assay_name switch (#341)

* ok

* sync

* snc

* removed shortcut transformation examples

* deprecating ZTransform and relAbundanceCounts

* final fixes

* news

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.7.8
+Version: 1.7.9
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "felix.gm.ernst@outlook.com",

NEWS

@@ -60,6 +60,8 @@ Changes in version 1.5.x
 + calculateUnifrac bugfix
 
 Changes in version 1.7.x
++ Deprecated assay_name arguments, replaced with assay.type
++ Removed abund_values argument
 + makePhyloseqFromTreeSE: added option for choosing a tree from multiple rowTrees
 + mergeSEs: match rows based on all available taxonomy level data on rowData
 + mergeSEs: fix bug related to equally named variables that are different class
@@ -69,5 +71,5 @@ Changes in version 1.7.x
 + calculateUnifrac: subset tree based on data
 + agglomerateByRank: take into account multiple trees
 + loadFromBiom: name columns of rowData based on prefixes
-+ Deprecate transformSamples, *Features, relabundance
++ Deprecate transformSamples, *Features, relabundance, ZTransform, relAbundanceCounts
 + mergeSEs: faster tree merging

R/calculateDMM.R

@@ -8,16 +8,16 @@
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
 #'   object.
 #'
-#' @param assay_name a single \code{character} value for specifying which
+#' @param assay.type a single \code{character} value for specifying which
 #'   assay to use for calculation.
 #'   
 #' @param exprs_values a single \code{character} value for specifying which
 #'   assay to use for calculation.
-#'   (Please use \code{assay_name} instead.)
+#'   (Please use \code{assay.type} instead.)
 #'   
-#' @param abund_values a single \code{character} value for specifying which
+#' @param assay_name a single \code{character} value for specifying which
 #'   assay to use for calculation.
-#'   (Please use \code{assay_name} instead. At some point \code{abund_values}
+#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
 #'   will be disabled.)
 #'
 #' @param k the number of Dirichlet components to fit. See
@@ -141,9 +141,9 @@ setMethod("calculateDMN", signature = c(x = "ANY"), .calculate_DMN)
 #' @rdname calculateDMN
 #' @export
 setMethod("calculateDMN", signature = c(x = "SummarizedExperiment"),
-    function(x, assay_name = abund_values, abund_values = exprs_values, exprs_values = "counts", 
+    function(x, assay.type = assay_name, assay_name = exprs_values, exprs_values = "counts", 
              transposed = FALSE, ...){
-        mat <- assay(x, assay_name)
+        mat <- assay(x, assay.type)
         if(!transposed){
             mat <- t(mat)
         }
@@ -276,9 +276,9 @@ setMethod("calculateDMNgroup", signature = c(x = "ANY"), .calculate_DMNgroup)
 #' @export
 setMethod("calculateDMNgroup", signature = c(x = "SummarizedExperiment"),
     function(x, variable, 
-             assay_name = abund_values, abund_values = exprs_values, exprs_values = "counts", 
+             assay.type = assay_name, assay_name = exprs_values, exprs_values = "counts", 
              transposed = FALSE, ...){
-        mat <- assay(x, assay_name)
+        mat <- assay(x, assay.type)
         if(!transposed){
             mat <- t(mat)
         }
@@ -327,9 +327,9 @@ setMethod("performDMNgroupCV", signature = c(x = "ANY"), .perform_DMNgroup_cv)
 #' @export
 setMethod("performDMNgroupCV", signature = c(x = "SummarizedExperiment"),
     function(x, variable, 
-             assay_name = abund_values, abund_values = exprs_values, exprs_values = "counts", 
+             assay.type = assay_name, assay_name = exprs_values, exprs_values = "counts", 
              transposed = FALSE, ...){
-        mat <- assay(x, assay_name)
+        mat <- assay(x, assay.type)
         if(!transposed){
             mat <- t(mat)
         }

R/calculateJSD.R

@@ -7,16 +7,16 @@
 #' @param x a numeric matrix or a
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}.
 #'   
-#' @param assay_name a single \code{character} value for specifying which
+#' @param assay.type a single \code{character} value for specifying which
 #'   assay to use for calculation.
 #'
 #' @param exprs_values a single \code{character} value for specifying which
 #'   assay to use for calculation.
-#'   (Please use \code{assay_name} instead.)
+#'   (Please use \code{assay.type} instead.)
 #'   
-#' @param abund_values a single \code{character} value for specifying which
+#' @param assay_name a single \code{character} value for specifying which
 #'   assay to use for calculation.
-#'   (Please use \code{assay_name} instead. At some point \code{abund_values}
+#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
 #'   will be disabled.)
 #'
 #' @param transposed Logical scalar, is x transposed with cells in rows?
@@ -85,9 +85,9 @@ setMethod("calculateJSD", signature = c(x = "ANY"),
 #'
 #' @export
 setMethod("calculateJSD", signature = c(x = "SummarizedExperiment"),
-    function(x, assay_name = abund_values, abund_values = exprs_values, 
+    function(x, assay.type = assay_name, assay_name = exprs_values, 
              exprs_values = "counts", transposed = FALSE, ...){
-        mat <- assay(x, assay_name)
+        mat <- assay(x, assay.type)
         if(!transposed){
             mat <- t(mat)
         }

R/calculateOverlap.R

@@ -8,13 +8,13 @@
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
 #'   object containing a tree.
 #'   
-#' @param assay_name A single character value for selecting the
+#' @param assay.type A single character value for selecting the
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{assay}}
 #'   to calculate the overlap.
 #'   
-#' @param abund_values a single \code{character} value for specifying which
+#' @param assay_name a single \code{character} value for specifying which
 #'   assay to use for calculation.
-#'   (Please use \code{assay_name} instead. At some point \code{abund_values}
+#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
 #'   will be disabled.)
 #'   
 #' @param detection A single numeric value for selecting detection threshold for 
@@ -53,7 +53,7 @@
 #' overlap
 #' 
 #' # Store result to reducedDim
-#' tse <- runOverlap(tse, assay_name = "relabundance", name = "overlap_between_samples")
+#' tse <- runOverlap(tse, assay.type = "relabundance", name = "overlap_between_samples")
 #' head(reducedDims(tse)$overlap_between_samples)
 #' 
 NULL
@@ -62,18 +62,18 @@ NULL
 #' @rdname calculateOverlap
 #' @export
 setGeneric("calculateOverlap", signature = c("x"),
-           function(x, assay_name = abund_values, abund_values = "counts", 
+           function(x, assay.type = assay_name, assay_name = "counts", 
                     detection = 0, ...)
              standardGeneric("calculateOverlap"))
 
 #' @rdname calculateOverlap
 #' @export
 setMethod("calculateOverlap", signature = c(x = "SummarizedExperiment"),
-    function(x, assay_name = abund_values, abund_values = "counts", 
+    function(x, assay.type = assay_name, assay_name = "counts", 
              detection = 0, ...){
         ############################# INPUT CHECK ##############################
-        # Check assay_name
-        .check_assay_present(assay_name, x)
+        # Check assay.type
+        .check_assay_present(assay.type, x)
         # Check detection
         if (!.is_numeric_string(detection)) {
           stop("'detection' must be a single numeric value or coercible to ",
@@ -83,7 +83,7 @@ setMethod("calculateOverlap", signature = c(x = "SummarizedExperiment"),
         detection <- as.numeric(detection)
         ########################### INPUT CHECK END ############################
         # Get assay
-        assay <- assay(x, assay_name)
+        assay <- assay(x, assay.type)
 
         # All the sample pairs
         sample_pairs <- as.matrix(expand.grid(colnames(x), colnames(x)))

R/calculateUnifrac.R

@@ -26,16 +26,16 @@
 #'   The length must equal the number of rows/columns of \code{x}. Furthermore, all the 
 #'   node labs must be present in \code{tree}.
 #'
-#' @param assay_name a single \code{character} value for specifying which
+#' @param assay.type a single \code{character} value for specifying which
 #'   assay to use for calculation.
 #'   
 #' @param exprs_values a single \code{character} value for specifying which
 #'   assay to use for calculation.
-#'   (Please use \code{assay_name} instead.)
+#'   (Please use \code{assay.type} instead.)
 #'   
-#' @param abund_values a single \code{character} value for specifying which
+#' @param assay_name a single \code{character} value for specifying which
 #'   assay to use for calculation.
-#'   (Please use \code{assay_name} instead. At some point \code{abund_values}
+#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
 #'   will be disabled.)
 #'
 #' @param tree_name a single \code{character} value for specifying which
@@ -146,11 +146,11 @@ setMethod("calculateUnifrac", signature = c(x = "ANY", tree = "phylo"),
 setMethod("calculateUnifrac",
           signature = c(x = "TreeSummarizedExperiment",
                         tree = "missing"),
-    function(x, assay_name = abund_values, abund_values = exprs_values, exprs_values = "counts", 
+    function(x, assay.type = assay_name, assay_name = exprs_values, exprs_values = "counts", 
              tree_name = "phylo", transposed = FALSE, ...){
-        # Check assay_name and get assay
-        .check_assay_present(assay_name, x)
-        mat <- assay(x, assay_name)
+        # Check assay.type and get assay
+        .check_assay_present(assay.type, x)
+        mat <- assay(x, assay.type)
         if(!transposed){
             # Check tree_name
             .check_rowTree_present(tree_name, x)

R/decontam.R

@@ -8,13 +8,13 @@
 #' @param seqtab,x
 #'   a \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
 #'
-#' @param assay_name A single character value for selecting the
+#' @param assay.type A single character value for selecting the
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{assay}}
 #'   to use.
 #'
-#' @param abund_values a single \code{character} value for specifying which
+#' @param assay_name a single \code{character} value for specifying which
 #'   assay to use for calculation.
-#'   (Please use \code{assay_name} instead. At some point \code{abund_values}
+#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
 #'   will be disabled.)
 #'
 #' @param name A name for the column of the colData in which the contaminant
@@ -89,7 +89,7 @@ NULL
 #' @export
 setMethod("isContaminant", signature = c(seqtab = "SummarizedExperiment"),
     function(seqtab,
-             assay_name = abund_values, abund_values = "counts",
+             assay.type = assay_name, assay_name = "counts",
              name = "isContaminant",
              concentration = NULL,
              control = NULL,
@@ -99,7 +99,7 @@ setMethod("isContaminant", signature = c(seqtab = "SummarizedExperiment"),
              detailed = TRUE,
              ...){
         # input check
-        .check_assay_present(assay_name, seqtab)
+        .check_assay_present(assay.type, seqtab)
         if(!.is_a_string(name)){
             stop("'name' must be single character value.",call. = FALSE)
         }
@@ -136,7 +136,7 @@ setMethod("isContaminant", signature = c(seqtab = "SummarizedExperiment"),
                                       search = "colData")$value
             batch <- factor(batch, sort(unique(batch)))
         }
-        mat <- assay(seqtab,assay_name)
+        mat <- assay(seqtab,assay.type)
         contaminant <- isContaminant(t(mat),
                                      conc = concentration,
                                      neg = control,
@@ -162,15 +162,15 @@ setMethod("isContaminant", signature = c(seqtab = "SummarizedExperiment"),
 #' @export
 setMethod("isNotContaminant", signature = c(seqtab = "SummarizedExperiment"),
     function(seqtab,
-             assay_name = abund_values, abund_values = "counts",
+             assay.type = assay_name, assay_name = "counts",
              name = "isNotContaminant",
              control = NULL,
              threshold = 0.5,
              normalize = TRUE,
              detailed = FALSE,
              ...){
         # input check
-        .check_assay_present(assay_name, seqtab)
+        .check_assay_present(assay.type, seqtab)
         if(!.is_a_string(name)){
             stop("'name' must be single character value.",call. = FALSE)
         }
@@ -193,7 +193,7 @@ setMethod("isNotContaminant", signature = c(seqtab = "SummarizedExperiment"),
                      call. = FALSE)
             }
         }
-        mat <- assay(seqtab,assay_name)
+        mat <- assay(seqtab,assay.type)
         not_contaminant <- isNotContaminant(t(mat),
                                             neg = control,
                                             threshold = threshold,

R/dominantTaxa.R

@@ -8,13 +8,13 @@
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
 #'   object.
 #'
-#' @param assay_name A single character value for selecting the
+#' @param assay.type A single character value for selecting the
 #'   \code{\link[SummarizedExperiment:SummarizedExperiment-class]{assay}}
 #'   to use for identifying dominant taxa.
 #'
-#' @param abund_values a single \code{character} value for specifying which
+#' @param assay_name a single \code{character} value for specifying which
 #'   assay to use for calculation.
-#'   (Please use \code{assay_name} instead. At some point \code{abund_values}
+#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
 #'   will be disabled.)
 #'   
 #' @param rank A single character defining a taxonomic rank. Must be a value of
@@ -63,7 +63,7 @@ NULL
 #' @aliases perSampleDominantFeatures
 #' @export
 setGeneric("perSampleDominantTaxa",signature = c("x"),
-           function(x, assay_name = abund_values, abund_values = "counts", 
+           function(x, assay.type = assay_name, assay_name = "counts", 
                     rank = NULL, ...)
                standardGeneric("perSampleDominantTaxa"))
 
@@ -72,11 +72,11 @@ setGeneric("perSampleDominantTaxa",signature = c("x"),
 #' @importFrom IRanges relist
 #' @export
 setMethod("perSampleDominantTaxa", signature = c(x = "SummarizedExperiment"),
-    function(x, assay_name = abund_values, abund_values = "counts", 
+    function(x, assay.type = assay_name, assay_name = "counts", 
              rank = NULL, ...){
         # Input check
-        # Check assay_name
-        .check_assay_present(assay_name, x)
+        # Check assay.type
+        .check_assay_present(assay.type, x)
         # rank check
         if(!is.null(rank)){
             if(!.is_a_string(rank)){
@@ -89,10 +89,10 @@ setMethod("perSampleDominantTaxa", signature = c(x = "SummarizedExperiment"),
         # taxonomic rank that is specified by user.
         if (!is.null(rank)) {
             x <- agglomerateByRank(x, rank, ...)
-            mat <- assay(x, assay_name)
+            mat <- assay(x, assay.type)
         } # Otherwise, if "rank" is NULL, abundances are stored without ranking
         else {
-            mat <- assay(x, assay_name)
+            mat <- assay(x, assay.type)
         }
         # apply() function finds the indices of taxa's that has the highest
         # abundance.

R/estimateDivergence.R

@@ -4,12 +4,12 @@
 #' 
 #' @param x a \code{\link{SummarizedExperiment}} object.
 #'
-#' @param assay_name the name of the assay used for calculation of the
+#' @param assay.type the name of the assay used for calculation of the
 #'   sample-wise estimates.
 #'   
-#' @param abund_values a single \code{character} value for specifying which
+#' @param assay_name a single \code{character} value for specifying which
 #'   assay to use for calculation.
-#'   (Please use \code{assay_name} instead. At some point \code{abund_values}
+#'   (Please use \code{assay.type} instead. At some point \code{assay_name}
 #'   will be disabled.)
 #'
 #' @param name a name for the column of the colData the results should be
@@ -83,21 +83,21 @@ NULL
 #' @rdname estimateDivergence
 #' @export
 setGeneric("estimateDivergence",signature = c("x"),
-           function(x, assay_name = abund_values, abund_values = "counts", 
+           function(x, assay.type = assay_name, assay_name = "counts", 
                     name = "divergence", reference = "median", 
                     FUN = vegan::vegdist, method = "bray", ...)
              standardGeneric("estimateDivergence"))
 
 #' @rdname estimateDivergence
 #' @export
 setMethod("estimateDivergence", signature = c(x="SummarizedExperiment"),
-    function(x, assay_name = abund_values, abund_values = "counts", 
+    function(x, assay.type = assay_name, assay_name = "counts", 
              name = "divergence", reference = "median", 
              FUN = vegan::vegdist, method = "bray", ...){
 
         ################### Input check ###############
-        # Check assay_name
-        .check_assay_present(assay_name, x)
+        # Check assay.type
+        .check_assay_present(assay.type, x)
         # Check name
         if(!.is_non_empty_character(name) || length(name) != 1L){
             stop("'name' must be a non-empty character value.",
@@ -125,7 +125,7 @@ setMethod("estimateDivergence", signature = c(x="SummarizedExperiment"),
         }
 
         ################# Input check end #############
-        divergence <- .calc_reference_dist(mat = assay(x, assay_name),
+        divergence <- .calc_reference_dist(mat = assay(x, assay.type),
                                        reference = reference, 
                                        FUN = FUN,
                                        method = method, ...)