@@ -10,7 +10,8 @@ Imports: circlize (>= 0.4.5), GetoptLong, colorspace, clue,

     RColorBrewer, GlobalOptions (>= 0.1.0), parallel

 Suggests: testthat (>= 1.0.0), knitr, markdown, dendsort, 

     Cairo, png, jpeg, tiff, fastcluster,

-    dendextend (>= 1.0.1), grImport, grImport2, glue

+    dendextend (>= 1.0.1), grImport, grImport2, glue,

+    GenomicRanges

 VignetteBuilder: knitr

 Description: Complex heatmaps are efficient to visualize associations 

     between different sources of data sets and reveal potential patterns. 

@@ -1,6 +1,7 @@

 CHANGES in VERSION 1.99.7

 * `UpSet()` supports adding complement sets.

+* `make_comb_set()`: add `universal_set` and `complement_size` arguments.

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

@@ -295,7 +295,8 @@ list_to_matrix = function(lt, universal_set = NULL) {

 # -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.

-# -universal_set The universal set. It if is specified, ``complement_size`` is ignored.

+# -universal_set The universal set. If it is set, the size of the complement set of all sets is also calculated.

+#                It if is specified, ``complement_size`` is ignored.

 # -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, 

@@ -7,21 +7,23 @@ Convert a List of Sets to a Binary Matrix

 Convert a List of Sets to a Binary Matrix

 }

 \usage{

-list_to_matrix(lt)

+list_to_matrix(lt, universal_set = NULL)

 }

 \arguments{

   \item{lt}{A list of vectors.}

+  \item{universal_set}{The universal set.}

 }

 \details{

 It converts the list which have m sets to a binary matrix with n rows and m columns

-where n is the number of union of all sets in the list.

+where n is the size of universal set.

 }

 \examples{

 set.seed(123)

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

-          b = sample(letters, 15),

-          c = sample(letters, 20))

+lt = list(a = sample(letters, 5),

+          b = sample(letters, 10),

+          c = sample(letters, 15))

 list_to_matrix(lt)

+list_to_matrix(lt, universal_set = letters)

 }

@@ -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, complement_size = NULL, value_fun)

+    top_n_sets = Inf, min_set_size = -Inf, universal_set = NULL, 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{universal_set}{The universal set. If it is set, the size of the complement set of all sets is also calculated. It if is specified, \code{complement_size} is ignored.}

   \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.}

@@ -54,10 +54,10 @@ test_that("test default make_comb_mat", {

 test_that("test default make_comb_mat with universal_set", {

 	m = make_comb_mat(lt, universal_set = letters)

-	expect_that(length(comb_size(m)), is_identical_to(8))

+	expect_that(length(comb_size(m)), equals(8))

 	expect_that("000" %in% comb_name(m), is_identical_to(TRUE))

 	expect_that(0 %in% comb_degree(m), is_identical_to(TRUE))

-

+	expect_that(sort(extract_comb(m, "000")), is_identical_to(sort(setdiff(letters, unlist(lt)))))

 })

@@ -65,8 +65,43 @@ test_that("test default make_comb_mat with universal_set which is smaller than t

 	m = make_comb_mat(lt, universal_set = letters[1:10])

 	expect_that("000" %in% comb_name(m), is_identical_to(TRUE))

-	expect_that(0 %in% comb_degree(m), is_identical_to(TRUE))

-

+	expect_that(sort(extract_comb(m, "000")), is_identical_to(sort(setdiff(letters[1:10], unlist(lt)))))

 })

-# test GRanges

\ No newline at end of file

+# test GRanges

+library(GenomicRanges)

+

+#  1        0         0         0         0

+#  ++++++++++++++++++++++++++++++++++++++++

+#     -------      ---------     ---------

+#   ------     ------    ------      ----

+#      -----     -----       ----------

+#       ++++++    +++++++     +++++++

+

+gr1 = GRanges(seqnames = "chr1",

+	ranges = IRanges(start = c(4, 17, 31), end = c(10, 25, 39)))

+gr2 = GRanges(seqnames = "chr1",

+	ranges = IRanges(start = c(2, 13, 23, 35), end = c(7, 18, 28, 38)))

+gr3 = GRanges(seqnames = "chr1",

+	ranges = IRanges(start = c(5, 15, 27), end = c(9, 19, 36)))

+universal = GRanges(seqnames = "chr1",

+	ranges = IRanges(start = 1, end = 40))

+bg = GRanges(seqnames = "chr1",

+	ranges = IRanges(start = c(6, 16, 28), end = c(11, 22, 34)))

+

+lt = list(gr1 = gr1, gr2 = gr2, gr3 = gr3)

+

+test_that("test default make_comb_mat with GRanges", {

+	m = make_comb_mat(lt)

+

+	expect_that(unname(set_size(m)), equals(c(sum(GenomicRanges::width(gr1)), sum(GenomicRanges::width(gr2)), sum(GenomicRanges::width(gr3)))))

+	expect_that(comb_size(m)[["111"]], equals(sum(GenomicRanges::width( GenomicRanges::intersect(GenomicRanges::intersect(gr1, gr2), gr3) ))))

+

+	m = make_comb_mat(lt, universal_set = universal)

+	expect_that(length(comb_size(m)), equals(8))

+	expect_that(comb_size(m)[["000"]], equals(sum(GenomicRanges::width( GenomicRanges::setdiff(universal, GenomicRanges::union(GenomicRanges::union(gr1, gr2), gr3))))))

+

+	m = make_comb_mat(lt, universal_set = bg)

+	expect_that(length(comb_size(m)), equals(8))

+	expect_that(comb_size(m)[["000"]], equals(sum(GenomicRanges::width( GenomicRanges::setdiff(bg, GenomicRanges::union(GenomicRanges::union(gr1, gr2), gr3))))))

+})