Merge pull request #160 from mojaveazure/fix/layer-slot

Update use of `GetAssayData()`

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SeuratObject
 Type: Package
 Title: Data Structures for Single Cell Data
-Version: 5.0.0
+Version: 5.0.0.9001
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = 'rsatija@nygenome.org', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
   person(given = 'Paul', family = 'Hoffman', email = 'seurat@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-7693-8957')),

NEWS.md

@@ -1,3 +1,8 @@
+# Unreleased
+
+## Changes:
+- Update internal calls to `GetAssayData()` to use `layer` instead of `slot` (#160)
+
 # SeuratObject 5.0.0
 ## Added
 - New `Assay5` class with support for layers; layers provide support for:

R/assay.R

@@ -319,7 +319,7 @@ Features.Assay <- function(
   }
   layer <- layer[1L] %||% 'data'
   layer <- match.arg(arg = layer)
-  features <- rownames(x = GetAssayData(object = x, slot = layer))
+  features <- rownames(x = GetAssayData(object = x, layer = layer))
   if (!length(x = features)) {
     features <- NULL
   }
@@ -370,7 +370,7 @@ FetchData.Assay <- function(
     x = vars
   )
   # Pull expression information
-  mat <- GetAssayData(object = object, slot = layer)
+  mat <- GetAssayData(object = object, layer = layer)
   if (IsMatrixEmpty(x = mat)) {
     abort(message = paste("Layer", sQuote(x = layer), "is empty in this assay"))
   }
@@ -736,7 +736,7 @@ RenameCells.Assay <- function(object, new.names = NULL, ...) {
   CheckDots(...)
   names(new.names) <- NULL
   for (data.slot in c("counts", "data", "scale.data")) {
-    old.data <- GetAssayData(object = object, slot = data.slot)
+    old.data <- GetAssayData(object = object, layer = data.slot)
     if (ncol(x = old.data) <= 1) {
       next
     }
@@ -1370,7 +1370,7 @@ merge.Assay <- function(
     }
     combined.assay <- SetAssayData(
       object = combined.assay,
-      slot = "data",
+      layer = "data",
       new.data = merged.data
     )
   }
@@ -1465,17 +1465,17 @@ subset.Assay <- function(x, cells = NULL, features = NULL, ...) {
   if (length(x = features) == 0) {
     abort(message = "Cannot find features provided")
   }
-  if (ncol(x = GetAssayData(object = x, slot = 'counts')) == ncol(x = x)) {
-    slot(object = x, name = "counts") <- GetAssayData(object = x, slot = "counts")[features, cells, drop = FALSE]
+  if (ncol(x = GetAssayData(object = x, layer = 'counts')) == ncol(x = x)) {
+    slot(object = x, name = "counts") <- GetAssayData(object = x, layer = "counts")[features, cells, drop = FALSE]
   }
-  slot(object = x, name = "data") <- GetAssayData(object = x, slot = "data")[features, cells, drop = FALSE]
-  cells.scaled <- colnames(x = GetAssayData(object = x, slot = "scale.data"))
+  slot(object = x, name = "data") <- GetAssayData(object = x, layer = "data")[features, cells, drop = FALSE]
+  cells.scaled <- colnames(x = GetAssayData(object = x, layer = "scale.data"))
   cells.scaled <- cells.scaled[cells.scaled %in% cells]
   cells.scaled <- cells.scaled[na.omit(object = match(x = colnames(x = x), table = cells.scaled))]
-  features.scaled <- rownames(x = GetAssayData(object = x, slot = 'scale.data'))
+  features.scaled <- rownames(x = GetAssayData(object = x, layer = 'scale.data'))
   features.scaled <- intersect(x = features, y = features.scaled)
   slot(object = x, name = "scale.data") <- if (length(x = cells.scaled) > 0 && length(x = features.scaled) > 0) {
-    GetAssayData(object = x, slot = "scale.data")[features.scaled, cells.scaled, drop = FALSE]
+    GetAssayData(object = x, layer = "scale.data")[features.scaled, cells.scaled, drop = FALSE]
   } else {
     new(Class = 'matrix')
   }
@@ -1625,7 +1625,7 @@ setMethod(
   signature = c(x = 'Assay'),
   definition = function(x, na.rm = FALSE, dims = 1, ..., slot = 'data') {
     return(Matrix::colMeans(
-      x = GetAssayData(object = x, slot = slot),
+      x = GetAssayData(object = x, layer = slot),
       na.rm = na.rm,
       dims = dims,
       ...
@@ -1649,7 +1649,7 @@ setMethod(
   signature = c(x = 'Assay'),
   definition = function(x, na.rm = FALSE, dims = 1, ..., slot = 'data') {
     return(Matrix::colSums(
-      x = GetAssayData(object = x, slot = slot),
+      x = GetAssayData(object = x, layer = slot),
       na.rm = na.rm,
       dims = dims,
       ...
@@ -1673,7 +1673,7 @@ setMethod(
   signature = c(x = 'Assay'),
   definition = function(x, na.rm = FALSE, dims = 1, ..., slot = 'data') {
     return(Matrix::rowMeans(
-      x = GetAssayData(object = x, slot = slot),
+      x = GetAssayData(object = x, layer = slot),
       na.rm = na.rm,
       dims = dims,
       ...
@@ -1697,7 +1697,7 @@ setMethod(
   signature = c(x = 'Assay'),
   definition = function(x, na.rm = FALSE, dims = 1, ..., slot = 'data') {
     return(Matrix::rowSums(
-      x = GetAssayData(object = x, slot = slot),
+      x = GetAssayData(object = x, layer = slot),
       na.rm = na.rm,
       dims = dims,
       ...
@@ -1927,11 +1927,11 @@ SubsetVST <- function(sct.info, cells, features) {
 #' @noRd
 #'
 ValidateDataForMerge <- function(assay, slot) {
-  mat <- GetAssayData(object = assay, slot = slot)
+  mat <- GetAssayData(object = assay, layer = slot)
   if (any(dim(x = mat) == c(0, 0))) {
     slots.to.check <- setdiff(x = c("counts", "data", "scale.data"), y = slot)
     for (ss in slots.to.check) {
-      data.dims <- dim(x = GetAssayData(object = assay, slot = ss))
+      data.dims <- dim(x = GetAssayData(object = assay, layer = ss))
       data.slot <- ss
       if (!any(data.dims == c(0, 0))) {
         break
@@ -1944,7 +1944,7 @@ ValidateDataForMerge <- function(assay, slot) {
       data = 0,
       nrow = data.dims[1],
       ncol = data.dims[2],
-      dimnames = dimnames(x = GetAssayData(object = assay, slot = data.slot))
+      dimnames = dimnames(x = GetAssayData(object = assay, layer = data.slot))
     )
     mat <- as.sparse(x = mat)
   }

R/assay5.R

@@ -2733,7 +2733,7 @@ setAs(
     # browser()
     # Add the expression matrices
     for (i in c('counts', 'data', 'scale.data')) {
-      adata <- GetAssayData(object = from, slot = i)
+      adata <- GetAssayData(object = from, layer = i)
       if (IsMatrixEmpty(x = adata)) {
         next
       }

R/seurat.R

@@ -1871,7 +1871,7 @@ FetchData.Seurat <- function(
 #'
 #' @examples
 #' # Get assay data from the default assay in a Seurat object
-#' GetAssayData(object = pbmc_small, slot = "data")[1:5,1:5]
+#' GetAssayData(object = pbmc_small, layer = "data")[1:5,1:5]
 #'
 GetAssayData.Seurat <- function(
   object,
@@ -2153,9 +2153,11 @@ LayerData.Seurat <- function(
     ...
 ) {
   if (is_present(arg = slot)) {
-    deprecate_stop(when = "5.0.0",
-                   what = "LayerData(slot = )",
-                   with = "LayerData(layer = )")
+    deprecate_stop(
+      when = "5.0.0",
+      what = "LayerData(slot = )",
+      with = "LayerData(layer = )"
+    )
   }
   assay <- assay %||% DefaultAssay(object = object)
   assay <- arg_match(arg = assay, values = Assays(object = object))
@@ -2465,13 +2467,20 @@ SetAssayData.Seurat <- function(
   ...
 ) {
   CheckDots(...)
+  if (is_present(arg = slot)) {
+    .Deprecate(
+      when = '5.0.0',
+      what = 'GetAssayData(slot = )',
+      with = 'GetAssayData(layer = )'
+    )
+    layer <- slot
+  }
   object <- UpdateSlots(object = object)
   assay <- assay %||% DefaultAssay(object = object)
   object[[assay]] <- SetAssayData(
     object = object[[assay]],
     layer = layer,
     new.data = new.data,
-    slot = slot,
     ...
   )
   return(object)
@@ -2795,7 +2804,7 @@ WhichCells.Seurat <- function(
       object = object,
       vars = unique(x = expr.char[vars.use]),
       cells = cells,
-      slot = slot
+      layer = slot
     )
     cells <- rownames(x = data.subset)[eval_tidy(expr = expr, data = data.subset)]
   }
@@ -3911,7 +3920,7 @@ setMethod( # because R doesn't allow S3-style [[<- for S4 classes
       # Ensure cell order stays the same
       if (all(Cells(x = value) %in% Cells(x = x)) && !all(Cells(x = value) == Cells(x = x))) {
         for (slot in c('counts', 'data', 'scale.data')) {
-          assay.data <- GetAssayData(object = value, slot = slot)
+          assay.data <- GetAssayData(object = value, layer = slot)
           if (!IsMatrixEmpty(x = assay.data)) {
             assay.data <- assay.data[, Cells(x = x), drop = FALSE]
           }
@@ -4113,8 +4122,8 @@ setMethod( # because R doesn't allow S3-style [[<- for S4 classes
       if (inherits(x = value, what = 'Assay')) {
         if ((!i %in% Assays(object = x)) |
             (i %in% Assays(object = x) && !identical(
-              x = GetAssayData(object = x, assay = i, slot = "counts"),
-              y = GetAssayData(object = value, slot = "counts"))
+              x = GetAssayData(object = x, assay = i, layer = "counts"),
+              y = GetAssayData(object = value, layer = "counts"))
             )) {
           n.calc <- CalcN(object = value)
           if (!is.null(x = n.calc)) {