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jokergoo · Mar 26, 2020 · c57f083 · c57f083
1 parent 4acbc10
commit c57f083
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Showing 5 changed files with 14 additions and 7 deletions.
diff --git a/R/Upset.R b/R/Upset.R
@@ -495,7 +495,13 @@ full_comb_code = function(n, complement = FALSE) {
             j = j + 1
         }
     }
-    sort(apply(comb_mat, 2, paste, collapse = ""))
+
+    lt = list(colSums(comb_mat))
+	lt = c(lt, as.list(as.data.frame(t(comb_mat))))
+	lt$decreasing = TRUE
+	od = do.call(order, lt)
+
+    apply(comb_mat[, od, drop = FALSE], 2, paste, collapse = "")
 }
 
 
@@ -874,7 +880,7 @@ subset_by_comb_ind = function(x, ind, margin = 2) {
 
 	class(x) = "matrix"
 	n = nrow(x)
-	if(is.numeric(ind)) {
+	if(is.numeric(ind) || is.logical(ind)) {
 		if(margin == 1) {
 			x2 = x[ind, , drop = FALSE]
 		} else {
@@ -918,7 +924,7 @@ subset_by_set_ind = function(x, ind) {
 
 	ind = unique(ind)
 
-	if(is.numeric(ind)) {
+	if(is.numeric(ind) || is.logical(ind)) {
 		sub_set = set_name(x)[ind]
 		if(is.matrix(env$data)) {
 			param$x = env$data[, sub_set, drop = FALSE]

diff --git a/man/UpSet.Rd b/man/UpSet.Rd
@@ -12,7 +12,7 @@ UpSet(m,
     pt_size = unit(3, "mm"), lwd = 2,
     bg_col = "#F0F0F0", bg_pt_col = "#CCCCCC",
     set_order = order(set_size(m), decreasing = TRUE),
-    comb_order = if(attr(m, "set_on_rows")) {
+    comb_order = if(attr(m, "param")$set_on_rows) {
     order.comb_mat(m[set_order, ], decreasing = TRUE)
     } else {
     order.comb_mat(m[, set_order], decreasing = TRUE)

diff --git a/man/anno_barplot.Rd b/man/anno_barplot.Rd
@@ -9,7 +9,7 @@ Barplot Annotation
 \usage{
 anno_barplot(x, baseline = 0, which = c("column", "row"), border = TRUE, bar_width = 0.6,
     gp = gpar(fill = "#CCCCCC"), ylim = NULL, extend = 0.05, axis = TRUE,
-    axis_param = default_axis_param(which), beside = FALSE,
+    axis_param = default_axis_param(which),
     width = NULL, height = NULL, ...)
 }
 \arguments{

diff --git a/man/make_comb_mat.Rd b/man/make_comb_mat.Rd
@@ -21,6 +21,7 @@ make_comb_mat(..., mode = c("distinct", "intersect", "union"),
   \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.}
+  \item{set_on_rows}{Used internally.}
 
 }
 \section{Input}{

diff --git a/tests/testthat/testthat-UpSet.R b/tests/testthat/testthat-UpSet.R
@@ -252,14 +252,14 @@ cm2 = make_comb_mat_from_matrix(m, "distinct")
 test_that("test subset method on sets and combination sets", {
 	expect_that(comb_size(cm1[, 1:5]), equals(comb_size(cm1)[1:5]))
 	expect_that(comb_size(cm1[1:5]), equals(comb_size(cm1)[1:5]))
-	expect_that(comb_size(cm1[full_comb_code(3, TRUE)]), equals(c("000" = 0, comb_size(cm1))))
+	expect_that(comb_size(cm1[full_comb_code(3, TRUE)]), equals(c(comb_size(cm1), "000" = 0)))
 
 	cm1_2sets = make_comb_mat_from_list(lt[1:2], "distinct")
 	expect_that(comb_size(cm1[c("a", "b"), ]), equals(comb_size(cm1_2sets)))
 
 	expect_that(comb_size(cm2[, 1:5]), equals(comb_size(cm2)[1:5]))
 	expect_that(comb_size(cm2[1:5]), equals(comb_size(cm2)[1:5]))
-	expect_that(comb_size(cm2[full_comb_code(3, TRUE)]), equals(c("000" = 0, comb_size(cm2))))
+	expect_that(comb_size(cm2[full_comb_code(3, TRUE)]), equals(c(comb_size(cm2), "000" = 0)))
 
 	cm2_2sets = make_comb_mat_from_matrix(m[, 1:2], "distinct")
 	expect_that(comb_size(cm2[c("a", "b"), ]), equals(comb_size(cm2_2sets)))