new generic function agglomerateByVariable (microbiome#507)

Co-authored-by: Tuomas Borman <[email protected]>
Co-authored-by: TuomasBorman <[email protected]>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.13.2
+Version: 1.13.3
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "[email protected]",

NAMESPACE

@@ -13,6 +13,7 @@ export(addPerSampleDominantTaxa)
 export(addTaxonomyTree)
 export(agglomerateByPrevalence)
 export(agglomerateByRank)
+export(agglomerateByVariable)
 export(bestDMNFit)
 export(calculateDMN)
 export(calculateDMNgroup)
@@ -124,6 +125,7 @@ exportMethods(addPerSampleDominantTaxa)
 exportMethods(addTaxonomyTree)
 exportMethods(agglomerateByPrevalence)
 exportMethods(agglomerateByRank)
+exportMethods(agglomerateByVariable)
 exportMethods(bestDMNFit)
 exportMethods(calculateCCA)
 exportMethods(calculateDMN)
@@ -288,7 +290,6 @@ importFrom(SummarizedExperiment,rowRanges)
 importFrom(ape,cophenetic.phylo)
 importFrom(ape,drop.tip)
 importFrom(ape,is.rooted)
-importFrom(ape,keep.tip)
 importFrom(ape,node.depth)
 importFrom(ape,node.depth.edgelength)
 importFrom(ape,prop.part)

NEWS

@@ -116,3 +116,4 @@ Changes in version 1.11.x
 Changes in version 1.13.x
 + Added new functions getMediation and addMediation
 + replace getExperiment* and testExperiment* functions with getCrossAssociation
++ Replace mergeRows and mergeCols with new function agglomerateByVariable

R/deprecate.R

@@ -60,6 +60,169 @@ setMethod("taxonomyTree", signature = c(x = "SummarizedExperiment"),
             }
 )
 
+#' @rdname deprecate
+#' @export
+setGeneric("mergeRows",
+            signature = "x",
+            function(x, ...)
+                standardGeneric("mergeRows"))
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeRows", signature = c(x = "SummarizedExperiment"),
+            function(x, ...){
+                .Deprecated(msg = paste0("'mergeRows' is deprecated. ",
+                                        "Use 'agglomerateByVariable' with ",
+                                        "parameter MARGIN = 'rows' instead."))
+                agglomerateByVariable(x, MARGIN = "rows", ...)
+            }
+)
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeRows", signature = c(x = "TreeSummarizedExperiment"),
+          function(x, ...){
+              .Deprecated(msg = paste0("'mergeRows' is deprecated. ",
+                                       "Use 'agglomerateByVariable' with ",
+                                        "parameter MARGIN = 'rows' instead."))
+              agglomerateByVariable(x, MARGIN = "rows", ...)
+          }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric("mergeCols",
+            signature = "x",
+            function(x, ...)
+                standardGeneric("mergeCols"))
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeCols", signature = c(x = "SummarizedExperiment"),
+            function(x, ...){
+                .Deprecated(msg = paste0("'mergeCols' is deprecated. ",
+                                        "Use 'agglomerateByVariable' with ", 
+                                        "parameter MARGIN = 'cols' instead."))
+                agglomerateByVariable(x, MARGIN = "cols", ...)
+            }
+)
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeCols", signature = c(x = "TreeSummarizedExperiment"),
+          function(x, ...){
+              .Deprecated(msg = paste0("'mergeCols' is deprecated. ",
+                                        "Use 'agglomerateByVariable' with ",
+                                        "parameter MARGIN = 'cols' instead."))
+              agglomerateByVariable(x, MARGIN = "cols", ...)
+          }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric("mergeFeatures",
+            signature = "x",
+            function(x, ...)
+                standardGeneric("mergeFeatures"))
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeFeatures", signature = c(x = "SummarizedExperiment"),
+            function(x, ...){
+                .Deprecated(msg = paste0("'mergeFeatures' is deprecated. ",
+                                        "Use 'agglomerateByVariable' with ", 
+                                        "parameter MARGIN = 'rows' instead."))
+                agglomerateByVariable(x, MARGIN = "rows", ...)
+            }
+)
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeFeatures", signature = c(x = "TreeSummarizedExperiment"),
+          function(x, ...){
+              .Deprecated(msg = paste0("'mergeFeatures' is deprecated. ",
+                                       "Use 'agglomerateByVariable' with ",
+                                        "parameter MARGIN = 'rows' instead."))
+              agglomerateByVariable(x, MARGIN = "rows", ...)
+          }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric("mergeSamples",
+            signature = "x",
+            function(x, ...)
+                standardGeneric("mergeSamples"))
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeSamples", signature = c(x = "SummarizedExperiment"),
+            function(x, ...){
+                .Deprecated(msg = paste0("'mergeSamples' is deprecated. ",
+                                        "Use 'agglomerateByVariable' with ",
+                                        "parameter MARGIN = 'cols' instead."))
+                agglomerateByVariable(x, MARGIN = "cols", ...)
+            }
+)
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeSamples", signature = c(x = "TreeSummarizedExperiment"),
+          function(x, ...){
+              .Deprecated(msg = paste0("'mergeSamples' is deprecated. ",
+                                       "Use 'agglomerateByVariable' with ", 
+                                        "parameter MARGIN = 'cols' instead."))
+              agglomerateByVariable(x, MARGIN = "cols", ...)
+          }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric("mergeFeaturesByRank",
+           signature = "x",
+           function(x, ...)
+               standardGeneric("mergeFeaturesByRank"))
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeFeaturesByRank", signature = c(x = "SummarizedExperiment"),
+          function(x, ...){
+              .Deprecated(msg = paste0("'mergeFeaturesByRank' is deprecated. ",
+                                        "Use 'agglomerateByRank' instead."))
+              x <- agglomerateByRank(x, ...)
+              x
+          }
+)
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeFeaturesByRank", signature = c(x = "SingleCellExperiment"),
+          function(x, ...){
+              .Deprecated(msg = paste0("'mergeFeaturesByRank' is deprecated. ",
+                                        "Use 'agglomerateByRank' instead."))
+              x <- agglomerateByRank(x, ...)
+              x
+          }
+)
+
+#' @rdname deprecate
+#' @export
+setGeneric("mergeFeaturesByPrevalence", signature = "x",
+           function(x, ...)
+               standardGeneric("mergeFeaturesByPrevalence"))
+
+#' @rdname deprecate
+#' @export
+setMethod("mergeFeaturesByPrevalence", signature = c(x = "SummarizedExperiment"),
+          function(x, ...){
+              .Deprecated(msg = paste0(
+                  "'mergeFeaturesByPrevalence' is deprecated. ",
+                  "Use agglomerateByPrevalence instead."))
+              x <- agglomerateByPrevalence(x, ...)
+              x 
+          }
+)
+
 #' @rdname deprecate
 #' @export
 setGeneric("getExperimentCrossAssociation", signature = c("x"),
@@ -89,6 +252,17 @@ setMethod("getExperimentCrossAssociation", signature = "SummarizedExperiment",
           }
 )
 
+#' @rdname deprecate
+#' @export
+setMethod("mergeFeaturesByRank", signature = c(x = "TreeSummarizedExperiment"),
+          function(x, ...){
+              .Deprecated(msg = paste0("'mergeFeaturesByRank' is deprecated. ",
+                                        "Use 'agglomerateByRank' instead."))
+              x <- agglomerateByRank(x, ...)
+              x
+          }
+)
+
 #' @rdname deprecate
 #' @export
 setGeneric("testExperimentCrossAssociation", signature = c("x"),
@@ -140,24 +314,6 @@ setMethod("getExperimentCrossCorrelation", signature = c(x = "ANY"),
           }
 )
 
-#' @rdname deprecate
-#' @export              
-setGeneric("mergeFeaturesByPrevalence", signature = "x",
-           function(x, ...)
-               standardGeneric("mergeFeaturesByPrevalence"))
-
-#' @rdname deprecate
-#' @export
-setMethod("mergeFeaturesByPrevalence", signature = c(x = "SummarizedExperiment"),
-          function(x, ...){
-              .Deprecated(msg = paste0(
-                  "'mergeFeaturesByPrevalence' is deprecated. ",
-                  "Use agglomerateByPrevalence instead."))
-              x <- agglomerateByPrevalence(x, ...)
-              x 
-          }
-)
-
 #' @rdname deprecate
 #' @export
 loadFromBiom <- function(...) {

R/getPrevalence.R

@@ -643,7 +643,9 @@ setMethod("agglomerateByPrevalence", signature = c(x = "SummarizedExperiment"),
         pr <- getPrevalentTaxa(x, rank = NULL, ...)
         f <- rownames(x) %in% pr
         if(any(!f)){
-            other_x <- mergeRows(x[!f,], factor(rep(1L,sum(!f))), check_assays = FALSE)
+            other_x <- agglomerateByVariable(x[!f,], MARGIN = "rows", 
+                                            factor(rep(1L,sum(!f))), 
+                                            check_assays = FALSE)
             rowData(other_x)[,colnames(rowData(other_x))] <- NA
             # set the other label
             rownames(other_x) <- other_label