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Automatically reset PCs based on var size #76

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Automatically reset PCs based on var size #76

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dd25d9e
reset PCs based on var size
Feb 21, 2020
aff91e4
Update _pca.py
pinin4fjords Feb 21, 2020
0340cea
Remove misplaced comment
pinin4fjords Feb 21, 2020
a452002
updated to n_comps
Feb 21, 2020
6bdb042
Merge branch 'develop' into fix_pca_defaults
pcm32 Feb 19, 2024
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8 changes: 8 additions & 0 deletions scanpy_scripts/lib/_pca.py
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Expand Up @@ -3,12 +3,20 @@
"""

import scanpy as sc
import math
from ..obj_utils import write_embedding

def pca(adata, key_added=None, export_embedding=None, **kwargs):
"""
Wrapper function for sc.pp.pca, for supporting named slot
"""

# Check the number of components (use_pc) less than floor(number of genes)/2
if 'use_pc' in kwargs and kwargs['use_pc'] is not None:
kwargs['use_pc'] = min(math.floor(adata.n_vars/2), kwargs['use_pc'])

# minimum of (<value calculated above>, n_pcs_supplied)

# omit "svd_solver" to let scanpy choose automatically
if 'svd_solver' in kwargs and kwargs['svd_solver'] == 'auto':
del kwargs['svd_solver']
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