Merge branch 'devel' into mediation

R/taxonomy.R

@@ -127,7 +127,6 @@
 #' 
 #' # getTaxonomyRanks is to get/check if the taxonomic ranks is set to "TAXA1"
 #' getTaxonomyRanks()
-#' 
 NULL
 
 #' @rdname taxonomy-methods
@@ -414,16 +413,23 @@ setMethod("getTaxonomyLabels", signature = c(x = "SummarizedExperiment"),
 #' \code{\link[TreeSummarizedExperiment:TreeSummarizedExperiment-class]{SummarizedExperiment}}
 #' object and add this hierarchy tree into the \code{rowTree}.
 #' 
-#' \code{addHierarchyTree} calculates hierarchy tree from the available taxonomic
-#'   information and add it to \code{rowTree}.
+#' @inheritParams taxonomy-methods
+#' 
+#' @details
+#' 
+#' \code{addHierarchyTree} calculates a hierarchy tree from the available 
+#'   taxonomic information and add it to \code{rowTree}.
 #'   
 #' \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.
-#' 
-#' @inheritParams taxonomy-methods
+#'   
+#' Please note that a hierarchy tree is not an actual phylogenetic tree.
+#' A phylogenetic tree represents evolutionary relationships among features.
+#' On the other hand, a hierarchy tree organizes species into a hierarchical 
+#' structure based on their taxonomic ranks. 
 #' 
 #' @return
 #' \itemize{
@@ -437,16 +443,15 @@ setMethod("getTaxonomyLabels", signature = c(x = "SummarizedExperiment"),
 #' @name hierarchy-tree
 #' 
 #' @examples
-#' # Generating a hierarchy tree based on available taxonomic information.
+#' # Generate a tree based on taxonomic rank hierarchy (a hierarchy tree).
 #' data(GlobalPatterns)
 #' tse <- GlobalPatterns
 #' getHierarchyTree(tse)
 #' 
-#' # Adding a hierarchy tree based on the available taxonomic information. 
+#' # Add a hierarchy tree to a TreeSummarizedExperiment.
 #' # Please note that any tree already stored in rowTree() will be overwritten.
 #' tse <- addHierarchyTree(tse)
 #' tse
-#' 
 NULL
 
 #' @rdname hierarchy-tree