Deprecate functions taxonomyTree and addTaxonomyTree

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.11.3
+Version: 1.11.4
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "[email protected]",
@@ -84,5 +84,5 @@ Suggests:
 URL: https://github.com/microbiome/mia
 BugReports: https://github.com/microbiome/mia/issues
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr

NAMESPACE

@@ -103,6 +103,7 @@ exportMethods(addNotContaminantQC)
 exportMethods(addPerSampleDominantFeatures)
 exportMethods(addPerSampleDominantTaxa)
 exportMethods(addTaxonomyTree)
+exportMethods(addTree)
 exportMethods(agglomerateByPrevalence)
 exportMethods(agglomerateByRank)
 exportMethods(bestDMNFit)
@@ -130,6 +131,7 @@ exportMethods(getBestDMNFit)
 exportMethods(getDMN)
 exportMethods(getExperimentCrossAssociation)
 exportMethods(getExperimentCrossCorrelation)
+exportMethods(getHierarchyTree)
 exportMethods(getPrevalence)
 exportMethods(getPrevalentAbundance)
 exportMethods(getPrevalentFeatures)

NEWS

@@ -97,3 +97,4 @@ Changes in version 1.9.x
 Changes in version 1.11.x
 + loadFromMetaphlan: support strain rank
 + agglomerateByRank: agglomerate tree fix
++ Deprecate taxonomyTree, addTaxonomyTree

R/deprecate.R

@@ -0,0 +1,40 @@
+#' These functions will be deprecated. Please use other functions instead.
+#' 
+#' @param x a \code{\link{SummarizedExperiment}} object -
+#' 
+#' @param ... -
+#' 
+#' @name deprecate
+NULL
+
+#' @rdname deprecate
+setGeneric("addTaxonomyTree",
+           signature = "x",
+           function(x, ...)
+               standardGeneric("addTaxonomyTree"))
+
+#' @rdname deprecate
+#' @export
+setMethod("addTaxonomyTree", signature = c(x = "SummarizedExperiment"),
+          function(x){
+              .Deprecated(msg = paste0("'addTaxonomyTree' is deprecated.\n",
+                                       "Use 'addTree' instead."))
+              addTree(x)
+          }
+)
+
+#' @rdname deprecate
+setGeneric("taxonomyTree",
+           signature = "x",
+           function(x, ...)
+               standardGeneric("taxonomyTree"))
+
+#' @rdname deprecate
+#' @export
+setMethod("taxonomyTree", signature = c(x = "SummarizedExperiment"),
+          function(x){
+              .Deprecated(msg = paste0("'taxonomyTree' is deprecated.\n",
+                                       "Use 'getHierarchyTree' instead."))
+              getHierarchyTree(x)
+          }
+)

R/splitOn.R

@@ -290,10 +290,10 @@ setMethod("splitOn", signature = c(x = "TreeSummarizedExperiment"),
         if( update_rowTree ){
             # If the returned value is a list, go through all of them
             if( class(x) == "SimpleList" ){
-                x <- SimpleList(lapply(x, addTaxonomyTree))
+                x <- SimpleList(lapply(x, addTree))
             } else {
                 # Otherwise, the returned value is TreeSE
-                x <- addTaxonomyTree(x)
+                x <- addTree(x)
             }
         }
         x
@@ -386,7 +386,7 @@ setGeneric("unsplitOn",
     if( class_x == "TreeSummarizedExperiment" ){
         # Update or add old tree from the first element of list
         if( update_rowTree ){
-            ans <- addTaxonomyTree(ans)
+            ans <- addTree(ans)
         } else{
             rowTree(ans) <- rowTree(ses[[1L]])
         }

R/taxonomy.R

@@ -18,12 +18,16 @@
 #'   the lowest taxonomic information possible. If data from different levels,
 #'   is to be mixed, the taxonomic level is prepended by default.
 #'
-#' \code{taxonomyTree} generates a \code{phylo} tree object from the available
+#' \code{getHierarchyTree} generates a hierarchy tree from the available
 #'   taxonomic information. Internally it uses
 #'   \code{\link[TreeSummarizedExperiment:toTree]{toTree}} and
 #'   \code{\link[TreeSummarizedExperiment:resolveLoop]{resolveLoop}} to sanitize
 #'   data if needed.
 #'
+#' \code{addTree} calculates hierarchy tree from the available taxonomic
+#'   information and add it to rowTree.
+#'   
+#'
 #' \code{IdTaxaToDataFrame} extracts taxonomic results from results of
 #'   \code{\link[DECIPHER:IdTaxa]{IdTaxa}}.
 #'
@@ -40,11 +44,11 @@
 #'   object
 #'
 #' @param rank a single character defining a taxonomic rank. Must be a value of
-#'   \code{taxonomyRanks()} function.
+#'   \code{taxonomyRanks()} function
 #'
 #' @param empty.fields a \code{character} value defining, which values should be
 #'   regarded as empty. (Default: \code{c(NA, "", " ", "\t")}). They will be
-#'   removed if \code{na.rm = TRUE} before agglomeration.
+#'   removed if \code{na.rm = TRUE} before agglomeration
 #'
 #' @param with_rank \code{TRUE} or \code{FALSE}: Should the level be add as a
 #'   suffix? For example: "Phylum:Crenarchaeota" (default:
@@ -126,7 +130,7 @@
 #' # adding a rowTree() based on the available taxonomic information. Please
 #' # note that any tree already stored in rowTree() will be overwritten.
 #' x <- GlobalPatterns
-#' x <- addTaxonomyTree(x)
+#' x <- addTree(x)
 #' x
 NULL
 
@@ -380,14 +384,14 @@ setMethod("getTaxonomyLabels", signature = c(x = "SummarizedExperiment"),
 }
 
 #' @rdname taxonomy-methods
-setGeneric("taxonomyTree",
+setGeneric("getHierarchyTree",
            signature = "x",
            function(x, ...)
-               standardGeneric("taxonomyTree"))
+               standardGeneric("getHierarchyTree"))
 
 #' @rdname taxonomy-methods
 #' @export
-setMethod("taxonomyTree", signature = c(x = "SummarizedExperiment"),
+setMethod("getHierarchyTree", signature = c(x = "SummarizedExperiment"),
     function(x){
         # Input check
         # If there is no rowData it is not possible to create rowTree
@@ -422,17 +426,17 @@ setMethod("taxonomyTree", signature = c(x = "SummarizedExperiment"),
 )
 
 #' @rdname taxonomy-methods
-setGeneric("addTaxonomyTree",
+setGeneric("addTree",
            signature = "x",
            function(x, ...)
-               standardGeneric("addTaxonomyTree"))
+               standardGeneric("addTree"))
 
 #' @rdname taxonomy-methods
 #' @export
-setMethod("addTaxonomyTree", signature = c(x = "SummarizedExperiment"),
+setMethod("addTree", signature = c(x = "SummarizedExperiment"),
     function(x){
         #
-        tree <- taxonomyTree(x)
+        tree <- getHierarchyTree(x)
         x <- as(x,"TreeSummarizedExperiment")
         rownames(x) <- getTaxonomyLabels(x, with_rank = TRUE,
                                          resolve_loops = TRUE,

tests/testthat/test-2taxonomy.R

@@ -69,9 +69,9 @@ test_that("taxonomy", {
                  c("Family:j","Phylum:a","Family:k","Family:l","Family:m",
                    "Family:n","Family:o_1","Phylum:c","Family:o_2"))
 
-    # addTaxonomyTree
+    # addTree
     data(GlobalPatterns, package="mia")
-    expect_warning(GlobalPatterns <- addTaxonomyTree(GlobalPatterns))
+    expect_warning(GlobalPatterns <- addTree(GlobalPatterns))
     expect_equal(dim(GlobalPatterns),c(19216,26))
     expect_equal(rowTree(GlobalPatterns)$Nnode, 1089)
     expect_equal(length(rowTree(GlobalPatterns)$tip.label), 1645)