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Add wrapper for agglomerateByRank/mergeRows #389

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merged 6 commits into from
Jul 25, 2023
Merged

Add wrapper for agglomerateByRank/mergeRows #389

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c586ee8
Add wrapper for agglomerateByRank/mergeRows
Daenarys8 Jul 13, 2023
a80ce25
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Daenarys8 Jul 15, 2023
358eec4
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Daenarys8 Jul 15, 2023
c36d9ef
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Daenarys8 Jul 15, 2023
891d849
Merge branch 'master' into mergeby
antagomir Jul 21, 2023
a8aea71
Merge branch 'master' into mergeby
antagomir Jul 24, 2023
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18 changes: 18 additions & 0 deletions R/utils.R
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Expand Up @@ -283,3 +283,21 @@

taxa_tab
}

################################################################################
# internal wrappers for agglomerateByRank/mergeRows
.merge_features <- function(x, merge.by, ...) {
# Check if merge.by parameter belongs to taxonomyRanks
if (is.character(merge.by) && length(merge.by) < 2 && merge.by %in% taxonomyRanks(x)) {
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#Merge using agglomerateByRank
x <- agglomerateByRank(x, rank = merge.by, ...)
} else {
# Merge using mergeRows
x <- mergeRows(x, f = merge.by, ...)
}

return(x)

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}


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3 changes: 3 additions & 0 deletions tests/testthat/test-2merge.R
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Expand Up @@ -102,11 +102,14 @@ test_that("merge", {
merged <- mergeRows(tse, f=rowData(tse)$group2, mergeTree=TRUE)
merged2 <- mergeRows(tse, f = rowData(tse)$group2, mergeTree = FALSE)
merged3 <- mergeRows(esophagus, f = rowData(esophagus)$group2, mergeTree = TRUE)
merged4 <- .merge_features(tse, merge.by = rowData(tse)$group2)
merged5 <- mergeRows(tse, f = rowData(tse)$group2)
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expect_equal( rowLinks(merged)$whichTree,
rowLinks(merged2)$whichTree )
expect_false( all(rowLinks(merged) == rowLinks(merged2)) )
expect_equal(rowTree(tse), rowTree(merged2))
expect_equal(rowTree(merged), rowTree(merged3))
expect_equal(merged4, merged5)

# Both datasets have group variable
merged <- mergeRows(tse, f = rowData(tse)$group, mergeTree = TRUE)
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5 changes: 5 additions & 0 deletions tests/testthat/test-3agglomerate.R
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Expand Up @@ -51,6 +51,11 @@ test_that("agglomerate", {
expect_equal(rowData(actual)$Family,c("c",NA,"d","e","f","g","h",NA))
actual <- agglomerateByRank(xtse,"Phylum")
expect_equivalent(rowData(actual),rowData(actual_phylum))

#
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actual1 <- agglomerateByRank(xtse,"Family")
actual2 <- .merge_features(xtse, merge.by = "Family")
expect_equal(actual1, actual2)

# Only one rank available in the object -
# the same dimensionality is retained
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