From f08da410ac87ce3cba7630ef62a87b0014b90052 Mon Sep 17 00:00:00 2001
From: thpralas <theotime.pralas@centrale-med.fr>
Date: Thu, 22 Feb 2024 11:13:45 +0200
Subject: [PATCH] add new man page 'get-values' (#474)

---
 R/taxonomy.R            | 27 ++++++++++++++++++---------
 man/get-values.Rd       | 30 ++++++++++++++++++++++++++++++
 man/taxonomy-methods.Rd | 13 ++-----------
 3 files changed, 50 insertions(+), 20 deletions(-)
 create mode 100644 man/get-values.Rd

diff --git a/R/taxonomy.R b/R/taxonomy.R
index 7852f3b45..09f1e9a31 100644
--- a/R/taxonomy.R
+++ b/R/taxonomy.R
@@ -18,15 +18,8 @@
 #'   the lowest taxonomic information possible. If data from different levels,
 #'   is to be mixed, the taxonomic level is prepended by default.
 #'
-#' \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}}.
@@ -383,13 +376,29 @@ setMethod("getTaxonomyLabels", signature = c(x = "SummarizedExperiment"),
     ans
 }
 
-#' @rdname taxonomy-methods
+#' Functions for accessing data  
+#' 
+#' These functions find and return data present in a 
+#' \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
+#' object.
+#' 
+#' \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
+#' 
+#' @name get-values
+
+#' @rdname get-values
 setGeneric("getHierarchyTree",
            signature = "x",
            function(x, ...)
                standardGeneric("getHierarchyTree"))
 
-#' @rdname taxonomy-methods
+#' @rdname get-values
 #' @export
 setMethod("getHierarchyTree", signature = c(x = "SummarizedExperiment"),
     function(x){
diff --git a/man/get-values.Rd b/man/get-values.Rd
new file mode 100644
index 000000000..ef6ae5dcb
--- /dev/null
+++ b/man/get-values.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/taxonomy.R
+\name{get-values}
+\alias{get-values}
+\alias{getHierarchyTree,SummarizedExperiment-method}
+\title{Functions for accessing data}
+\usage{
+getHierarchyTree(x, ...)
+
+\S4method{getHierarchyTree}{SummarizedExperiment}(x)
+}
+\arguments{
+\item{x}{a
+\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
+object}
+
+\item{...}{optional arguments not used currently.}
+}
+\description{
+These functions find and return data present in a
+\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
+object.
+}
+\details{
+\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.
+}
diff --git a/man/taxonomy-methods.Rd b/man/taxonomy-methods.Rd
index 4cd296cbf..ab24f1b84 100644
--- a/man/taxonomy-methods.Rd
+++ b/man/taxonomy-methods.Rd
@@ -12,7 +12,6 @@
 \alias{checkTaxonomy,SummarizedExperiment-method}
 \alias{getTaxonomyLabels}
 \alias{getTaxonomyLabels,SummarizedExperiment-method}
-\alias{getHierarchyTree,SummarizedExperiment-method}
 \alias{addTree}
 \alias{addTree,SummarizedExperiment-method}
 \alias{mapTaxonomy}
@@ -57,8 +56,6 @@ getTaxonomyLabels(x, ...)
   ...
 )
 
-\S4method{getHierarchyTree}{SummarizedExperiment}(x)
-
 addTree(x, ...)
 
 \S4method{addTree}{SummarizedExperiment}(x)
@@ -75,11 +72,11 @@ IdTaxaToDataFrame(from)
 object}
 
 \item{rank}{a single character defining a taxonomic rank. Must be a value of
-\code{taxonomyRanks()} function.}
+\code{taxonomyRanks()} function}
 
 \item{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}
 
 \item{...}{optional arguments not used currently.}
 
@@ -143,12 +140,6 @@ creation.
 the lowest taxonomic information possible. If data from different levels,
 is to be mixed, the taxonomic level is prepended by default.
 
-\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.