fix: Ignore NaNs when calculating scatter plot dot size (#3771)

Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Philipp A. <[email protected]>

Author: 3 people

src/scanpy/plotting/_tools/scatterplots.py

@@ -226,7 +226,8 @@ def embedding(  # noqa: PLR0912, PLR0913, PLR0915
         ):
             size = np.array(size, dtype=float)
     else:
-        size = 120000 / adata.shape[0]
+        # if the basis has NaNs, ignore the corresponding cells for size calcluation
+        size = 120000 / (~np.isnan(basis_values).any(axis=1)).sum()
 
     ##########
     # Layout #