Merge pull request #48 from quadbio/fix/joint_pca

Fix hvg mask to joint_pca

Author: Marius1311

CHANGELOG.md

@@ -10,6 +10,17 @@ and this project adheres to [Semantic Versioning][].
 
 ## [Unreleased]
 
+## [v0.2.2]
+### Added
+- Enabled subsetting categories before mapping .obs values {pr}`46`
+
+### Changed
+- Updated the README a bit {pr}`44`
+- Updated tutorials to work with new parameter names {pr}`43`
+
+### Fices
+- Fixed a small bug where hvg masks would not be propagated correctly to joint pca computation {pr}`48`
+
 ## [v0.2.1]
 ### Changed
 - Move some duplicated docstrings into a central _docs.py file {pr}`41`

src/cellmapper/model/embedding.py

@@ -32,7 +32,9 @@ def compute_joint_pca(self, n_comps: int | None = None, key_added: str = "X_pca"
         improved cross-dataset integration.
         """
         # Concatenate with inner join on genes
-        joint = ad.concat([self.reference, self.query], join="inner", label="batch", keys=["reference", "query"])
+        joint = ad.concat(
+            [self.reference, self.query], join="inner", label="batch", keys=["reference", "query"], merge="same"
+        )
 
         # Compute PCA using scanpy
         sc.pp.pca(joint, n_comps=n_comps, **kwargs)