Merge pull request #112 from stemangiola/ECCB2024

fixes to aggregate and as_SE
stemangiola · Sep 17, 2024 · 4cef707 · 4cef707
2 parents 38b69e5 + b340b74
commit 4cef707
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.15.4
+Version: 1.15.5
 Authors@R: c(person("Stefano", "Mangiola", 
     comment=c(ORCID="0000-0001-7474-836X"),
     email="[email protected]",

diff --git a/R/methods.R b/R/methods.R
@@ -232,12 +232,12 @@ setMethod("aggregate_cells", "SingleCellExperiment", function(.data,
       subset(!!.sample) |>
       unite("my_id_to_split_by___", !!.sample, remove=FALSE, sep = "___") 
 
-    new_col_data = new_col_data |> DataFrame(row.names = new_col_data$my_id_to_split_by___) |> _[,-1]
+    new_col_data = new_col_data |> DataFrame(row.names = new_col_data$my_id_to_split_by___) |> _[,-1,drop=FALSE]
 
     colData(aggregated_sce) = 
       colData(aggregated_sce) |> 
       cbind(
-        new_col_data[match(rownames(colData(aggregated_sce)), rownames(new_col_data)),]
+        new_col_data[match(rownames(colData(aggregated_sce)), rownames(new_col_data)),,drop=FALSE]
       )
 
     rowData(aggregated_sce)  = rowData(.data)

diff --git a/R/tidybulk_utilities.R b/R/tidybulk_utilities.R
@@ -132,7 +132,7 @@ as_SummarizedExperiment <- function(.data,
         tidyr::nest(`data`=-`assay`) %>%
         mutate(`data`=`data` %>%  map(
             ~ .x %>%
-                spread(!!sample__$symbol, .a) %>%
+                pivot_wider(names_from =  !!sample__$symbol, values_from = .a) %>%
 
                 # arrange sample
                 select(!!feature__$symbol, any_of(rownames(colData))) |>