Fix tests issues, improve performance and fialsafes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ComplexUpset
 Type: Package
 Title: Create Complex UpSet Plots Using 'ggplot2' Components
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: person(
   "Michał", "Krassowski", email = "[email protected]", role = c("aut", "cre"),
   comment = c(ORCID = "0000-0002-9638-7785"))

NEWS.md

@@ -1,3 +1,13 @@
+# Version 1.0.3
+
+2021-01-05
+
+Bug fixes:
+- Major performance and memory use improvements, especially when using `intersections = 'all'`
+- The `max_combinations_n` fail-safe was replaced by a more useful `max_combinations_datapoints_n` with more precise error message
+- The atypical use case of filtering with `max_degree = 0` is now accepted again
+- Fix tests using all the data (effectively union mode) rather than chosen mode data only
+
 # Version 1.0.2
 
 2021-01-04

R/tests.R

@@ -8,11 +8,20 @@ NULL
 #' @param tests a named list with tests for specific variables, overwriting the default test
 #' @param ignore a list with names of variables to exclude from testing
 #' @param ignore_mode_columns whether the membership columns and size columns for all modes should be ignored
+#' @param mode region selection mode; note that modes other than `exclusive_intersection` repeat observations in different test group, introducing dependencies. See `get_size_mode()` for accepted values.
 #' @param ... passed to `upset_data()`
 #' @export
-compare_between_intersections = function(data, intersect, test=kruskal.test, tests=list(), ignore=list(), ignore_mode_columns=TRUE, ...) {
-  data = upset_data(data, intersect, ...)
+compare_between_intersections = function(
+    data, intersect, test=kruskal.test, tests=list(),
+    ignore=list(), ignore_mode_columns=TRUE,
+    mode='exclusive_intersection', ...
+) {
+  data = upset_data(data, intersect, mode=mode, ...)
+
   isect = data$with_sizes
+  isect = isect[
+      (isect[, paste0('in_', mode)] == 1) & (isect$intersection %in% data$plot_intersections_subset),
+  ]
 
   modes = c(
       'exclusive_intersection',

tests/testthat/test-data.R

@@ -334,6 +334,20 @@ test_that("upset_data() filters by min_size, max_size, min_degree and max_degree
     Sys.setlocale("LC_COLLATE", old_locale)
 })
 
+
+test_that("fail-safe protects from out of memory errors when sing observations='all'", {
+    set_data <- create_upset_abc_example()
+
+    expect_error(
+        upset_data(set_data, colnames(set_data), intersections='all', max_combinations_datapoints_n=100),
+        'The number of combinations with degrees between 0 and3 (8.0e+00) multiplied by the number of observations (325) and columns (4) accounts to an upper bound of 1.0e+04 datapoints; such a high number may lead to out of memory errors (depending on the available RAM size). Please adjust `min_degree` and `max_degree`, remove unused columns, or adjust `max_combinations_datapoints_n` (if you wish to proceed anyways).
+Note: filtering by size (`min_size` and/or `max_size`) or setting `n_intersections` reduces the memory requirements and if you already do that it may be safe to increase `max_combinations_datapoints_n`.',
+        fixed=TRUE
+    )
+
+})
+
+
 test_that("upset_data() works with a tibble", {
     # see https://github.com/krassowski/complex-upset/issues/20
     df = data.frame(

tests/testthat/test-other-visual.R

@@ -300,3 +300,16 @@ test_that("Sets of generated intersections are ok when sets not observed alone",
         )
     )
 })
+
+
+test_that("Inclusive union filtering works ok", {
+    expect_doppelganger(
+        "Inclusive union filtering works ok",
+        upset(
+            movies, genres,
+            n_intersections=5,
+            mode='exclusive_union',
+            keep_empty_groups=FALSE
+        )
+    )
+})

tests/testthat/test-plot.R

@@ -94,7 +94,7 @@ test_that("upset throws an informative error if filtering leads to empty dataset
     )
     expect_error(
         upset(df, c('a', 'b', 'c', 'd'), max_degree=-1),
-        'No intersections left after filtering: provide `max_degree` >= 1 \\(you provoided: -1\\)'
+        'No intersections left after filtering: provide `max_degree` >= 0 \\(you provoided: -1\\)'
     )
 })