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Ignore NaNs when calculating scatter plot dot size #3771

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Ignore NaNs when calculating scatter plot dot size #3771

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Ignore NaNs when calculating scatter plot dot size
MLubetzki Aug 22, 2025
1bd3b19
Merge branch 'main' into embedding_size_ignore_nans
Zethson Oct 3, 2025
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3 changes: 2 additions & 1 deletion src/scanpy/plotting/_tools/scatterplots.py
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Expand Up @@ -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()

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# Layout #
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