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Harmony 64bit #2655

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merged 4 commits into from Sep 14, 2023
Merged

Harmony 64bit #2655

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d6a5aab
harmony runs with 64 bit
Intron7 Sep 5, 2023
afdc1db
add harmony
Intron7 Sep 5, 2023
df1c96f
Update 1.10.0.md
Intron7 Sep 5, 2023
9e142c8
Merge branch 'master' into harmony-64
Intron7 Sep 5, 2023
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1 change: 1 addition & 0 deletions docs/release-notes/1.10.0.md
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Expand Up @@ -8,6 +8,7 @@
* {func}`scanpy.pp.neighbors` now has a `transformer` argument allowing for more flexibility {pr}`2536` {smaller}`P Angerer`
* {func}`scanpy.experimental.pp.highly_variable_genes` using `flavor='pearson_residuals'`
now uses numba for variance computation {pr}`2612` {smaller}`S Dicks & P Angerer`
* {func}`scanpy.external.pp.harmony_integrate` now runs with 64 bit floats improving reproducibility {pr}`2655` {smaller}`S Dicks`

```{rubric} Docs
```
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5 changes: 4 additions & 1 deletion scanpy/external/pp/_harmony_integrate.py
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Expand Up @@ -5,6 +5,7 @@
from typing import Optional

from anndata import AnnData
import numpy as np


def harmony_integrate(
Expand Down Expand Up @@ -79,6 +80,8 @@ def harmony_integrate(
except ImportError:
raise ImportError("\nplease install harmonypy:\n\n\tpip install harmonypy")

harmony_out = harmonypy.run_harmony(adata.obsm[basis], adata.obs, key, **kwargs)
X = adata.obsm[basis].astype(np.float64)

harmony_out = harmonypy.run_harmony(X, adata.obs, key, **kwargs)

adata.obsm[adjusted_basis] = harmony_out.Z_corr.T