up

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.15.16
+Version: 1.15.17
 Authors@R:
     c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"),
              email = "tuomas.v.borman@utu.fi",

NEWS

@@ -165,3 +165,4 @@ Changes in version 1.15.x
 + Add functions for classifying taxa based on their average abundance
 + Add addPrevalence function that adds results of getPrevalence to rowData
 + Added support for dimred to getCrossAssociation
++ Add wrapper for PhILR transformation

R/transformCounts.R

@@ -48,6 +48,12 @@
 #'   difference threshold and determines the first point where the relative
 #'   change in  differences between consecutive quantiles exceeds this
 #'   threshold. (Default: \code{0.1}).
+#'   \item \code{tree}: \code{phylo}. Phylogeny used in PhILR transformation.
+#'   If \code{NULL}, the tree is retrieved from \code{x}.
+#'   (Default: \code{NULL}).
+#'   \item \code{node.labels}: \code{Character vector}. Linkages between
+#'   \code{tree} and \code{x}. Used in PhILR transformation.
+#'   (Default: \code{NULL}).
 #' }
 #' @details
 #'
@@ -691,7 +697,7 @@ setMethod("transformAssay", signature = c(x = "SingleCellExperiment"),
     # Check that node.label is NULL or it specifies links between rownames and
     # node labs
     if( !( is.null(node.label) ||
-           is.character(node.label) && length(node.label) == n_FUN(x) ) ){
+            is.character(node.label) && length(node.label) == n_FUN(x) ) ){
         stop("'node.label' must be NULL or a vector specifying links between ",
             "features and node labs of 'tree'.", call. = FALSE)
     }

tests/testthat/test-5transformCounts.R

@@ -406,6 +406,40 @@ test_that("transformAssay", {
         test <- transformAssay(tse, method = "relabundance", altexp = altExpNames(tse))
         test <- altExp(test, "Genus")
         expect_equal(assay(test, "relabundance"), assay(ref, "relabundance"))
+
+        # Check that philt transformation works
+        skip_if_not(require("philr", quietly = TRUE))
+        data("GlobalPatterns")
+        tse <- GlobalPatterns
+        # The default is columns, and colTree is not present
+        expect_error(transformAssay(tse, method = "philr", pseudocount = 1))
+        # There must not be 0s
+        expect_error(transformAssay(tse, method = "philr", MARGIN = 1))
+        # Give error if tree does not match
+        data("esophagus")
+        expect_error(transformAssay(
+            tse, method = "philr", MARGIN = 1, pseudocount = 1,
+            tree = rowTree(esophagus)))
+        tse <- agglomerateByRank(tse, rank = "Phylum")
+        tse <- transformAssay(
+            tse, method = "philr", pseudocount = 1, MARGIN = 1L,
+            part.weights = "enorm.x.gm.counts",
+            ilr.weights = "blw.sqrt") |>
+            expect_message()
+        expect_true( "philr" %in% altExpNames(tse) )
+        #
+        test <- philr::philr(
+            t(assay(tse, "counts")+1),
+            rowTree(tse),
+            part.weights = "enorm.x.gm.counts",
+            ilr.weights = "blw.sqrt"
+            ) |> t()
+        expect_equal(
+            assay(altExp(tse, "philr"), "philr"),
+            test,
+            check.attributes = FALSE
+        )
+        expect_equal(colData(tse), colData(altExp(tse, "philr")))
     }
 
     # TSE object