Merge pull request #21 from quadbio/feat/input_imputed

Work with pre-computed objects for imputed values and k-NN graphs

Author: Marius1311

pyproject.toml

@@ -58,6 +58,7 @@ optional-dependencies.doc = [
 optional-dependencies.test = [
   "coverage",
   "pytest",
+  "squidpy",
 ]
 optional-dependencies.tutorials = [
   "harmony-pytorch",

src/cellmapper/cellmapper.py

@@ -57,14 +57,17 @@ def check(self) -> None:
 
 
 INSTALL_HINTS = types.SimpleNamespace(
-    rapids="To speed up k-NN search on GPU, you may install rapids following the guide from "
-    "https://docs.rapids.ai/install/. Note that you will only need cuML.",
+    cuml="To speed up k-NN search on GPU, you may install cuML following the guide from "
+    "https://docs.rapids.ai/install/.",
+    cupy="To speed up k-NN search on GPU, you may install cuPy following the guide from "
+    "https://docs.rapids.ai/install/.",
     faiss="To speed up k-NN search on GPU, you may install faiss following the guide from "
     "https://github.com/facebookresearch/faiss/blob/main/INSTALL.md",
 )
 
 CHECKERS = {
-    "rapids": Checker("rapids", vmin=None, install_hint=INSTALL_HINTS.rapids),
+    "cuml": Checker("cuml", vmin=None, install_hint=INSTALL_HINTS.cuml),
+    "cupy": Checker("cupy", vmin=None, install_hint=INSTALL_HINTS.cupy),
     "faiss": Checker("faiss", package_name="faiss", vmin="1.7.0", install_hint=INSTALL_HINTS.faiss),
 }
 

src/cellmapper/check.py

@@ -35,8 +35,6 @@ def _jensen_shannon_divergence(p: np.ndarray, q: np.ndarray) -> float:
     q = np.clip(q, 0, None)
     if p.sum() == 0 or q.sum() == 0:
         return np.nan
-    p = p / p.sum()
-    q = q / q.sum()
     return jensenshannon(p, q, base=10)
 
 
@@ -226,7 +224,11 @@ def evaluate_expression_transfer(
 
         # Helper to compute metrics for a given mask of cells
         def compute_metrics(mask):
-            return np.array([metric_func(original_x[mask, i], imputed_x[mask, i]) for i in range(imputed_x.shape[1])])
+            # Explicitly return as float32 to match DataFrame's dtype
+            return np.array(
+                [metric_func(original_x[mask, i], imputed_x[mask, i]) for i in range(imputed_x.shape[1])],
+                dtype=np.float32,
+            )
 
         # Compute metrics for all cells
         overall_mask = np.ones(original_x.shape[0], dtype=bool)
@@ -273,7 +275,9 @@ def _get_aligned_expression_arrays(self, layer_key: str) -> tuple[np.ndarray, np
         imputed_x, original_x, shared_genes
         """
         if self.query_imputed is None:
-            raise ValueError("Imputed query data not found. Run transfer_expression() first.")
+            raise ValueError(
+                "Imputed query data not found. Either run transfer_expression() first or set query_imputed manually."
+            )
         shared_genes = list(self.query_imputed.var_names.intersection(self.query.var_names))
         if len(shared_genes) == 0:
             raise ValueError("No shared genes between query_imputed and query.")
@@ -376,8 +380,8 @@ def estimate_presence_score(
         groupby
             Column in self.query.obs to group query cells by (e.g., cell type, batch). If None, computes a single score for all query cells.
         key_added
-            Key to store the presence score: always writes the score across all query cells to self.ref.obs[key_added].
-            If groupby is not None, also writes per-group scores as a DataFrame to self.ref.obsm[key_added].
+            Key to store the presence score: always writes the score across all query cells to self.reference.obs[key_added].
+            If groupby is not None, also writes per-group scores as a DataFrame to self.reference.obsm[key_added].
         log
             Whether to apply log1p transformation to the scores.
         percentile
@@ -387,30 +391,30 @@ def estimate_presence_score(
             raise ValueError("Neighbors must be computed before estimating presence scores.")
 
         conn = self.knn.yx.knn_graph_connectivities()
-        ref_names = self.ref.obs_names
+        reference_names = self.reference.obs_names
 
         # Always compute and post-process the overall score (all query cells)
         scores_all = np.array(conn.sum(axis=0)).flatten()
-        df_all = pd.DataFrame({"all": scores_all}, index=ref_names)
+        df_all = pd.DataFrame({"all": scores_all}, index=reference_names)
         df_all_processed = process_presence_scores(df_all, log=log, percentile=percentile)
-        self.ref.obs[key_added] = df_all_processed["all"]
-        logger.info("Presence score across all query cells computed and stored in `ref.obs['%s']`", key_added)
+        self.reference.obs[key_added] = df_all_processed["all"]
+        logger.info("Presence score across all query cells computed and stored in `reference.obs['%s']`", key_added)
 
         # If groupby, also compute and post-process per-group scores
         if groupby is not None:
             group_labels = self.query.obs[groupby]
             groups = group_labels.unique()
-            score_matrix = np.zeros((len(ref_names), len(groups)), dtype=np.float32)
+            score_matrix = np.zeros((len(reference_names), len(groups)), dtype=np.float32)
             for i, group in enumerate(groups):
                 mask = group_labels == group
                 group_conn = conn[mask.values, :]
                 score_matrix[:, i] = np.array(group_conn.sum(axis=0)).flatten()
-            df_groups = pd.DataFrame(score_matrix, index=ref_names, columns=groups)
+            df_groups = pd.DataFrame(score_matrix, index=reference_names, columns=groups)
             df_groups_processed = process_presence_scores(df_groups, log=log, percentile=percentile)
-            self.ref.obsm[key_added] = df_groups_processed
+            self.reference.obsm[key_added] = df_groups_processed
 
             logger.info(
-                "Presence scores per group defined in `query.obs['%s']` computed and stored in `ref.obsm['%s']`",
+                "Presence scores per group defined in `query.obs['%s']` computed and stored in `reference.obsm['%s']`",
                 groupby,
                 key_added,
             )