Merge remote-tracking branch 'origin/development' into allyhawkins/al…

…texp-merged-objects

templates/qc_report/celltypes_supplemental_report.rmd

@@ -339,18 +339,20 @@ if (has_singler) {
 }
 
 if (has_cellassign) {
-  tissue_type <- stringr::word(
-    # eg, "blood-compartment"
-    metadata(processed_sce)$cellassign_reference,
-    1,
-    sep = "-"
-  )
+  
+  organs <- metadata(processed_sce)$cellassign_reference_organs |>
+    stringr::str_to_lower()
+  # split up and add an `and` before the final organ
+  organs_string <- stringr::str_split_1(organs, pattern = ", ") |> 
+    stringr::str_flatten_comma(last = ", and ")
+  
+  ref_name <- metadata(processed_sce)$cellassign_reference
 
   methods_text <- glue::glue(
     "{methods_text}
     * Annotations from [`CellAssign`](https://github.com/Irrationone/cellassign), a marker-gene-based approach ([Zhang _et al._ 2019](https://doi.org/10.1038/s41592-019-0529-1)).
-    Marker genes associated with `{tissue_type}` tissue were obtained from [PanglaoDB](https://panglaodb.se/).\n
-    "
+    Marker genes for cell types were obtained from [PanglaoDB](https://panglaodb.se/) and compiled into a reference named `{ref_name}`. 
+    This reference includes the following organs and tissue compartments: {organs_string}.\n"
   )
 }