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Robustify utility check #92

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369b02e
Allow this check, even though I assay names might not be present
stemangiola Apr 22, 2024
ac4b6bc
update dependencies
stemangiola Apr 22, 2024
a799194
Add tests for check_if_assays_are_NOT_consistently_ordered function i…
stemangiola Jul 10, 2025
482beff
version UP
stemangiola Jul 10, 2025
52c4b6d
update docs
stemangiola Jul 10, 2025
3ee3c2b
Merge branch 'master' into robustify-utility-check
stemangiola Jul 10, 2025
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1 change: 1 addition & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -114,6 +114,7 @@ importFrom(rlang,is_spliced)
importFrom(rlang,quo_is_null)
importFrom(rlang,quo_name)
importFrom(rlang,quo_squash)
importFrom(rlang,set_names)
importFrom(stringr,regex)
importFrom(stringr,str_detect)
importFrom(stringr,str_replace)
Expand Down
27 changes: 23 additions & 4 deletions R/utilities.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1297,10 +1297,12 @@ is_filer_columns_in_column_selection <- function(.data, ...) {
error = function(e) FALSE)
}

#' @importFrom rlang set_names
check_if_assays_are_NOT_consistently_ordered <- function(se) {

# If I have any assay at all
assays(se) |> length() |> gt(0) &&
do_I_have_assays =
assays(se) |> length() |> gt(0) &&

# If I have more than one assay with colnames
Filter(
Expand All @@ -1310,9 +1312,24 @@ check_if_assays_are_NOT_consistently_ordered <- function(se) {
map(colnames)
) |>
length() |>
gt(0) &&

# If I have lack of consistency

gt(0)

# If I have lack of consistency
# Forcing assay names otherwise fails if assay is unnamed
if(
se |>
assays(withDimnames = FALSE) |>
as.list() |>
names()
)
assays(se) =
se |>
assays(withDimnames = FALSE) |>
as.list() |>
set_names(se |> assays() |> as.list() |> length() |> seq_len())

lack_of_consistency =
se |>
assays(withDimnames = FALSE) |>
as.list() |>
Expand All @@ -1321,6 +1338,8 @@ check_if_assays_are_NOT_consistently_ordered <- function(se) {
equals(1) |>
all() |>
not()

do_I_have_assays && lack_of_consistency
}

check_if_any_dimnames_duplicated <- function(se, dim = "cols") {
Expand Down
306 changes: 306 additions & 0 deletions tests/testthat/test-utilities.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
})
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