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add reference samples to divergence outputs #100

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Jan 22, 2025
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TuomasBorman committed Jan 22, 2025
commit fb680a48199dbcec120e65478dcf4768420a0ff9
2 changes: 1 addition & 1 deletion tests/testthat/test-getBaselineDivergence.R
Original file line number Diff line number Diff line change
@@ -113,7 +113,7 @@ test_that("Test altExp", {
tse, group = "subject", time.col = "time", altexp = "Family")
altExp(tse, "Family_test") <- addBaselineDivergence(
altExp(tse, "Family"), group = "subject", time.col = "time",
name = "val", name.time = "time_val")
name = c("val", "time_val", "ref"))
# Time differences should still match
expect_equal(
altExp(tse, "Family")$divergence, altExp(tse, "Family_test")$val)
10 changes: 5 additions & 5 deletions tests/testthat/test-getStepwiseDivergence.R
Original file line number Diff line number Diff line change
@@ -93,7 +93,7 @@ test_that("Comparing vegan distances (bray vs euclidean)", {
tse2 <- addStepwiseDivergence(
tse2, group = "subject", time.interval = 1, time.col = "time",
assay.type = "counts", dis.fun = vegan::vegdist, method = "euclidean",
name = c("timedivergence2", "timedifference2", "ref_samples"))
name = c("timedivergence2", "timedifference2", "ref_samples2"))
expect_true(identical(tse2$timedifference, tse2$timedifference2))
expect_true(!identical(tse2$timedivergence, tse2$timedivergence2))
})
@@ -107,16 +107,16 @@ test_that("AltExp functionality in addStepwiseDivergence", {
tse, group = "subject", time.interval = 1, time.col = "time",
altexp = "Family")

altExp(tse, "Family_test") <- addStepwiseDivergence(
altExp(tse, "Family") <- addStepwiseDivergence(
altExp(tse, "Family"), group = "subject", time.interval = 1,
time.col = "time",
name = c("timedivergence", "timedifference", "ref_samples"))
name = c("timedivergence", "timedifference", "ref_samples2"))
expect_equal(
altExp(tse, "Family")$time_diff,
altExp(tse, "Family_test")$timedifference)
altExp(tse, "Family")$timedifference)
expect_equal(
altExp(tse, "Family")$divergence,
altExp(tse, "Family_test")$timedivergence)
altExp(tse, "Family")$timedivergence)
})

# Test: getStepwiseDivergence output type