#392 Deprecate mergeRows/mergeCols and agglomerateByRank/Prevalence (#…

…404)

Signed-off-by: Daenarys8 <[email protected]>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.9.9
+Version: 1.9.10
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "[email protected]",

NAMESPACE

@@ -59,8 +59,11 @@ export(makeTreeSummarizedExperimentFromDADA2)
 export(makeTreeSummarizedExperimentFromPhyloseq)
 export(meltAssay)
 export(mergeCols)
+export(mergeFeatures)
+export(mergeFeaturesByPrevalence)
 export(mergeRows)
 export(mergeSEs)
+export(mergeSamples)
 export(perSampleDominantFeatures)
 export(perSampleDominantTaxa)
 export(performDMNgroupCV)
@@ -149,8 +152,12 @@ exportMethods(makeTreeSummarizedExperimentFromPhyloseq)
 exportMethods(mapTaxonomy)
 exportMethods(meltAssay)
 exportMethods(mergeCols)
+exportMethods(mergeFeatures)
+exportMethods(mergeFeaturesByPrevalence)
+exportMethods(mergeFeaturesByRank)
 exportMethods(mergeRows)
 exportMethods(mergeSEs)
+exportMethods(mergeSamples)
 exportMethods(perSampleDominantFeatures)
 exportMethods(perSampleDominantTaxa)
 exportMethods(performDMNgroupCV)

NEWS

@@ -83,3 +83,4 @@ Changes in version 1.9.x
 + Added Tengeler2020 dataset
 + *RDA & *CCA: calculate also statistical significance
 + altExp support for meltAssay
++ Deprecate mergeRows, mergeCols, agglomerateByRank, agglomerateByPrevalence

R/agglomerate.R

@@ -130,13 +130,22 @@
 #' taxonomyRanks(enterotype)
 NULL
 
+#' @rdname agglomerate-methods
+#' @aliases mergeFeaturesByRank
 setGeneric("agglomerateByRank",
             signature = "x",
             function(x, ...)
                 standardGeneric("agglomerateByRank"))
 
 #' @rdname agglomerate-methods
 #' @aliases agglomerateByRank
+setGeneric("mergeFeaturesByRank",
+           signature = "x",
+           function(x, ...)
+               standardGeneric("mergeFeaturesByRank"))
+
+#' @rdname agglomerate-methods
+#' @aliases mergeFeaturesByRank
 #'
 #' @importFrom SummarizedExperiment rowData rowData<-
 #'
@@ -209,6 +218,22 @@ setMethod("agglomerateByRank", signature = c(x = "SummarizedExperiment"),
     }
 )
 
+#' @rdname agglomerate-methods
+#' @aliases agglomerateByRank
+#'
+#' @importFrom SummarizedExperiment rowData rowData<-
+#'
+#' @export
+setMethod("mergeFeaturesByRank", signature = c(x = "SummarizedExperiment"),
+          function(x, rank = taxonomyRanks(x)[1], onRankOnly = FALSE, na.rm = FALSE,
+                   empty.fields = c(NA, "", " ", "\t", "-", "_"), ...){
+              .Deprecated(old="agglomerateByRank", new="mergeFeaturesByRank", "Now agglomerateByRank is deprecated. Use mergeFeaturesByRank instead.")
+              x <- agglomerateByRank(x, rank = rank, onRankOnly = onRankOnly, na.rm = na.rm,
+                                     empty.fields = empty.fields, ...)
+              x
+          }
+)
+
 #' @rdname agglomerate-methods
 #' @importFrom SingleCellExperiment altExp altExp<- altExps<-
 #' @export
@@ -229,6 +254,18 @@ setMethod("agglomerateByRank", signature = c(x = "SingleCellExperiment"),
     }
 )
 
+#' @rdname agglomerate-methods
+#' @aliases agglomerateByRank
+#' @importFrom SingleCellExperiment altExp altExp<- altExps<-
+#' @export
+setMethod("mergeFeaturesByRank", signature = c(x = "SingleCellExperiment"),
+          function(x, ..., altexp = NULL, strip_altexp = TRUE){
+              .Deprecated(old="agglomerateByRank", new="mergeFeaturesByRank", "Now agglomerateByRank is deprecated. Use mergeFeaturesByRank instead.")
+              x <- agglomerateByRank(x, ..., altexp = altexp, strip_altexp = strip_altexp)
+              x
+          }
+)
+
 
 #' @rdname agglomerate-methods
 #' @export
@@ -263,6 +300,16 @@ setMethod("agglomerateByRank", signature = c(x = "TreeSummarizedExperiment"),
           }
 )
 
+#' @rdname agglomerate-methods
+#' @aliases agglomerateByRank
+#' @export
+setMethod("mergeFeaturesByRank", signature = c(x = "TreeSummarizedExperiment"),
+          function(x, ..., agglomerateTree = FALSE){
+              .Deprecated(old="agglomerateByRank", new="mergeFeaturesByRank", "Now agglomerateByRank is deprecated. Use mergeFeaturesByRank instead.")
+              x <- agglomerateByRank(x, ..., agglomerateTree = agglomerateTree)
+              x
+          }
+)
 ################################ HELP FUNCTIONS ################################
 
 .remove_with_empty_taxonomic_info <-

R/getPrevalence.R

@@ -564,13 +564,22 @@ setMethod("getPrevalentAbundance", signature = c(x = "SummarizedExperiment"),
 ############################# agglomerateByPrevalence ##########################
 
 #' @rdname getPrevalence
+#' @aliases mergeFeaturesByPrevalence
 #' @export
 setGeneric("agglomerateByPrevalence", signature = "x",
            function(x, ...)
                standardGeneric("agglomerateByPrevalence"))
 
+#' @rdname getPrevalence
+#' @aliases agglomerateByPrevalence
+#' @export
+setGeneric("mergeFeaturesByPrevalence", signature = "x",
+           function(x, ...)
+               standardGeneric("mergeFeaturesByPrevalence"))
+
 
 #' @rdname getPrevalence
+#' @aliases mergeFeaturesByPRevalence
 #' @export
 setMethod("agglomerateByPrevalence", signature = c(x = "SummarizedExperiment"),
     function(x, rank = taxonomyRanks(x)[1L], other_label = "Other", ...){
@@ -608,3 +617,14 @@ setMethod("agglomerateByPrevalence", signature = c(x = "SummarizedExperiment"),
     }
 )
 
+
+#' @rdname getPrevalence
+#' @aliases agglomerateByPrevalence
+#' @export
+setMethod("mergeFeaturesByPrevalence", signature = c(x = "SummarizedExperiment"),
+          function(x, rank = taxonomyRanks(x)[1L], other_label = "Other", ...){
+              .Deprecated(old="agglomerateByPrevalence", new="mergeFeaturesByPrevalence", "Now agglomerateByPrevalence is deprecated. Use mergeFeaturesByPrevalence instead.")
+              x <- agglomerateByPrevalence(x, rank = rank, other_label = other_label, ...)
+              x 
+          })
+

R/merge.R

@@ -72,19 +72,37 @@
 NULL
 
 #' @rdname merge-methods
+#' @aliases mergeFeatures
 #' @export
 setGeneric("mergeRows",
            signature = "x",
            function(x, f, archetype = 1L, ...)
                standardGeneric("mergeRows"))
 
 #' @rdname merge-methods
+#' @aliases mergeSamples
 #' @export
 setGeneric("mergeCols",
            signature = "x",
            function(x, f, archetype = 1L, ...)
                standardGeneric("mergeCols"))
 
+#' @rdname merge-methods
+#' @aliases mergeRows
+#' @export
+setGeneric("mergeFeatures",
+           signature = "x",
+           function(x, f, archetype = 1L, ...)
+               standardGeneric("mergeFeatures"))
+
+#' @rdname merge-methods
+#' @aliases mergeCols
+#' @export
+setGeneric("mergeSamples",
+           signature = "x",
+           function(x, f, archetype = 1L, ...)
+               standardGeneric("mergeSamples"))
+
 .norm_f <- function(i, f, dim_type = c("rows","columns")){
     dim_type <- match.arg(dim_type)
     if(!is.character(f) && !is.factor(f)){
@@ -230,6 +248,7 @@ setGeneric("mergeCols",
 }
 
 #' @rdname merge-methods
+#' @aliases mergeFeatures
 #' @export
 setMethod("mergeRows", signature = c(x = "SummarizedExperiment"),
           function(x, f, archetype = 1L, ...){
@@ -238,13 +257,34 @@ setMethod("mergeRows", signature = c(x = "SummarizedExperiment"),
 )
 
 #' @rdname merge-methods
+#' @aliases mergeSmaples
 #' @export
 setMethod("mergeCols", signature = c(x = "SummarizedExperiment"),
           function(x, f, archetype = 1L, ...){
               .merge_cols(x, f, archetype = archetype, ...)
           }
 )
 
+#' @rdname merge-methods
+#' @aliases mergeRows
+#' @export
+setMethod("mergeFeatures", signature = c(x = "SummarizedExperiment"),
+          function(x, f, archetype = 1L, ...){
+              .Deprecated(old="mergeRows", new="mergeFeatures", "Now mergeRows is deprecated. Use mergeFeatures instead.")
+              .merge_rows(x, f, archetype = archetype, ...)
+          }
+)
+
+#' @rdname merge-methods
+#' @aliases mergeCols
+#' @export
+setMethod("mergeSamples", signature = c(x = "SummarizedExperiment"),
+          function(x, f, archetype = 1L, ...){
+              .Deprecated(old="mergeCols", new="mergeSamples", "Now mergeCols is deprecated. Use mergeSamples instead.")
+              .merge_cols(x, f, archetype = archetype, ...)
+          }
+)
+
 .merge_tree <- function(tree, links){
     tips <- sort(setdiff(tree$edge[, 2], tree$edge[, 1]))
     drop_tip <- tips[!(tips %in% unique(links$nodeNum[links$isLeaf]))]
@@ -371,3 +411,27 @@ setMethod("mergeCols", signature = c(x = "TreeSummarizedExperiment"),
               return(x)
           }
 )
+
+#' @rdname merge-methods
+#' @importFrom ape keep.tip
+#' @aliases mergeRows
+#' @export
+setMethod("mergeFeatures", signature = c(x = "TreeSummarizedExperiment"),
+          function(x, f, archetype = 1L, mergeTree = FALSE, mergeRefSeq = FALSE, ...){
+             .Deprecated(old="mergeRows", new="mergeFeatures", "Now mergeRows is deprecated. Use mergeFeatures instead.")
+             x <- mergeRows(x = x, f = f, archetype = 1L, mergeTree = mergeTree, mergeRefSeq = mergeRefSeq, ...)
+              return(x)
+          }
+)
+
+#' @rdname merge-methods
+#' @importFrom ape keep.tip
+#' @aliases mergeCols
+#' @export
+setMethod("mergeSamples", signature = c(x = "TreeSummarizedExperiment"),
+          function(x, f, archetype = 1L, mergeTree = FALSE, ...){
+              .Deprecated(old="mergeCols", new="mergeSamples", "Now mergeCols is deprecated. Use mergeSamples instead.")
+              x <- mergeCols(x, f, archetype = 1L, mergeTree =mergeTree, ...)
+              return(x)
+          }
+)