Merge pull request #147 from rcannood/patch-1

Fix `tfidf` to always use correct counts when from_layer is specified
scverse · Oct 17, 2024 · d52b60d · d52b60d
2 parents ff3c0e1 + 782d85c
commit d52b60d
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/muon/_atac/preproc.py b/muon/_atac/preproc.py
@@ -96,14 +96,14 @@ def tfidf(
         tf = np.dot(n_peaks, counts)
     else:
         n_peaks = np.asarray(counts.sum(axis=1)).reshape(-1, 1)
-        tf = adata.X / n_peaks
+        tf = counts / n_peaks
 
     if scale_factor is not None and scale_factor != 0 and scale_factor != 1:
         tf = tf * scale_factor
     if log_tf:
         tf = np.log1p(tf)
 
-    idf = np.asarray(adata.shape[0] / adata.X.sum(axis=0)).reshape(-1)
+    idf = np.asarray(adata.shape[0] / counts.sum(axis=0)).reshape(-1)
     if log_idf:
         idf = np.log1p(idf)