rename calculateDPCoA, calculateNMDS, calculateRDA, calculateCCA (mic…

…robiome#524)

Co-authored-by: Leo Lahti <[email protected]>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.13.18
+Version: 1.13.19
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "[email protected]",

NAMESPACE

@@ -5,9 +5,11 @@ export(TAXONOMY_RANKS)
 export(ZTransform)
 export(addCluster)
 export(addContaminantQC)
+export(addDPCoA)
 export(addDivergence)
 export(addDominant)
 export(addMediation)
+export(addNMDS)
 export(addNotContaminantQC)
 export(addPerSampleDominantFeatures)
 export(addPerSampleDominantTaxa)
@@ -17,12 +19,14 @@ export(agglomerateByRank)
 export(agglomerateByRanks)
 export(agglomerateByVariable)
 export(bestDMNFit)
+export(calculateCCA)
 export(calculateDMN)
 export(calculateDMNgroup)
 export(calculateDPCoA)
 export(calculateJSD)
 export(calculateNMDS)
 export(calculateOverlap)
+export(calculateRDA)
 export(calculateUnifrac)
 export(cluster)
 export(countDominantFeatures)
@@ -37,10 +41,12 @@ export(full_join)
 export(getBestDMNFit)
 export(getCrossAssociation)
 export(getDMN)
+export(getDPCoA)
 export(getDominant)
 export(getExperimentCrossAssociation)
 export(getExperimentCrossCorrelation)
 export(getMediation)
+export(getNMDS)
 export(getPrevalence)
 export(getPrevalent)
 export(getPrevalentAbundance)
@@ -95,11 +101,13 @@ export(readQZA)
 export(relAbundanceCounts)
 export(relabundance)
 export(right_join)
+export(runCCA)
 export(runDMN)
 export(runDPCoA)
 export(runJSD)
 export(runNMDS)
 export(runOverlap)
+export(runRDA)
 export(runUnifrac)
 export(setTaxonomyRanks)
 export(splitByRanks)
@@ -126,6 +134,7 @@ export(unsplitByRanks)
 export(unsplitOn)
 exportMethods("relabundance<-")
 exportMethods(ZTransform)
+exportMethods(addCCA)
 exportMethods(addCluster)
 exportMethods(addContaminantQC)
 exportMethods(addDivergence)
@@ -135,20 +144,17 @@ exportMethods(addMediation)
 exportMethods(addNotContaminantQC)
 exportMethods(addPerSampleDominantFeatures)
 exportMethods(addPerSampleDominantTaxa)
+exportMethods(addRDA)
 exportMethods(addTaxonomyTree)
 exportMethods(agglomerateByPrevalence)
 exportMethods(agglomerateByRank)
 exportMethods(agglomerateByRanks)
 exportMethods(agglomerateByVariable)
 exportMethods(bestDMNFit)
-exportMethods(calculateCCA)
 exportMethods(calculateDMN)
 exportMethods(calculateDMNgroup)
-exportMethods(calculateDPCoA)
 exportMethods(calculateJSD)
-exportMethods(calculateNMDS)
 exportMethods(calculateOverlap)
-exportMethods(calculateRDA)
 exportMethods(calculateUnifrac)
 exportMethods(checkTaxonomy)
 exportMethods(cluster)
@@ -162,18 +168,22 @@ exportMethods(estimateFaith)
 exportMethods(estimateRichness)
 exportMethods(full_join)
 exportMethods(getBestDMNFit)
+exportMethods(getCCA)
 exportMethods(getCrossAssociation)
 exportMethods(getDMN)
+exportMethods(getDPCoA)
 exportMethods(getDominant)
 exportMethods(getExperimentCrossAssociation)
 exportMethods(getExperimentCrossCorrelation)
 exportMethods(getHierarchyTree)
 exportMethods(getMediation)
+exportMethods(getNMDS)
 exportMethods(getPrevalence)
 exportMethods(getPrevalent)
 exportMethods(getPrevalentAbundance)
 exportMethods(getPrevalentFeatures)
 exportMethods(getPrevalentTaxa)
+exportMethods(getRDA)
 exportMethods(getRare)
 exportMethods(getRareFeatures)
 exportMethods(getRareTaxa)
@@ -208,9 +218,7 @@ exportMethods(rarefyAssay)
 exportMethods(relAbundanceCounts)
 exportMethods(relabundance)
 exportMethods(right_join)
-exportMethods(runCCA)
 exportMethods(runOverlap)
-exportMethods(runRDA)
 exportMethods(splitOn)
 exportMethods(subsampleCounts)
 exportMethods(subsetByPrevalent)

NEWS

@@ -109,7 +109,7 @@ Changes in version 1.11.x
 + rename importers loadFromBiom, loadFromQIIME2, readQZA, loadFromMothur, loadFromMetaphlan, loadFromHumann
 + fix typo in loadFromBiom definition (deprecate file)
 + deprecate subsetSamples, subsetFeatures and subsetTaxa
-+ deprecate plotNMDS after moving it to miaViz package
++ deprecate plotNMDS after moving it to miaViz 
 + rename estimateDivergence to addDivergence
 + Add details to documentation of function agglomerateByPrevalence
 
@@ -134,3 +134,5 @@ Changes in version 1.13.x
 + Explain that rarefyAssay returns a new SummarizedExperiment object that 
   includes the newly added subsampled assay.
 + Fix bug in mergeFeaturesByPrevalence
++ new aliases calculateDPCoA to getDPCoA, calculateNMDS to getNMDS, calculateRDA to getRDA, 
+calculateCCA to getCCA

R/deprecate.R

@@ -3,7 +3,7 @@
 #' @param x A
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
 #'   object.
-#'   
+#'    
 #' @param ... Additional parameters. See dedicated function.
 #' 
 #' @name deprecate
@@ -17,7 +17,6 @@ setGeneric("cluster", signature = c("x"),
 
 #' @rdname deprecate
 #' @export
-#' @importFrom bluster clusterRows
 setMethod("cluster", signature = c(x = "SummarizedExperiment"),
             function(x,...){
                 .Deprecated(msg = paste0("'cluster' is deprecated. ",
@@ -471,12 +470,12 @@ setGeneric("full_join", signature = c("x"),
 #' @rdname deprecate
 #' @export
 setMethod("full_join", signature = c(x = "ANY"),
-            function(x, ...){
-                .Deprecated(msg = paste0("'full_join' is deprecated. ",
-                                        "Use 'mergeSEs' with 'join = full' ",
-                                        "instead."))
-                mergeSEs(x, join = "full", ...)
-            }
+          function(x, ...){
+              .Deprecated(msg = paste0("'full_join' is deprecated. ",
+                                       "Use 'mergeSEs' with 'join = full' ",
+                                       "instead."))
+              mergeSEs(x, join = "full", ...)
+          }
 )
 
 #' @rdname deprecate

R/runCCA.R

@@ -85,11 +85,11 @@
 #'   specified by \code{homogeneity.test} parameter.
 #'
 #' @return
-#' For \code{calculateCCA} a matrix with samples as rows and CCA dimensions as
+#' For \code{getCCA} a matrix with samples as rows and CCA dimensions as
 #' columns. Attributes include calculated \code{cca}/\code{rda} object and
 #' significance analysis results.
 #'
-#' For \code{runCCA} a modified \code{x} with the results stored in
+#' For \code{addCCA} a modified \code{x} with the results stored in
 #' \code{reducedDim} as the given \code{name}.
 #'
 #' @name runCCA
@@ -100,18 +100,18 @@
 #' @examples
 #' library(scater)
 #' data(GlobalPatterns)
-#' GlobalPatterns <- runCCA(GlobalPatterns, data ~ SampleType)
+#' GlobalPatterns <- addCCA(GlobalPatterns, data ~ SampleType)
 #' plotReducedDim(GlobalPatterns,"CCA", colour_by = "SampleType")
 #' 
 #' # Fetch significance results
 #' attr(reducedDim(GlobalPatterns, "CCA"), "significance")
 #'
-#' GlobalPatterns <- runRDA(GlobalPatterns, data ~ SampleType)
+#' GlobalPatterns <- addRDA(GlobalPatterns, data ~ SampleType)
 #' plotReducedDim(GlobalPatterns,"CCA", colour_by = "SampleType")
 #' 
 #' # Specify dissimilarity measure
 #' GlobalPatterns <- transformAssay(GlobalPatterns, method = "relabundance")
-#' GlobalPatterns <- runRDA(
+#' GlobalPatterns <- addRDA(
 #'     GlobalPatterns, data ~ SampleType, assay.type = "relabundance",  method = "bray")
 #' 
 #' # To scale values when using *RDA functions, use transformAssay(MARGIN = "features", ...) 
@@ -121,36 +121,36 @@
 #' # their value is NA
 #' tse <- tse[ rowSums( is.na( assay(tse, "z") ) ) == 0, ]
 #' # Calculate RDA
-#' tse <- runRDA(tse, formula = data ~ SampleType,
+#' tse <- addRDA(tse, formula = data ~ SampleType,
 #'               assay.type = "z", name = "rda_scaled", na.action = na.omit)
 #' # Plot
 #' plotReducedDim(tse,"rda_scaled", colour_by = "SampleType")
 #' # A common choice along with PERMANOVA is ANOVA when statistical significance
 #' # of homogeneity of groups is analysed. Moreover, full signficance test results
 #' # can be returned.
-#'  tse <- runRDA(tse, data ~ SampleType, homogeneity.test = "anova", full = TRUE)
+#'  tse <- addRDA(tse, data ~ SampleType, homogeneity.test = "anova", full = TRUE)
 #' 
 NULL
 
 #' @rdname runCCA
-setGeneric("calculateCCA", signature = c("x"),
+setGeneric("getCCA", signature = c("x"),
            function(x, ...)
-               standardGeneric("calculateCCA"))
+               standardGeneric("getCCA"))
 
 #' @rdname runCCA
-setGeneric("runCCA", signature = c("x"),
+setGeneric("addCCA", signature = c("x"),
            function(x, ...)
-               standardGeneric("runCCA"))
+               standardGeneric("addCCA"))
 
 #' @rdname runCCA
-setGeneric("calculateRDA", signature = c("x"),
+setGeneric("getRDA", signature = c("x"),
            function(x, ...)
-               standardGeneric("calculateRDA"))
+               standardGeneric("getRDA"))
 
 #' @rdname runCCA
-setGeneric("runRDA", signature = c("x"),
+setGeneric("addRDA", signature = c("x"),
            function(x, ...)
-               standardGeneric("runRDA"))
+               standardGeneric("addRDA"))
 
 .remove_special_functions_from_terms <- function(terms){
     names(terms) <- terms
@@ -210,7 +210,7 @@ setGeneric("runRDA", signature = c("x"),
 
 #' @export
 #' @rdname runCCA
-setMethod("calculateCCA", "ANY",
+setMethod("getCCA", "ANY",
       function(x, ...){
           .calculate_cca(x, ...)
       })
@@ -250,7 +250,7 @@ setMethod("calculateCCA", "ANY",
 
 #' @export
 #' @rdname runCCA
-setMethod("calculateCCA", "SummarizedExperiment",
+setMethod("getCCA", "SummarizedExperiment",
     function(x, formula, variables, test.signif = TRUE,
              assay.type = assay_name, assay_name = exprs_values, exprs_values = "counts",
              scores = "wa", ...)
@@ -289,10 +289,17 @@ setMethod("calculateCCA", "SummarizedExperiment",
     }
 )
 
+#' @export
+#' @rdname runCCA
+#' @aliases getCCA
+calculateCCA <- function(x,...){
+    getCCA(x,...)
+}
+
 #' @export
 #' @rdname runCCA
 #' @importFrom SingleCellExperiment reducedDim<-
-setMethod("runCCA", "SingleCellExperiment",
+setMethod("addCCA", "SingleCellExperiment",
     function(x, formula, variables, altexp = NULL, name = "CCA", ...)
     {
         if (!is.null(altexp)) {
@@ -301,13 +308,20 @@ setMethod("runCCA", "SingleCellExperiment",
           y <- x
         }
         # Calculate CCA
-        cca <- calculateCCA(y, formula, variables, ...)
+        cca <- getCCA(y, formula, variables, ...)
         # Add object to reducedDim
         x <- .add_object_to_reduceddim(x, cca, name = name, ...)
         return(x)
     }
 )
 
+#' @export
+#' @rdname runCCA
+#' @aliases addCCA
+runCCA <- function(x,...){
+    addCCA(x,...)
+}
+
 #' @importFrom vegan sppscores<-
 .calculate_rda <- function(
         x, formula, variables, scores, method = distance, distance = "euclidean", ...){
@@ -548,14 +562,14 @@ setMethod("runCCA", "SingleCellExperiment",
 
 #' @export
 #' @rdname runCCA
-setMethod("calculateRDA", "ANY",
+setMethod("getRDA", "ANY",
       function(x, ...){
           .calculate_rda(x, ...)
       })
 
 #' @export
 #' @rdname runCCA
-setMethod("calculateRDA", "SummarizedExperiment",
+setMethod("getRDA", "SummarizedExperiment",
     function(x, formula, variables, test.signif = TRUE,
              assay.type = assay_name, assay_name = exprs_values, exprs_values = "counts",
              scores = "wa", ...)
@@ -595,10 +609,17 @@ setMethod("calculateRDA", "SummarizedExperiment",
     }
 )
 
+#' @export
+#' @rdname runCCA
+#' @aliases getRDA
+calculateRDA <- function(x,...){
+    getRDA(x,...)
+}
+
 #' @export
 #' @rdname runCCA
 #' @importFrom SingleCellExperiment reducedDim<-
-setMethod("runRDA", "SingleCellExperiment",
+setMethod("addRDA", "SingleCellExperiment",
     function(x, formula, variables, altexp = NULL, name = "RDA", ...)
     {
         if (!is.null(altexp)) {
@@ -607,9 +628,16 @@ setMethod("runRDA", "SingleCellExperiment",
           y <- x
         }
         # Calculate RDA
-        rda <- calculateRDA(y, formula, variables, ...)
+        rda <- getRDA(y, formula, variables, ...)
         # Add object to reducedDim
         x <- .add_object_to_reduceddim(x, rda, name = name, ...)
         return(x)
     }
 )
+
+#' @export
+#' @rdname runCCA
+#' @aliases addRDA
+runRDA <- function(x,...){
+    addRDA(x,...)
+}