Merge pull request #76 from stemangiola/aggregate-fix-assay-subset-fo…

…r-complex-seurats use DietSeurat instead of manual subsetting
stemangiola · Oct 30, 2023 · c4aafa8 · c4aafa8
2 parents 81ddf3f + 1af3dae
commit c4aafa8
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidyseurat
 Title: Brings Seurat to the Tidyverse 
-Version: 0.7.4
+Version: 0.7.5
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")),
             person("Maria", "Doyle", email = "[email protected]",
@@ -15,7 +15,7 @@ Depends:
     ttservice (>= 0.3.8),
     SeuratObject
 Imports:
-    Seurat,
+    Seurat (>= 4.3.0),
     tibble,
     dplyr,
     magrittr,

diff --git a/NAMESPACE b/NAMESPACE
@@ -54,6 +54,7 @@ exportMethods(aggregate_cells)
 exportMethods(join_features)
 importFrom(Matrix,rowSums)
 importFrom(Seurat,Assays)
+importFrom(Seurat,DietSeurat)
 importFrom(Seurat,GetAssayData)
 importFrom(Seurat,SplitObject)
 importFrom(Seurat,VariableFeatures)

diff --git a/R/methods.R b/R/methods.R
@@ -126,6 +126,7 @@ setMethod("join_features", "Seurat", function(.data,
 #' @importFrom Matrix rowSums
 #' @importFrom ttservice aggregate_cells
 #' @importFrom SeuratObject DefaultAssay
+#' @importFrom Seurat DietSeurat
 #' @importFrom purrr map_int
 #' @export
 setMethod("aggregate_cells", "Seurat",  function(.data,
@@ -140,7 +141,7 @@ setMethod("aggregate_cells", "Seurat",  function(.data,
     # Subset only wanted assays
     if(!is.null(assays)){
         DefaultAssay(.data) <- assays[1]
-        .data@assays <- .data@assays[assays]
+        .data = .data |> DietSeurat(assays = assays)
     }
 
     .data %>%
@@ -159,9 +160,9 @@ setMethod("aggregate_cells", "Seurat",  function(.data,
                         ) %>%
                         mutate(.feature=as.character(.feature)) 
                 ) %>%
-                Reduce(function(...) full_join(..., by=c(".feature")), .)            
-            )
-        ) %>%
+                Reduce(function(...) full_join(..., by=c(".feature")), .), 
+                .progress = TRUE          
+        )) %>%
         left_join(
             .data %>%
                 as_tibble() %>%