@@ -1,8 +1,8 @@

 Package: ComplexHeatmap

 Type: Package

 Title: Make Complex Heatmaps

-Version: 1.99.4

-Date: 2018-12-10

+Version: 1.99.5

+Date: 2018-12-26

 Author: Zuguang Gu

 Maintainer: Zuguang Gu <z.gu@dkfz.de>

 Depends: R (>= 3.1.2), methods, grid, graphics, stats, grDevices

@@ -10,6 +10,8 @@ S3method("[", "HeatmapList")

 export("[.HeatmapList")

 S3method("[", "SingleAnnotation")

 export("[.SingleAnnotation")

+S3method("[", "comb_mat")

+export("[.comb_mat")

 S3method("c", "HeatmapAnnotation")

 export("c.HeatmapAnnotation")

 S3method("dim", "Heatmap")

@@ -62,6 +64,8 @@ S3method("nobs", "SingleAnnotation")

 export("nobs.SingleAnnotation")

 S3method("nrow", "Heatmap")

 export("nrow.Heatmap")

+S3method("print", "comb_mat")

+export("print.comb_mat")

 S3method("size", "AnnotationFunction")

 export("size.AnnotationFunction")

 S3method("size", "HeatmapAnnotation")

@@ -78,6 +82,8 @@ S3method("summary", "Heatmap")

 export("summary.Heatmap")

 S3method("summary", "HeatmapList")

 export("summary.HeatmapList")

+S3method("t", "comb_mat")

+export("t.comb_mat")

 S3method("width", "AnnotationFunction")

 export("width.AnnotationFunction")

 S3method("width", "Heatmap")

@@ -114,6 +120,7 @@ export("HeatmapList")

 export("Legend")

 export("Legends")

 export("SingleAnnotation")

+export("UpSet")

 export("adjust_dend_by_x")

 export("anno_barplot")

 export("anno_block")

@@ -136,6 +143,9 @@ export("anno_zoom")

 export("annotation_axis_grob")

 export("cluster_within_group")

 export("columnAnnotation")

+export("comb_degree")

+export("comb_name")

+export("comb_size")

 export("decorate_annotation")

 export("decorate_column_dend")

 export("decorate_column_names")

@@ -154,6 +164,7 @@ export("dend_xy")

 export("dendrogramGrob")

 export("densityHeatmap")

 export("dist2")

+export("extract_comb")

 export("getXY_in_parent_vp")

 export("grid.annotation_axis")

 export("grid.boxplot")

@@ -162,6 +173,8 @@ export("ht_global_opt")

 export("ht_opt")

 export("is_abs_unit")

 export("list_components")

+export("list_to_matrix")

+export("make_comb_mat")

 export("max_text_height")

 export("max_text_width")

 export("merge_dendrogram")

@@ -176,6 +189,8 @@ export("row_anno_histogram")

 export("row_anno_link")

 export("row_anno_points")

 export("row_anno_text")

+export("set_name")

+export("set_size")

 export("smartAlign2")

 export("subset_gp")

 export("subset_matrix_by_row")

@@ -245,6 +260,7 @@ importFrom("circlize", rand_color)

 importFrom("circlize", smartAlign)

 importFrom("colorspace", diverge_hcl)

 importFrom("colorspace", rainbow_hcl)

+importFrom("utils", "combn")

 importFrom("utils", "getFromNamespace")

 importFrom("utils", "packageDescription")

 importFrom("utils", "str")

@@ -48,7 +48,7 @@ make_comb_mat_from_matrix = function(x, mode, top_n_sets = Inf, min_set_size = -

 	comb_mat = t(comb_mat)

 	nc = ncol(comb_mat)

-	comb_mat2 = matrix(nr = nrow(comb_mat), nc = nc*(nc-1)/2)

+	comb_mat2 = matrix(nrow = nrow(comb_mat), ncol = nc*(nc-1)/2)

 	rownames(comb_mat2) = rownames(comb_mat)

 	if(mode == "intersect") {

 		if(nc > 1) {

@@ -112,11 +112,11 @@ make_comb_mat_from_list = function(lt, mode, value_fun = length, top_n_sets = In

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

     	set_size = sapply(lt, function(x) {

-	    	value_fun(union(x, GRanges()))

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

 	    })

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

     	set_size = sapply(lt, function(x) {

-	    	value_fun(union(x, IRanges()))

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

 	    })

     } else {

 	    set_size = sapply(lt, function(x) {

@@ -213,11 +213,94 @@ list_to_matrix = function(lt) {

 # Make a Combination matrix for UpSet Plot

 #

 # == param

-# -...

-# -mode

-# -top_n_sets

-# -min_set_size

-# -value_fun

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

+#     or a list. If it is multiple variables, it should be name-value pairs, see Input section for explanation.

+# -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, 

+#      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.

+#

+# == Input

+# To represent multiple sets, the variable can be represented as: 

+#

+# 1. A list of sets where each set is a vector, e.g.:

+#

+#     list(set1 = c("a", "b", "c"),

+#          set2 = c("b", "c", "d", "e"),

+#          ...)

+#

+# 2. A binary matrix/data frame where rows are elements and columns are sets, e.g.:

+#

+#       a b c

+#     h 1 1 1

+#     t 1 0 1

+#     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.

+#

+# The set can be genomic regions, then it can only be represented as a list of ``GRanges`` objects.

+#

+# == Mode

+# E.g. for three sets (A, B, C), the UpSet approach splits the combination of selecting elements

+# in the set or not in the set and calculates the sizes of the combination sets. For three sets,

+# all possible combinations are:

+#

+#     A B C

+#     1 1 1

+#     1 1 0

+#     1 0 1

+#     0 1 1

+#     1 0 0

+#     0 1 0

+#     0 0 1

+# 

+# A value of 1 means to select that set and 0 means not to select that set. E.g., "1 1 0"

+# means to select set A, B while not set C. Note there is no "0 0 0", because the background 

+# size is not of interest here. With the code of selecting and not selecting the sets, next

+# 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

+# 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.

+#

+# 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.

+#

+# == value

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

+#

+# == example

+# set.seed(123)

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

+# 	      b = sample(letters, 15),

+# 	      c = sample(letters, 20))

+# m = make_comb_mat(lt)

+#

+# mat = list_to_matrix(lt)

+# mat

+# m = make_comb_mat(mat)

+#

+# \dontrun{

+# library(circlize)

+# library(GenomicRanges)

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

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

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

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

+# m = make_comb_mat(lt)

+# }

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

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

@@ -368,6 +451,13 @@ comb_degree = function(m) {

 	}

 }

+# == title

+# Extract Elements in a Combination set

+#

+# == param

+# -m

+# -comb_name

+#

 extract_comb = function(m, comb_name) {

 	all_comb_names = comb_name(m)

 	if(!comb_name %in% all_comb_names) {

@@ -463,6 +553,26 @@ t.comb_mat = function(x) {

 # -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

+# 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.

+#

+# 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

+# by the size.

+#

+# == example

+# set.seed(123)

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

+# 	      b = sample(letters, 15),

+# 	      c = sample(letters, 20))

+# m = make_comb_mat(lt)

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

+# comb_size(m2)

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

 	set_size = attr(x, "set_size")

 	comb_size = attr(x, "comb_size")

@@ -537,6 +647,13 @@ print.comb_mat = function(x, ...) {

 # == title

 # Make the UpSet plot

 #

+# == param

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

+#    the position of sets and combination sets.

+# -set_order The order of sets.

+# -comb_order The order of combination sets.

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

+#

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

 	comb_order = order(comb_size(m), decreasing = TRUE), ...) {

new file mode 100644

@@ -0,0 +1,41 @@

+\name{[.comb_mat}

+\alias{[.comb_mat}

+\alias{Extract.comb_mat}

+\title{

+Subset the Combination Matrix

+}

+\description{

+Subset the Combination Matrix

+}

+\usage{

+\method{[}{comb_mat}(x, i, j, drop = FALSE)

+}

+\arguments{

+

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

+  \item{i}{Indices on rows.}

+  \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

+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.

+

+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

+by the size.

+}

+\examples{

+set.seed(123)

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

+	      b = sample(letters, 15),

+	      c = sample(letters, 20))

+m = make_comb_mat(lt)

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

+comb_size(m2)

+}

new file mode 100644

@@ -0,0 +1,25 @@

+\name{UpSet}

+\alias{UpSet}

+\title{

+Make the UpSet plot

+}

+\description{

+Make the UpSet plot

+}

+\usage{

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

+    comb_order = order(comb_size(m), decreasing = TRUE), ...)

+}

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

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

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

+

+}

+\examples{

+# There is no example

+NULL

+

+}

new file mode 100644

@@ -0,0 +1,30 @@

+\name{comb_degree}

+\alias{comb_degree}

+\title{

+Degrees of the Combination sets

+}

+\description{

+Degrees of the Combination sets

+}

+\usage{

+comb_degree(m)

+}

+\arguments{

+

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

+

+}

+\details{

+The degree for a combination set is the number of sets that are selected.

+}

+\value{

+A vector of degrees of the combination sets.

+}

+\examples{

+set.seed(123)

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

+	      b = sample(letters, 15),

+	      c = sample(letters, 20))

+m = make_comb_mat(lt)

+comb_degree(m)

+}

new file mode 100644

@@ -0,0 +1,34 @@

+\name{comb_name}

+\alias{comb_name}

+\title{

+Names of the Combination sets

+}

+\description{

+Names of the Combination sets

+}

+\usage{

+comb_name(m)

+}

+\arguments{

+

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

+

+}

+\details{

+The name of the combination sets are formatted as a string

+of binary bits. E.g. for three sets of "a", "b", "c", the combination

+set with name "101" corresponds to select set a, not select set b

+and select set c. The definition of "select" depends on the value of

+\code{mode} from \code{\link{make_comb_mat}}.

+}

+\value{

+A vector of names of the combination sets.

+}

+\examples{

+set.seed(123)

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

+	      b = sample(letters, 15),

+	      c = sample(letters, 20))

+m = make_comb_mat(lt)

+comb_name(m)

+}

new file mode 100644

@@ -0,0 +1,27 @@

+\name{comb_size}

+\alias{comb_size}

+\title{

+Sizes of the Combination sets

+}

+\description{

+Sizes of the Combination sets

+}

+\usage{

+comb_size(m)

+}

+\arguments{

+

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

+

+}

+\value{

+A vector of sizes of the combination sets.

+}

+\examples{

+set.seed(123)

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

+	      b = sample(letters, 15),

+	      c = sample(letters, 20))

+m = make_comb_mat(lt)

+comb_size(m)

+}

new file mode 100644

@@ -0,0 +1,22 @@

+\name{extract_comb}

+\alias{extract_comb}

+\title{

+Extract Elements in a Combination set

+}

+\description{

+Extract Elements in a Combination set

+}

+\usage{

+extract_comb(m, comb_name)

+}

+\arguments{

+

+  \item{m}{-m}

+  \item{comb_name}{-comb_name}

+

+}

+\examples{

+# There is no example

+NULL

+

+}

new file mode 100644

@@ -0,0 +1,27 @@

+\name{list_to_matrix}

+\alias{list_to_matrix}

+\title{

+Convert a List of Sets to a Binary Matrix

+}

+\description{

+Convert a List of Sets to a Binary Matrix

+}

+\usage{

+list_to_matrix(lt)

+}

+\arguments{

+

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

+

+}

+\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.

+}

+\examples{

+set.seed(123)

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

+	      b = sample(letters, 15),

+	      c = sample(letters, 20))

+list_to_matrix(lt)

+}

new file mode 100644

@@ -0,0 +1,101 @@

+\name{make_comb_mat}

+\alias{make_comb_mat}

+\title{

+Make a Combination matrix for UpSet Plot

+}

+\description{

+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)

+}

+\arguments{

+

+  \item{...}{The input sets. If it is represented as a single variable, it should be a matrix/data frame or a list. If it is multiple variables, it should be name-value pairs, see Input section for explanation.}

+  \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{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.}

+

+}

+\section{Input}{

+To represent multiple sets, the variable can be represented as:

+

+1. A list of sets where each set is a vector, e.g.:

+

+  \preformatted{

+    list(set1 = c("a", "b", "c"),

+         set2 = c("b", "c", "d", "e"),

+         ...)  }

+

+2. A binary matrix/data frame where rows are elements and columns are sets, e.g.:

+

+  \preformatted{

+      a b c

+    h 1 1 1

+    t 1 0 1

+    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.

+

+The set can be genomic regions, then it can only be represented as a list of \code{GRanges} objects.}

+\section{Mode}{

+E.g. for three sets (A, B, C), the UpSet approach splits the combination of selecting elements

+in the set or not in the set and calculates the sizes of the combination sets. For three sets,

+all possible combinations are:

+

+  \preformatted{

+    A B C

+    1 1 1

+    1 1 0

+    1 0 1

+    0 1 1

+    1 0 0

+    0 1 0

+    0 0 1  }

+

+A value of 1 means to select that set and 0 means not to select that set. E.g., "1 1 0"

+means to select set A, B while not set C. Note there is no "0 0 0", because the background 

+size is not of interest here. With the code of selecting and not selecting the sets, next

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

+

+1. \code{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 (\code{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. \code{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 (\code{intersect(A, B)}).

+Under this mode, the seven combinatio sets can overlap.

+

+3. \code{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 (\code{union(A, B)}).

+Under this mode, the seven combinatio sets can overlap.}

+\value{

+A matrix also in a class of \code{comb_mat}.

+}

+\examples{

+set.seed(123)

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

+	      b = sample(letters, 15),

+	      c = sample(letters, 20))

+m = make_comb_mat(lt)

+

+mat = list_to_matrix(lt)

+mat

+m = make_comb_mat(mat)

+

+\dontrun{

+library(circlize)

+library(GenomicRanges)

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

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

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

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

+m = make_comb_mat(lt)

+}

+}

new file mode 100644

@@ -0,0 +1,22 @@

+\name{print.comb_mat}

+\alias{print.comb_mat}

+\title{

+Print the comb_mat Object

+}

+\description{

+Print the comb_mat Object

+}

+\usage{

+\method{print}{comb_mat}(x, ...)

+}

+\arguments{

+

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

+  \item{...}{Other arguments}

+

+}

+\examples{

+# There is no example

+NULL

+

+}

new file mode 100644

@@ -0,0 +1,27 @@

+\name{set_name}

+\alias{set_name}

+\title{

+Set Names

+}

+\description{

+Set Names

+}

+\usage{

+set_name(m)

+}

+\arguments{

+

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

+

+}

+\value{

+A vector of set names.

+}

+\examples{

+set.seed(123)

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

+	      b = sample(letters, 15),

+	      c = sample(letters, 20))

+m = make_comb_mat(lt)

+set_name(m)

+}

new file mode 100644

@@ -0,0 +1,27 @@

+\name{set_size}

+\alias{set_size}

+\title{

+Set Sizes

+}

+\description{

+Set Sizes

+}

+\usage{

+set_size(m)

+}

+\arguments{

+

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

+

+}

+\value{

+A vector of set sizes.

+}

+\examples{

+set.seed(123)

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

+	      b = sample(letters, 15),

+	      c = sample(letters, 20))

+m = make_comb_mat(lt)

+set_size(m)

+}

new file mode 100644

@@ -0,0 +1,24 @@

+\name{t.comb_mat}

+\alias{t.comb_mat}

+\title{

+Transpost the Combination Matrix

+}

+\description{

+Transpost the Combination Matrix

+}

+\usage{

+\method{t}{comb_mat}(x)

+}

+\arguments{

+

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

+

+}

+\examples{

+set.seed(123)

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

+	      b = sample(letters, 15),

+	      c = sample(letters, 20))

+m = make_comb_mat(lt)

+t(m)

+}

@@ -51,7 +51,6 @@ m = make_comb_mat(movies, top_n_sets = 6, mode = "intersect")

 m = make_comb_mat(movies, top_n_sets = 6, mode = "union")

-

 library(circlize)

 library(GenomicRanges)

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

@@ -60,3 +59,53 @@ names(lt) = letters[1:4]

 m = make_comb_mat(lt)

+set.seed(123)

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

+	      b = sample(letters, 15),

+	      c = sample(letters, 20))

+v = gplots::venn(lt, show.plot = FALSE)

+rownames(v) = apply(v[, -1], 1, paste, collapse = "")

+m = make_comb_mat(lt)

+cs = structure(comb_size(m), names = comb_name(m))

+

+library(testthat)

+test_that("test to the output from gplots::venn", {

+	expect_that(cs[["111"]], equals(v["111", 1]))

+	expect_that(cs[["110"]], equals(v["110", 1]))

+	expect_that(cs[["101"]], equals(v["101", 1]))

+	expect_that(cs[["011"]], equals(v["011", 1]))

+	expect_that(cs[["100"]], equals(v["100", 1]))

+	expect_that(cs[["010"]], equals(v["010", 1]))

+	expect_that(cs[["001"]], equals(v["001", 1]))

+})

+

+m = make_comb_mat(lt, mode = "intersect")

+cs = structure(comb_size(m), names = comb_name(m))

+test_that("test to the output from gplots::venn", {

+	expect_that(cs[["111"]], equals(v["111", 1]))

+	expect_that(cs[["110"]], equals(v["110", 1] + v["111", 1]))

+	expect_that(cs[["101"]], equals(v["101", 1] + v["111", 1]))

+	expect_that(cs[["011"]], equals(v["011", 1] + v["111", 1]))

+	expect_that(cs[["100"]], equals(v["100", 1] + v["110", 1] + v["101", 1] + v["111", 1]))

+	expect_that(cs[["010"]], equals(v["010", 1] + v["110", 1] + v["111", 1] + v["011", 1]))

+	expect_that(cs[["001"]], equals(v["001", 1] + v["111", 1] + v["101", 1] + v["011", 1]))

+})

+

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

+cs = structure(comb_size(m), names = comb_name(m))

+test_that("test to the output from gplots::venn", {

+	expect_that(cs[["111"]], equals(sum(v[, 1])))

+	expect_that(cs[["110"]], equals(sum(v[, 1]) - v["001", 1]))

+	expect_that(cs[["101"]], equals(sum(v[, 1]) - v["010", 1]))

+	expect_that(cs[["011"]], equals(sum(v[, 1]) - v["100", 1]))

+	expect_that(cs[["100"]], equals(v["100", 1] + v["101", 1] + v["110", 1] + v["111", 1]))

+	expect_that(cs[["010"]], equals(v["010", 1] + v["110", 1] + v["011", 1] + v["111", 1]))

+	expect_that(cs[["001"]], equals(v["001", 1] + v["101", 1] + v["011", 1] + v["111", 1]))

+})

+

+m = make_comb_mat(lt)

+cs = comb_size(m)

+test_that("test comb_size and extract_comb", {

+	expect_that(cs, equals(unname(sapply(comb_name(m), function(nm) length(extract_comb(m, nm))))))

+})

+