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handle Mapping cohorts in pca #1329

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handle Mapping cohorts in pca #1329

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5a0567a
handle Mapping cohorts in pca
31puneet Jun 1, 2026
0de092b
running ci again
31puneet Jun 1, 2026
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10 changes: 7 additions & 3 deletions malariagen_data/anoph/pca.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@

from ..util import CacheMiss, _check_types, _jitter
from . import base_params, pca_params, plotly_params
from .sample_metadata import _locate_cohorts
from .snp_data import AnophelesSnpData


Expand Down Expand Up @@ -89,7 +90,7 @@ def pca(
) -> Tuple[pca_params.df_pca, pca_params.evr]:
# Change this name if you ever change the behaviour of this function, to
# invalidate any previously cached data.
name = "pca_v8"
name = "pca_v9"

# Check that either sample_query xor sample_indices are provided.
base_params._validate_sample_selection_params(
Expand Down Expand Up @@ -118,9 +119,12 @@ def pca(
sample_query_options=sample_query_options,
)
# N.B., we are going to overwrite the sample_indices parameter here.
groups = df_samples.groupby(cohorts, sort=False)
coh_dict = _locate_cohorts(
cohorts=cohorts, data=df_samples, min_cohort_size=0
)
ix = []
for _, group in groups:
for _label, loc_coh in coh_dict.items():
group = df_samples[loc_coh]
if len(group) > max_cohort_size:
ix.extend(
group.sample(
Expand Down
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