microbiome#392 Up

Signed-off-by: Daenarys8 <rysdaena8@gmail.com>
Daenarys8 · Jul 25, 2023 · dc8f6c1 · dc8f6c1
1 parent 31307f8
commit dc8f6c1
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/R/agglomerate.R b/R/agglomerate.R
@@ -224,7 +224,7 @@ setMethod("mergeFeaturesByRank", signature = c(x = "SummarizedExperiment"),
           function(x, rank = taxonomyRanks(x)[1], onRankOnly = FALSE, na.rm = FALSE,
                    empty.fields = c(NA, "", " ", "\t", "-", "_"), ...){
               .Deprecated(old="agglomerateByRank", new="mergeFeaturesByRank", "Now agglomerateByRank is deprecated. Use mergeFeaturesByRank instead.")
-              x <- agglomerateByRank(x)
+              x <- agglomerateByRank(x, ...)
               x
           }
 )
@@ -256,7 +256,7 @@ setMethod("agglomerateByRank", signature = c(x = "SingleCellExperiment"),
 setMethod("mergeFeaturesByRank", signature = c(x = "SingleCellExperiment"),
           function(x, ..., altexp = NULL, strip_altexp = TRUE){
               .Deprecated(old="agglomerateByRank", new="mergeFeaturesByRank", "Now agglomerateByRank is deprecated. Use mergeFeaturesByRank instead.")
-              x <- agglomerateByRank(x)
+              x <- agglomerateByRank(x, ...)
               x
           }
 )
@@ -301,7 +301,7 @@ setMethod("agglomerateByRank", signature = c(x = "TreeSummarizedExperiment"),
 setMethod("mergeFeaturesByRank", signature = c(x = "TreeSummarizedExperiment"),
           function(x, ..., agglomerateTree = FALSE){
               .Deprecated(old="agglomerateByRank", new="mergeFeaturesByRank", "Now agglomerateByRank is deprecated. Use mergeFeaturesByRank instead.")
-              x <- agglomerateByRank(x)
+              x <- agglomerateByRank(x,...)
               x
           }
 )

diff --git a/tests/testthat/test-2merge.R b/tests/testthat/test-2merge.R
@@ -110,6 +110,7 @@ test_that("merge", {
     expect_equal(rowTree(tse), rowTree(merged2))
     expect_equal(rowTree(merged), rowTree(merged3))
     expect_equal(merged4, merged5)
+    expect_equal(mergeRows(tse, f=rowData(tse)$group2), mergeFeatures(tse, f=rowData(tse)$group2))
 
     # Both datasets have group variable
     merged <- mergeRows(tse, f = rowData(tse)$group, mergeTree = TRUE)

diff --git a/tests/testthat/test-3agglomerate.R b/tests/testthat/test-3agglomerate.R
@@ -55,6 +55,7 @@ test_that("agglomerate", {
     actual1 <- agglomerateByRank(xtse,"Family")
     actual2 <- .merge_features(xtse, merge.by = "Family")
     expect_equal(actual1, actual2)
+    expect_equal(agglomerateByRank(xtse,"Family"), mergeFeaturesByRank(xtse,"Family"))
 
     # Only one rank available in the object -
     # the same dimensionality is retained