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Signed-off-by: Daena Rys <[email protected]>
microbiome · May 22, 2024 · e5b3461 · e5b3461
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.13.16
+Version: 1.13.17
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "[email protected]",

diff --git a/tests/testthat/test-3agglomerate.R b/tests/testthat/test-3agglomerate.R
@@ -120,6 +120,40 @@ test_that("agglomerate", {
     not_uniq <- mergeFeaturesByRank(se, rank = "Species", make_unique = FALSE)
     expect_true( !any( duplicated(rownames(uniq)) ) )
     expect_true( any( duplicated(rownames(not_uniq)) ) )
+
+
+    data(GlobalPatterns, package="mia")
+    tse <- GlobalPatterns
+    tse <- transformAssay(tse, assay.type="counts", method="relabundance")
+    altExp(tse, "Family") <- agglomerateByRank(tse, rank="Family")
+    altExp(tse, "Family1") <- agglomerateByRank(tse, rank="Family", onRankOnly = TRUE)
+    altExp(tse, "Family2") <- agglomerateByRank(tse, rank="Family", onRankOnly = FALSE)
+    altExp(tse, "Family3") <- agglomerateByRank(tse, rank="Family", onRankOnly = TRUE, na.rm = TRUE)
+    altExp(tse, "Family4") <- agglomerateByRank(tse, rank="Family", onRankOnly = TRUE, na.rm = FALSE)
+    altExp(tse, "Family5") <- agglomerateByVariable(tse, f="Family", MARGIN = 'row')
+
+    # Other group is added by agglomerateByPrevalence function to collect features under threshold
+    actual <- agglomerateByPrevalence(tse, rank="Family", assay.type="relabundance", 
+                                         detection  = 0.5/100, prevalence  = 20/100)
+    actual0 <- agglomerateByPrevalence(altExp(tse, "Family"), assay.type="relabundance", 
+                                       detection  = 0.5/100, prevalence  = 20/100)
+    actual1 <- agglomerateByPrevalence(altExp(tse, "Family1"), assay.type="relabundance", 
+                                       detection  = 0.5/100, prevalence  = 20/100)
+    actual2 <- agglomerateByPrevalence(altExp(tse, "Family2"), assay.type="relabundance", 
+                                       detection  = 0.5/100, prevalence  = 20/100)
+    actual3 <- agglomerateByPrevalence(altExp(tse, "Family3"), assay.type="relabundance", 
+                                       detection  = 0.5/100, prevalence  = 20/100)
+    actual4 <- agglomerateByPrevalence(altExp(tse, "Family4"), assay.type="relabundance", 
+                                       detection  = 0.5/100, prevalence  = 20/100)
+    actual5 <- agglomerateByPrevalence(altExp(tse, "Family5"), assay.type="relabundance", 
+                                       detection  = 0.5/100, prevalence  = 20/100)
+
+    expect_equal(nrow(actual), nrow(actual0))
+    expect_equal(nrow(actual), nrow(actual1))
+    expect_equal(nrow(actual2), 27)
+    expect_equal(nrow(actual3), 20)
+    expect_equal(nrow(actual), nrow(actual4))
+    expect_equal(nrow(actual), nrow(actual5))
 })