up

NAMESPACE

@@ -426,6 +426,7 @@ importFrom(stats,na.omit)
 importFrom(stats,p.adjust)
 importFrom(stats,runif)
 importFrom(stats,sd)
+importFrom(stats,setNames)
 importFrom(stats,terms)
 importFrom(tibble,rownames_to_column)
 importFrom(tibble,tibble)

R/addAlpha.R

@@ -5,7 +5,7 @@
 #'
 #' @inheritParams calculateDMN
 #'
-#' @param x a \code{\link{SummarizedExperiment}} object.
+#' @param x a \code{\link[SummarizedExperiment]{SummarizedExperiment}} object.
 #'
 #' @param assay.type \code{Character scalar}. Specifies the name of assay
 #'   used in calculation. (Default: \code{"counts"})

R/addDivergence.R

@@ -1,11 +1,11 @@
 #' Estimate divergence
 #'
 #' Estimate divergence against a given reference sample.
-#' 
+#'
 #' @inheritParams addDissimilarity
-#' 
-#' @param x a \code{\link{SummarizedExperiment}} object.
-#'   
+#'
+#' @param x a \code{\link[SummarizedExperiment]{SummarizedExperiment}} object.
+#'
 #' @param assay_name Deprecated. Use \code{assay.type} instead.
 #'
 #' @param reference \code{Character scalar}. A column name from
@@ -20,53 +20,54 @@
 #'   values are used to calculate divergence instead of the assay. Can be
 #'   disabled with \code{NULL}. (Default: \code{NULL})
 #' }
-#' 
-#' @return \code{x} with additional \code{\link{colData}} named \code{name}
-#' 
+#'
+#' @return \code{x} with additional
+#' \code{\link[SummarizedExperiment:colData]{colData}} named \code{name}
+#'
 #' @details
 #'
 #' Microbiota divergence (heterogeneity / spread) within a given sample
 #' set can be quantified by the average sample dissimilarity or beta
 #' diversity with respect to a given reference sample.
 #'
 #' The calculation makes use of the function \code{getDissimilarity()}. The
-#' divergence 
-#' measure is sensitive to sample size. Subsampling or bootstrapping can be 
+#' divergence
+#' measure is sensitive to sample size. Subsampling or bootstrapping can be
 #' applied to equalize sample sizes between comparisons.
-#' 
+#'
 #' @seealso
 #' \itemize{
 #'   \item \code{\link[=addAlpha]{addAlpha}}
 #'   \item \code{\link[=addDissimilarity]{addDissimilarity}}
 #'   \item \code{\link[scater:plotColData]{plotColData}}
 #' }
-#' 
+#'
 #' @name addDivergence
 #' @export
-#' 
+#'
 #' @examples
 #' data(GlobalPatterns)
 #' tse <- GlobalPatterns
-#' 
+#'
 #' # By default, reference is median of all samples. The name of column where
-#' # results is "divergence" by default, but it can be specified. 
+#' # results is "divergence" by default, but it can be specified.
 #' tse <- addDivergence(tse)
-#' 
-#' # The method that are used to calculate distance in divergence and 
+#'
+#' # The method that are used to calculate distance in divergence and
 #' # reference can be specified. Here, euclidean distance is used. Reference is
 #' # the first sample. It is recommended # to add reference to colData.
 #' tse[["reference"]] <- rep(colnames(tse)[[1]], ncol(tse))
 #' tse <- addDivergence(
-#'     tse, name = "divergence_first_sample", 
+#'     tse, name = "divergence_first_sample",
 #'     reference = "reference",
 #'     method = "euclidean")
-#' 
+#'
 #' # Here we compare samples to global mean
 #' tse <- addDivergence(tse, name = "divergence_average", reference = "mean")
-#' 
+#'
 #' # All three divergence results are stored in colData.
 #' colData(tse)
-#' 
+#'
 NULL
 
 #' @rdname addDivergence
@@ -91,7 +92,7 @@ setMethod("addDivergence", signature = c(x="SummarizedExperiment"),
 #' @export
 setMethod("getDivergence", signature = c(x="SummarizedExperiment"),
     function(
-        x, assay.type = assay_name, assay_name = "counts", 
+        x, assay.type = assay_name, assay_name = "counts",
         reference = "median", method = "bray", ...){
         ################### Input check ###############
         # Get altExp if user has specified
@@ -182,7 +183,7 @@ setMethod("getDivergence", signature = c(x="SummarizedExperiment"),
     } else{
         mat <- t(reducedDim(x, dimred))
     }
-    
+
     # If reference type is median or mean, calculate it
     if( ref_type %in% c("median", "mean") ){
         reference <- apply(mat, 1, ref_type)
@@ -231,7 +232,7 @@ setMethod("getDivergence", signature = c(x="SummarizedExperiment"),
         temp <- temp[[1]]
         return(temp)
     })
-    # Add values to data.frame that holds sample pairs 
+    # Add values to data.frame that holds sample pairs
     temp <- unlist(temp)
     reference[["value"]] <- temp
     return(reference)

R/cluster.R

@@ -1,42 +1,41 @@
 #' Clustering wrapper
 #'
-#' This function returns a \code{SummarizedExperiment} with clustering 
+#' This function returns a \code{SummarizedExperiment} with clustering
 #'   information in its colData or rowData
 #'
 #' @param x A
 #' \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
 #' object.
-#' 
+#'
 #' @param by \code{Character scalar}. Determines if association is calculated
 #'   row-wise / for features ('rows') or column-wise / for samples ('cols').
 #'   Must be \code{'rows'} or \code{'cols'}.
-#'   
+#'
 #' @param MARGIN Deprecated. Use \code{by} instead.
-#'   
-#' @param clust.col \code{Character scalar}. Indicates the name of the 
+#'
+#' @param clust.col \code{Character scalar}. Indicates the name of the
 #'   \code{rowData} (or \code{colData}) where the data will be stored.
 #'   (Default: \code{"clusters"})
-#'   
+#'
 #' @param ... Additional parameters to use altExps for example
 #' @inheritParams bluster::clusterRows
 #' @inheritParams runDMN
 #' @inheritParams transformAssay
-#'   
-#'   
+#'
+#'
 #' @details
-#' This is a wrapper for the \code{clusterRows} function from the 
-#' \link[https://bioconductor.org/packages/release/bioc/html/bluster.html]{bluster} 
-#' package.
+#' This is a wrapper for the \code{clusterRows} function from the
+#' \link[bluster]{bluster} package.
 #'
 #' When setting \code{full = TRUE}, the clustering information will be stored in
 #' the metadata of the object.
-#' 
+#'
 #' By default, clustering is done on the features.
 #'
 #' @return
 #' \code{addCluster} returns an object of the same type as the \code{x}
 #' parameter with clustering information named \code{clusters} stored in
-#' \code{colData} or \code{rowData}. 
+#' \code{colData} or \code{rowData}.
 #'
 #' @name addCluster
 #' @export
@@ -48,24 +47,24 @@
 #'
 #' # Cluster on rows using Kmeans
 #' tse <- addCluster(tse, KmeansParam(centers = 3))
-#' 
+#'
 #' # Clustering done on the samples using Hclust
-#' tse <- addCluster(tse, 
-#'                by = "samples", 
+#' tse <- addCluster(tse,
+#'                by = "samples",
 #'                HclustParam(metric = "bray", dist.fun = vegan::vegdist))
-#' 
+#'
 #' # Getting the clusters
 #' colData(tse)$clusters
-#' 
+#'
 NULL
 
 #' @rdname addCluster
 #' @export
 #' @importFrom bluster clusterRows
 setMethod("addCluster", signature = c(x = "SummarizedExperiment"),
     function(
-            x, BLUSPARAM, assay.type = assay_name, 
-            assay_name = "counts", by = MARGIN, MARGIN = "rows", full = FALSE, 
+            x, BLUSPARAM, assay.type = assay_name,
+            assay_name = "counts", by = MARGIN, MARGIN = "rows", full = FALSE,
             name = "clusters", clust.col = "clusters", ...) {
         .require_package("bluster")
         # Checking parameters

R/getPrevalence.R

@@ -1,7 +1,7 @@
 #' Calculation prevalence information for features across samples
 #'
 #' These functions calculate the population prevalence for taxonomic ranks in a
-#' \code{\link{SummarizedExperiment-class}} object.
+#' \code{\link[SummarizedExperiment]{SummarizedExperiment}} object.
 #'
 #' @inheritParams getDissimilarity
 #'

R/mergeSEs.R

@@ -3,8 +3,9 @@
 #' @inheritParams rarefyAssay
 #' @inheritParams getDominant
 #'
-#' @param y a \code{\link{SummarizedExperiment}} object when \code{x} is a
-#' \code{\link{SummarizedExperiment}} object. Disabled when \code{x} is a list.
+#' @param y a \code{\link[SummarizedExperiment]{SummarizedExperiment}} object
+#' when \code{x} is a \code{\link[SummarizedExperiment]{SummarizedExperiment}}
+#' object. Disabled when \code{x} is a list.
 #'
 #' @param join \code{Character scalar}. A value for selecting the joining
 #' method. Must be 'full', 'inner', 'left', or 'right'. 'left' and 'right' are

R/runDPCoA.R

@@ -8,9 +8,10 @@
 #' @inheritParams getDissimilarity
 #'
 #' @details
-#'   For \code{addDPCoA} a \linkS4class{TreeSummarizedExperiment} containing the
-#'   expression values as well as a \code{rowTree} to calculate \code{y} using
-#'   \code{\link[ape:cophenetic.phylo]{cophenetic.phylo}}.
+#' For \code{addDPCoA} a
+#' \code{\link[TreeSummarizedExperiment]{TreeSummarizedExperiment}} containing
+#' the expression values as well as a \code{rowTree} to calculate \code{y} using
+#' \code{\link[ape:cophenetic.phylo]{cophenetic.phylo}}.
 #'
 #' @param y a \code{dist} or a symmetric \code{matrix} compatible with
 #'   \code{ade4:dpcoa}
@@ -26,24 +27,24 @@
 #' to use for dimensionality reduction. This can be a character vector of row
 #' names, an integer vector of row indices or a logical vector.
 #' (Default: \code{NULL})
-#' 
+#'
 #' @param subset_row Deprecated. Use \code{subset.row} instead.
 #'
 #' @param scale \code{Logical scalar}. Should the expression values be
 #' standardized? (Default: \code{FALSE})
-#' 
-#' @param name \code{Character scalar}. A name for the column of the 
+#'
+#' @param name \code{Character scalar}. A name for the column of the
 #'   \code{colData} where results will be stored. (Default: \code{"DPCoA"})
-#' 
+#'
 #' @param altexp \code{Character scalar} or \code{integer scalar}. Specifies an
 #'   alternative experiment containing the input data. (Default: \code{NULL})
-#'   
+#'
 #' @param exprs_values Deprecated. Use \code{assay.type} instead.
-#' 
+#'
 #' @param tree.name \code{Character scalar}. Specifies the name of the
-#'   tree to be included in the phyloseq object that is created, 
+#'   tree to be included in the phyloseq object that is created,
 #'   (Default: \code{"phylo"})
-#'   
+#'
 #' @param tree_name Deprecated. Use \code{tree.name} instead.
 #'
 #' @param ... Currently not used.
@@ -142,7 +143,7 @@ setMethod("getDPCoA", c("ANY","ANY"), .calculate_dpcoa)
 #' @importFrom ape cophenetic.phylo
 #' @rdname runDPCoA
 setMethod("getDPCoA", signature = c("TreeSummarizedExperiment","missing"),
-    function(x, ..., assay.type = assay_name, assay_name = exprs_values, 
+    function(x, ..., assay.type = assay_name, assay_name = exprs_values,
         exprs_values = "counts", tree.name = tree_name, tree_name = "phylo")
     {
         .require_package("ade4")

R/runNMDS.R

@@ -5,15 +5,16 @@
 #'
 #' @inheritParams getDominant
 #' @inheritParams runDPCoA
-#' 
+#'
 #' @details
-#'   For \code{addNMDS} a \linkS4class{SingleCellExperiment}
+#' For \code{addNMDS} a
+#' \code{\link[TreeSummarizedExperiment]{TreeSummarizedExperiment}}
 #'
 #' @param keep.dist \code{Logical scalar}. Indicates whether the \code{dist}
 #' object calculated by \code{FUN} should be stored as \sQuote{dist} attribute
-#' of the matrix returned/stored by \code{getNMDS}/ \code{addNMDS}. (Default: 
+#' of the matrix returned/stored by \code{getNMDS}/ \code{addNMDS}. (Default:
 #' \code{FALSE})
-#' 
+#'
 #' @param keep_dist Deprecated. Use \code{keep.dist} instead.
 #'
 #' @param FUN \code{Function} or \code{Character scalar}. A value with a
@@ -23,10 +24,10 @@
 #'   implementation, either \dQuote{isoMDS} for
 #'   \code{\link[MASS:isoMDS]{MASS::isoMDS}} or \dQuote{monoMDS} for
 #'   \code{\link[vegan:monoMDS]{vegan::monoMDS}}
-#'   
+#'
 #' @param nmdsFUN Deprecated. Use \code{nmds.fun} instead.
-#' 
-#' @param name \code{Character scalar}. A name for the column of the 
+#'
+#' @param name \code{Character scalar}. A name for the column of the
 #' \code{colData} where results will be stored. (Default: \code{"NMDS"})
 #'
 #' @param ... additional arguments to pass to \code{FUN} and
@@ -37,9 +38,9 @@
 #'
 #' @param ndimred \code{integer vector}. Specifies the dimensions to use if
 #'   dimred is specified.
-#' 
+#'
 #' @param n_dimred Deprecated. Use \code{ndimred} instead.
-#' 
+#'
 #' @param exprs_values Deprecated. Use \code{assay.type} instead.
 #'
 #' @return For \code{getNMDS}, a matrix is returned containing the MDS
@@ -125,10 +126,10 @@ NULL
 #' @importFrom stats cmdscale
 #' @importFrom vegan vegdist monoMDS
 .calculate_nmds <- function(
-        x, FUN = vegdist, 
+        x, FUN = vegdist,
         nmds.fun = nmdsFUN,
         nmdsFUN = c("isoMDS","monoMDS"),
-        ncomponents = 2, ntop = 500, subset.row = subset_row, 
+        ncomponents = 2, ntop = 500, subset.row = subset_row,
         subset_row = NULL, scale = FALSE, transposed = FALSE,
         keep.dist = keep_dist,
         keep_dist = FALSE, ...){
@@ -162,7 +163,7 @@ setMethod("getNMDS", "ANY", .calculate_nmds)
 #' @importFrom SummarizedExperiment assay
 #' @export
 setMethod("getNMDS", "SummarizedExperiment",
-    function(x, ..., assay.type = assay_name, assay_name = exprs_values, 
+    function(x, ..., assay.type = assay_name, assay_name = exprs_values,
         exprs_values = "counts", FUN = vegdist) {
         .calculate_nmds(assay(x, assay.type), FUN = FUN, ...)
     }
@@ -171,8 +172,8 @@ setMethod("getNMDS", "SummarizedExperiment",
 #' @rdname runNMDS
 #' @export
 setMethod("getNMDS", "SingleCellExperiment",
-    function(x, ..., assay.type = assay_name, assay_name = exprs_values, 
-            exprs_values = "counts", dimred = NULL, ndimred = n_dimred, 
+    function(x, ..., assay.type = assay_name, assay_name = exprs_values,
+            exprs_values = "counts", dimred = NULL, ndimred = n_dimred,
             n_dimred = NULL, FUN = vegdist){
         mat <- .get_mat_from_sce(
             x, exprs_values = assay.type, dimred = dimred, n_dimred = ndimred)