Correctly assign levels to factors in R reader

Fixes #122
theislab · Oct 4, 2024 · 03c28f8 · 03c28f8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: zellkonverter
 Title: Conversion Between scRNA-seq Objects
-Version: 1.15.2
-Date: 2024-10-02
+Version: 1.15.3
+Date: 2024-10-04
 Authors@R: c(
     person("Luke", "Zappia", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7744-8565")),

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,10 @@
 
 * Bioconductor 3.20, October 2024
 
+## zellkonverter 1.15.3 (2024-10-04)
+
+* Correctly assign levels to factors in R reader (Fixes #122)
+
 ## zellkonverter 1.15.2 (2024-10-02)
 
 * Correctly set `filepath` in the R reader with reading `adata.raw` with `use_hdf5 = TRUE` (PR #124 @GabrielHoffman, Fixes #123)

diff --git a/R/read.R b/R/read.R
@@ -368,8 +368,7 @@ readH5AD <- function(file, X_name = NULL, use_hdf5 = FALSE,
         levels <- as.vector(
             rhdf5::h5read(file, file.path(path, "__categories", cat_name))
         )
-        out_cols[[cat_name]] <- factor(out_cols[[cat_name]])
-        levels(out_cols[[cat_name]]) <- levels
+        out_cols[[cat_name]] <- factor(out_cols[[cat_name]], levels = levels)
     }
 
     ## rhdf5::h5readAttributes(file, "var") |> str()