Comments (3)
Thanks for opening the issue!
harmonypy version 0.0.4 (and later versions) supports multiple covariates.
Please see #4 for discussion of this issue.
from harmonypy.
Hello @slowkow
Thank you! Has this been added to the Scanpy function?
I assume the line will look like: sce.pp.harmony_integrate(adata, ['batch1', 'batch2'])
from harmonypy.
Try it! If it doesn't work, then please consider reporting the issue to scanpy developers.
Please also consider reading the source code for the packages that you use:
Here is what I see inside the harmony_integrate()
scanpy function (lines 77-84):
try:
import harmonypy
except ImportError:
raise ImportError("\nplease install harmonypy:\n\n\tpip install harmonypy")
harmony_out = harmonypy.run_harmony(adata.obsm[basis], adata.obs, key, **kwargs)
adata.obsm[adjusted_basis] = harmony_out.Z_corr.T
from harmonypy.
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