}'."))

+	}

+

 	all_comb_names = comb_name(m)

 	if(!comb_name %in% all_comb_names) {

 		stop_wrap(paste0("Cannot find a combination name:	", comb_name, ", valid combination name should be in `comb_name(m)`."))

@@ -8,7 +8,7 @@ Make a Combination Matrix for UpSet Plot

 }

 \usage{

 make_comb_mat(..., mode = c("distinct", "intersect", "union"),

-    top_n_sets = Inf, min_set_size = -Inf, value_fun)

+    top_n_sets = Inf, min_set_size = -Inf, complement_size = NULL, value_fun)

 }

 \arguments{

@@ -16,6 +16,7 @@ make_comb_mat(..., mode = c("distinct", "intersect", "union"),

   \item{mode}{The mode for forming the combination set, see Mode section.}

   \item{top_n_sets}{Number of sets with largest size.}

   \item{min_set_size}{Ths minimal set size that is used for generating the combination matrix.}

+  \item{complement_size}{The size for the complement of all sets. If it is specified, the combination set name will be like "00...".}

   \item{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. \code{GRanges} or \code{IRanges} object), the sum of widths of regions in the set is calculated as the size of the set.}

 }