From 7ac9ee488b36c8d2bddf4cb50530d87e16e7918b Mon Sep 17 00:00:00 2001
From: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com>
Date: Fri, 20 Oct 2023 13:14:43 -0500
Subject: [PATCH] track singler label in singler objects

---
 bin/add_celltypes_to_sce.R | 8 ++++++--
 bin/classify_SingleR.R     | 2 ++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/bin/add_celltypes_to_sce.R b/bin/add_celltypes_to_sce.R
index fb3cf0a3..85337b52 100755
--- a/bin/add_celltypes_to_sce.R
+++ b/bin/add_celltypes_to_sce.R
@@ -62,6 +62,9 @@ if(!is.null(opt$singler_results)){
   }
 
   singler_results <- readr::read_rds(opt$singler_results)
+  
+  # get label type from metadata of singler object
+  label_type <- metadata(singler_results)$reference_label
 
   # create a tibble with annotations and barcode
   # later we'll add the annotations into colData by joining on barcodes column
@@ -71,8 +74,8 @@ if(!is.null(opt$singler_results)){
   )
 
   # map ontology labels to cell type names, as needed
-  # we can tell if ontologies were used because this will exist:
-  if ("cell_ontology_df" %in% names(singler_results)) {
+  # label type will be label.ont if ontology is present
+  if (label_type == "label.ont") {
 
     # end up with columns: barcode, singler_celltype_annotation, singler_celltype_ontology
     colData(sce) <- annotations_df |>
@@ -100,6 +103,7 @@ if(!is.null(opt$singler_results)){
   # add singler info to metadata
   metadata(sce)$singler_results <- singler_results
   metadata(sce)$singler_reference <- metadata(singler_results)$reference_name
+  metadata(sce)$singler_reference_label <- label_type
 
   # add note about cell type method to metadata
   metadata(sce)$celltype_methods <- c(metadata(sce)$celltype_methods, "singler")
diff --git a/bin/classify_SingleR.R b/bin/classify_SingleR.R
index 54862131..1337df0e 100755
--- a/bin/classify_SingleR.R
+++ b/bin/classify_SingleR.R
@@ -94,6 +94,8 @@ singler_results <- SingleR::classifySingleR(
 
 # add reference name to singler_results DataFrame metadata
 metadata(singler_results)$reference_name <- reference_name
+# add label name to metadata
+metadata(singler_results)$reference_label <- metadata(singler_model)$reference_label
 
 # export results ---------------