Add tests for check_if_assays_are_NOT_consistently_ordered function in test-utilities.R

stemangiola · stemangiola · commit a79919408a34 · 2025-07-10T18:26:42.000+09:30
Implemented a comprehensive suite of tests to validate the behavior of the check_if_assays_are_NOT_consistently_ordered function across various scenarios, including cases with empty assays, inconsistent colnames, and different ordering of colnames. This enhances the robustness of the utility checks in the package.
diff --git a/tests/testthat/test-utilities.R b/tests/testthat/test-utilities.R
@@ -351,3 +351,309 @@ test_that("get_count_datasets works", {
     # )
     # expect_error(cds <- get_count_datasets(se1), "assays must be named")
 })
+
+test_that("check_if_assays_are_NOT_consistently_ordered works correctly", {
+    # Use testthat edition 3
+    local_edition(3)
+    
+    # Test 1: SE with no assays - should return FALSE
+    se_empty <- SummarizedExperiment::SummarizedExperiment(
+        assays = list()
+    )
+    expect_false(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_empty))
+    
+    # Test 2: SE with assays but no colnames - should return FALSE
+    se_no_colnames <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3)
+        )
+    )
+    expect_false(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_no_colnames))
+    
+    # Test 3: SE with assays, some with colnames, some without - should return FALSE
+    se_mixed <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3)
+        )
+    )
+    colnames(assay(se_mixed, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    expect_false(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_mixed))
+    
+    # Test 4: SE with assays, all with same colnames in same order - should return FALSE
+    se_consistent <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3)
+        )
+    )
+    colnames(assay(se_consistent, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_consistent, "mat2", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    expect_false(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_consistent))
+    
+    # Test 5: SE with assays, all with same colnames but different order - should return TRUE
+    se_inconsistent <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3)
+        )
+    )
+    colnames(assay(se_inconsistent, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_inconsistent, "mat2", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_inconsistent))
+    
+    # Test 6: SE with assays, all with same colnames but different order (reverse) - should return TRUE
+    se_reverse <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3)
+        )
+    )
+    colnames(assay(se_reverse, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_reverse, "mat2", withDimnames = FALSE)) <- paste0("S", c(3, 2, 1))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_reverse))
+    
+    # Test 7: SE with assays, all with same colnames but different order (middle swap) - should return TRUE
+    se_middle_swap <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3)
+        )
+    )
+    colnames(assay(se_middle_swap, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_middle_swap, "mat2", withDimnames = FALSE)) <- paste0("S", c(1, 3, 2))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_middle_swap))
+    
+    # Test 8: SE with 3 assays, first two consistent, third different - should return TRUE
+    se_three_assays <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_three_assays, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_three_assays, "mat2", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_three_assays, "mat3", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_three_assays))
+    
+    # Test 9: SE with 3 assays, all consistent - should return FALSE
+    se_three_consistent <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_three_consistent, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_three_consistent, "mat2", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_three_consistent, "mat3", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    expect_false(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_three_consistent))
+    
+    # Test 10: SE with assays, all with same colnames but different order (complex permutation) - should return TRUE
+    se_complex <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(12), nrow = 3),
+            mat2 = matrix(seq(13, 24), nrow = 3)
+        )
+    )
+    colnames(assay(se_complex, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(4))
+    colnames(assay(se_complex, "mat2", withDimnames = FALSE)) <- paste0("S", c(4, 2, 1, 3))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_complex))
+    
+    # Test 11: SE with assays, all with same colnames but different order (all different) - should return TRUE
+    se_all_different <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_all_different, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_all_different, "mat2", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    colnames(assay(se_all_different, "mat3", withDimnames = FALSE)) <- paste0("S", c(2, 3, 1))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_all_different))
+    
+    # Test 12: SE with assays, all with same colnames but different order (pairwise different) - should return TRUE
+    se_pairwise <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_pairwise, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_pairwise, "mat2", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    colnames(assay(se_pairwise, "mat3", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_pairwise))
+    
+    # Test 13: SE with assays, all with same colnames but different order (first and last same) - should return TRUE
+    se_first_last <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_first_last, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_first_last, "mat2", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    colnames(assay(se_first_last, "mat3", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_first_last))
+    
+    # Test 14: SE with assays, all with same colnames but different order (middle different) - should return TRUE
+    se_middle_different <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_middle_different, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_middle_different, "mat2", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_middle_different, "mat3", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_middle_different))
+    
+    # Test 15: SE with assays, all with same colnames but different order (first different) - should return TRUE
+    se_first_different <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_first_different, "mat1", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    colnames(assay(se_first_different, "mat2", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_first_different, "mat3", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_first_different))
+    
+    # Test 16: SE with assays, all with same colnames but different order (last different) - should return TRUE
+    se_last_different <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_last_different, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_last_different, "mat2", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_last_different, "mat3", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_last_different))
+    
+    # Test 17: SE with assays, all with same colnames but different order (all different) - should return TRUE
+    se_all_different_2 <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_all_different_2, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_all_different_2, "mat2", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    colnames(assay(se_all_different_2, "mat3", withDimnames = FALSE)) <- paste0("S", c(2, 3, 1))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_all_different_2))
+    
+    # Test 18: SE with assays, all with same colnames but different order (all different) - should return TRUE
+    se_all_different_3 <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_all_different_3, "mat1", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    colnames(assay(se_all_different_3, "mat2", withDimnames = FALSE)) <- paste0("S", c(2, 3, 1))
+    colnames(assay(se_all_different_3, "mat3", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_all_different_3))
+    
+    # Test 19: SE with assays, all with same colnames but different order (all different) - should return TRUE
+    se_all_different_4 <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_all_different_4, "mat1", withDimnames = FALSE)) <- paste0("S", c(2, 3, 1))
+    colnames(assay(se_all_different_4, "mat2", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_all_different_4, "mat3", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_all_different_4))
+    
+    # Test 20: SE with assays, all with same colnames but different order (all different) - should return TRUE
+    se_all_different_5 <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_all_different_5, "mat1", withDimnames = FALSE)) <- paste0("S", c(2, 3, 1))
+    colnames(assay(se_all_different_5, "mat2", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    colnames(assay(se_all_different_5, "mat3", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_all_different_5))
+    
+    # Test 21: SE with assays, all with same colnames but different order (all different) - should return TRUE
+    se_all_different_6 <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_all_different_6, "mat1", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    colnames(assay(se_all_different_6, "mat2", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_all_different_6, "mat3", withDimnames = FALSE)) <- paste0("S", c(2, 3, 1))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_all_different_6))
+    
+    # Test 22: SE with assays, all with same colnames but different order (all different) - should return TRUE
+    se_all_different_7 <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_all_different_7, "mat1", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_all_different_7, "mat2", withDimnames = FALSE)) <- paste0("S", c(2, 3, 1))
+    colnames(assay(se_all_different_7, "mat3", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_all_different_7))
+    
+    # Test 23: SE with assays, all with same colnames but different order (all different) - should return TRUE
+    se_all_different_8 <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_all_different_8, "mat1", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    colnames(assay(se_all_different_8, "mat2", withDimnames = FALSE)) <- paste0("S", c(2, 3, 1))
+    colnames(assay(se_all_different_8, "mat3", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_all_different_8))
+    
+    # Test 24: SE with assays, all with same colnames but different order (all different) - should return TRUE
+    se_all_different_9 <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_all_different_9, "mat1", withDimnames = FALSE)) <- paste0("S", c(2, 3, 1))
+    colnames(assay(se_all_different_9, "mat2", withDimnames = FALSE)) <- paste0("S", seq_len(3))
+    colnames(assay(se_all_different_9, "mat3", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_all_different_9))
+    
+    # Test 25: SE with assays, all with same colnames but different order (all different) - should return TRUE
+    se_all_different_10 <- SummarizedExperiment::SummarizedExperiment(
+        assays = list(
+            mat1 = matrix(seq_len(9), nrow = 3),
+            mat2 = matrix(seq(10, 18), nrow = 3),
+            mat3 = matrix(seq(19, 27), nrow = 3)
+        )
+    )
+    colnames(assay(se_all_different_10, "mat1", withDimnames = FALSE)) <- paste0("S", c(3, 1, 2))
+    colnames(assay(se_all_different_10, "mat2", withDimnames = FALSE)) <- paste0("S", c(2, 3, 1))
+    colnames(assay(se_all_different_10, "mat3", withDimnames = FALSE)) <- paste0("S", c(1, 2, 3))
+    expect_true(tidySummarizedExperiment:::check_if_assays_are_NOT_consistently_ordered(se_all_different_10))
+})
