Remove droplevels call from subset, revert #251

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SeuratObject
 Title: Data Structures for Single Cell Data
-Version: 5.2.0
+Version: 5.2.0.9000
 Authors@R: c(
   person(given = 'Paul', family = 'Hoffman', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-7693-8957')),
   person(given = 'Rahul', family = 'Satija', email = '[email protected]', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-9448-8833')),

NEWS.md

@@ -1,6 +1,7 @@
 # Unreleased
 
 ## Changes
+ - Update `subset.Seurat` to no longer call `droplevels` on the input's cell-level `meta.data` slot; update `subset.Assay` to no longer call `droplevels` on the input's feature-level `meta.features` slot; update `subset.StdAssay` to no longer call `droplevels` on the input's feature-level `meta.data` slot (reverting #251, see discussion in #247)
 
 # SeuratObject 5.2.0
 

R/assay.R

@@ -1488,13 +1488,7 @@ subset.Assay <- function(x, cells = NULL, features = NULL, ...) {
     new(Class = 'matrix')
   }
   VariableFeatures(object = x) <- VariableFeatures(object = x)[VariableFeatures(object = x) %in% features]
-
-  # Subset feature-level metadata.
-  meta.features <- x[[]]
-  meta.features <- meta.features[features, , drop = FALSE]
-  meta.features <- droplevels(meta.features)
-  slot(object = x, name = 'meta.features') <- meta.features
-
+  slot(object = x, name = 'meta.features') <- x[[]][features, , drop = FALSE]
   validObject(object = x)
   return(x)
 }

R/assay5.R

@@ -2484,12 +2484,8 @@ subset.StdAssay <- function(
     orig = features,
     ordered = TRUE
   )
-
-  # Subset feature-level metadata.
-  meta.data <- slot(x, name = "meta.data")
-  meta.data <- meta.data[mfeatures, , drop = FALSE]
-  meta.data <- droplevels(meta.data)
-  slot(x, name = "meta.data") <- meta.data
+  # subset the meta.data slot accordingly
+  slot(x, name = "meta.data") <- slot(x, name = "meta.data")[mfeatures, , drop = FALSE]
 
   # ensure the object is valid
   validObject(x)

R/seurat.R

@@ -3727,13 +3727,7 @@ subset.Seurat <- function(
   # Remove metadata for cells not present
   orig.cells <- colnames(x = x)
   cells <- intersect(x = orig.cells, y = cells)
-
-  # Subset cell-level metadata.
-  meta.data <- x[[]]
-  meta.data <- meta.data[cells, , drop = FALSE]
-  meta.data <- droplevels(meta.data)
-  slot(object = x, name = 'meta.data') <- meta.data
-
+  slot(object = x, name = 'meta.data') <- x[[]][cells, , drop = FALSE]
   if (!all(orig.cells %in% cells)) {
     # Remove neighbors
     slot(object = x, name = 'neighbors') <- list()