Merge pull request #85 from stemangiola/hotfix-Seurat5-one-cell-bug

Hotfix seurat5 one cell bug
stemangiola · Jul 18, 2024 · 82b6aec · 82b6aec
2 parents 74a7cca + 5780b87
commit 82b6aec
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Showing 5 changed files with 30 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidyseurat
 Title: Brings Seurat to the Tidyverse 
-Version: 0.8.1
+Version: 0.8.2
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")),
             person("Maria", "Doyle", email = "[email protected]",
@@ -49,6 +49,6 @@ Biarch: true
 biocViews: AssayDomain, Infrastructure, RNASeq, DifferentialExpression, GeneExpression, Normalization, Clustering, QualityControl, Sequencing, Transcription, Transcriptomics
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 URL: https://github.com/stemangiola/tidyseurat, https://stemangiola.github.io/tidyseurat/
 BugReports: https://github.com/stemangiola/tidyseurat/issues
diff --git a/R/methods.R b/R/methods.R
@@ -108,7 +108,6 @@ setMethod("join_features", "Seurat", function(.data,
 
 })
 
-
 #' @name aggregate_cells
 #' @rdname aggregate_cells
 #' @inherit ttservice::aggregate_cells
@@ -128,6 +127,7 @@ setMethod("join_features", "Seurat", function(.data,
 #' @importFrom ttservice aggregate_cells
 #' @importFrom SeuratObject DefaultAssay
 #' @importFrom Seurat DietSeurat
+#' @importFrom Seurat GetAssayData
 #' @importFrom purrr map_int
 #' @export
 setMethod("aggregate_cells", "Seurat",  function(.data,
@@ -153,7 +153,7 @@ setMethod("aggregate_cells", "Seurat",  function(.data,
                 # Loop over assays
                 map2(.x@assays, names(.x@assays),
                     # Get counts
-                    ~ GetAssayData(.x, layer=slot) %>%
+                    ~ GetAssayData_robust(.x, layer=slot) %>%
                         aggregation_function(na.rm=T) %>%
                         tibble::enframe(
                             name=".feature",

diff --git a/R/utilities.R b/R/utilities.R
@@ -496,8 +496,26 @@ subset_tidyseurat <- function(.data, .column) {
         stop("tidyseurat says: some of the .column specified",
             " do not exist in the input data frame.")
 
+
     .data %>%
     # Selecting the right columns
         select(!!.column, get_specific_annotation_columns(.data, !!.column)) %>%
         distinct()
 }
+
+#' @importFrom Seurat GetAssayData
+GetAssayData_robust = function(seurat_assay, layer = NULL){
+
+  if(
+    seurat_assay |> is("Assay5") & 
+    seurat_assay |> ncol() == 1
+  ){
+    m = seurat_assay@layers[[layer]] |> as.matrix()
+    rownames(m) = rownames(seurat_assay)
+    colnames(m) = colnames(seurat_assay)
+    m
+  }
+
+  else 
+    GetAssayData(seurat_assay, layer=layer)
+}
diff --git a/README.md b/README.md
@@ -105,7 +105,7 @@ pbmc_small
 ```
 
     ## # A Seurat-tibble abstraction: 80 × 15
-    ## # [90mFeatures=230 | Cells=80 | Active assay=RNA | Assays=RNA[0m
+    ## # [90mFeatures=230 | Cells=80 | Active assay=RNA | Assays=RNA[0m
     ##    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
     ##    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
     ##  1 ATGC… SeuratPro…         70           47 0               A             g2    
@@ -217,7 +217,7 @@ pbmc_small_pca
 ```
 
     ## # A Seurat-tibble abstraction: 80 × 17
-    ## # [90mFeatures=220 | Cells=80 | Active assay=SCT | Assays=RNA, SCT[0m
+    ## # [90mFeatures=220 | Cells=80 | Active assay=SCT | Assays=RNA, SCT[0m
     ##    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
     ##    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
     ##  1 ATGC… SeuratPro…         70           47 0               A             g2    
@@ -262,7 +262,7 @@ pbmc_small_cluster
 ```
 
     ## # A Seurat-tibble abstraction: 80 × 19
-    ## # [90mFeatures=220 | Cells=80 | Active assay=SCT | Assays=RNA, SCT[0m
+    ## # [90mFeatures=220 | Cells=80 | Active assay=SCT | Assays=RNA, SCT[0m
     ##    .cell orig.ident nCount_RNA nFeature_RNA RNA_snn_res.0.8 letter.idents groups
     ##    <chr> <fct>           <dbl>        <int> <fct>           <fct>         <chr> 
     ##  1 ATGC… SeuratPro…         70           47 0               A             g2    

diff --git a/tests/testthat/test-methods.R b/tests/testthat/test-methods.R
@@ -52,6 +52,11 @@ test_that("aggregate_cells() returns expected values", {
                                   pull(.cell)] |>
         LayerData() |> 
         sum())
+
+  # Aggregate with tidyselect
+  pbmc_small |>
+    aggregate_cells(c(any_of("groups"), letter.idents), assays = "RNA") |> 
+    expect_no_error()
 })
 
 test_that("get_abundance_sc_wide", {