Retreive within_group from mdata OR adata (#459)

* Retreive within_group from mdata OR adata

* udpate changelog

* Fix _validate_parameters for ir_query

* Fix sphinx warning

CHANGELOG.md

@@ -10,6 +10,10 @@ and this project adheres to [Semantic Versioning][].
 
 ## [Unreleased]
 
+### Fixes
+
+-   Fix that `define_clonotype_clusters` could not retreive `within_group` columns from MuData ([#459](https://github.com/scverse/scirpy/pull/459))
+
 ## v0.13.1
 
 ### Fixes

docs/conf.py

@@ -138,6 +138,7 @@
     "repository_url": repository_url,
     "use_repository_button": True,
     "path_to_docs": "docs/",
+    "navigation_with_keys": False,
 }
 
 pygments_style = "default"

src/scirpy/ir_dist/_clonotype_neighbors.py

@@ -77,7 +77,7 @@ def _make_clonotype_table(self, params: DataHandler) -> tuple[Mapping, pd.DataFr
         obs = obs.loc[_has_ir(params) & np.any(~pd.isnull(obs), axis=1), :]
         if self.match_columns is not None:
             obs = obs.join(
-                params.adata.obs.loc[:, self.match_columns],
+                params.get_obs(self.match_columns),
                 validate="one_to_one",
                 how="inner",
             )

src/scirpy/tl/_clonotypes.py

@@ -123,11 +123,11 @@
 
 
 def _validate_parameters(
-    adata,
-    reference,
+    params: DataHandler,
+    reference: DataHandler,
     receptor_arms,
     dual_ir,
-    match_columns,
+    within_group,
     distance_key,
     sequence,
     metric,
@@ -137,7 +137,7 @@ def _validate_parameters(
 
     def _get_db_name():
         try:
-            return reference.uns["DB"]["name"]
+            return reference.adata.uns["DB"]["name"]
         except KeyError:
             raise ValueError(
                 'If reference does not contain a `.uns["DB"]["name"]` entry, '
@@ -153,22 +153,24 @@ def _get_db_name():
     if dual_ir not in ["primary_only", "all", "any"]:
         raise ValueError("Invalid value for `dual_ir")
 
-    if match_columns is not None:
-        if isinstance(match_columns, str):
-            match_columns = [match_columns]
-        for group_col in match_columns:
-            if group_col not in adata.obs.columns:
-                msg = f"column `{match_columns}` not found in `adata.obs`. "
+    if within_group is not None:
+        if isinstance(within_group, str):
+            within_group = [within_group]
+        for group_col in within_group:
+            try:
+                params.get_obs(group_col)
+            except KeyError:
+                msg = f"column `{group_col}` not found in `obs`. "
                 if group_col in ("receptor_type", "receptor_subtype"):
                     msg += "Did you run `tl.chain_qc`? "
-                raise ValueError(msg)
+                raise ValueError(msg) from None
 
     if distance_key is None:
         if reference is not None:
             distance_key = f"ir_dist_{_get_db_name()}_{sequence}_{_get_metric_key(metric)}"
         else:
             distance_key = f"ir_dist_{sequence}_{_get_metric_key(metric)}"
-    if distance_key not in adata.uns:
+    if distance_key not in params.adata.uns:
         raise ValueError("Sequence distances were not found in `adata.uns`. Did you run `pp.ir_dist`?")
 
     if key_added is None:
@@ -177,7 +179,7 @@ def _get_db_name():
         else:
             key_added = f"cc_{sequence}_{_get_metric_key(metric)}"
 
-    return match_columns, distance_key, key_added
+    return within_group, distance_key, key_added
 
 
 @DataHandler.inject_param_docs(
@@ -271,7 +273,7 @@ def define_clonotype_clusters(
     """
     params = DataHandler(adata, airr_mod, airr_key, chain_idx_key)
     within_group, distance_key, key_added = _validate_parameters(
-        params.adata,
+        params,
         None,
         receptor_arms,
         dual_ir,

src/scirpy/tl/_ir_query.py

@@ -178,8 +178,8 @@ def ir_query(
         DataHandler(reference, airr_mod_ref, airr_key_ref, chain_idx_key_ref) if reference is not None else None
     )
     match_columns, distance_key, key_added = _validate_parameters(
-        params.adata,
-        params_ref.adata if params_ref is not None else None,
+        params,
+        params_ref if params_ref is not None else None,
         receptor_arms,
         dual_ir,
         match_columns,