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Allow set random seed for reproducibility in CompositionalAnalysis objects #49

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Allow set random seed for reproducibility in CompositionalAnalysis objects #49

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9462fa1
Add random seed for reproducibility
yihming Feb 13, 2022
30a24ea
Merge branch 'theislab:master' into master
yihming Mar 3, 2022
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4 changes: 4 additions & 0 deletions sccoda/model/scCODA_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -615,6 +615,7 @@ class scCODAModel(CompositionalModel):
def __init__(
self,
reference_cell_type: int,
seed: Optional[int] = None,
*args,
**kwargs):
"""
Expand Down Expand Up @@ -708,6 +709,9 @@ def target_log_prob_fn(*argsl):
self.target_log_prob_fn = target_log_prob_fn

# MCMC starting values
if seed is not None:
tf.random.set_seed(seed)

self.init_params = [
tf.ones(sigma_size, name="init_sigma_d", dtype=dtype),
tf.random.normal(beta_nobl_size, 0, 1, name='init_b_offset', dtype=dtype),
Expand Down
4 changes: 4 additions & 0 deletions sccoda/util/comp_ana.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@ def __new__(
formula: str,
reference_cell_type: Union[str, int] = "automatic",
automatic_reference_absence_threshold: float = 0.05,
seed: Optional[int] = None,
) -> dm.scCODAModel:
"""
Builds count and covariate matrix, returns a CompositionalModel object
Expand Down Expand Up @@ -100,6 +101,7 @@ def __new__(
covariate_names=covariate_names,
reference_cell_type=ref_index,
formula=formula,
seed=seed,
)

# Column name as reference cell type
Expand All @@ -112,6 +114,7 @@ def __new__(
covariate_names=covariate_names,
reference_cell_type=num_index,
formula=formula,
seed=seed,
)

# Numeric reference cell type
Expand All @@ -123,6 +126,7 @@ def __new__(
covariate_names=covariate_names,
reference_cell_type=reference_cell_type,
formula=formula,
seed=seed,
)

# None of the above: Throw error
Expand Down