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adding posterior quantile #19

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Nov 25, 2023
Merged

adding posterior quantile #19

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31 changes: 25 additions & 6 deletions schierarchy/logistic/_logistic_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -389,9 +389,18 @@ def export_posterior(
self.adata = self._validate_anndata(adata)
# self.adata = adata

# generate samples from posterior distributions for all parameters
# and compute mean, 5%/95% quantiles and standard deviation
self.samples = self.sample_posterior(**sample_kwargs)
if use_quantiles:
add_to_varm = [i for i in add_to_varm if (i not in ["means", "stds"]) and ("q" in i)]
if len(add_to_varm) == 0:
raise ValueError("No quantiles to export - please add add_to_obsm=['q05', 'q50', 'q95'].")
self.samples = dict()
for i in add_to_varm:
q = float(f"0.{i[1:]}")
self.samples[f"post_sample_{i}"] = self.posterior_quantile(q=q, **sample_kwargs)
else:
# generate samples from posterior distributions for all parameters
# and compute mean, 5%/95% quantiles and standard deviation
self.samples = self.sample_posterior(**sample_kwargs)

# revert adata object substitution
self.adata = adata_train
Expand All @@ -403,9 +412,18 @@ def export_posterior(
)
obs_names = adata.obs_names
else:
# generate samples from posterior distributions for all parameters
# and compute mean, 5%/95% quantiles and standard deviation
self.samples = self.sample_posterior(**sample_kwargs)
if use_quantiles:
add_to_varm = [i for i in add_to_varm if (i not in ["means", "stds"]) and ("q" in i)]
if len(add_to_varm) == 0:
raise ValueError("No quantiles to export - please add add_to_obsm=['q05', 'q50', 'q95'].")
self.samples = dict()
for i in add_to_varm:
q = float(f"0.{i[1:]}")
self.samples[f"post_sample_{i}"] = self.posterior_quantile(q=q, **sample_kwargs)
else:
# generate samples from posterior distributions for all parameters
# and compute mean, 5%/95% quantiles and standard deviation
self.samples = self.sample_posterior(**sample_kwargs)
obs_names = self.adata.obs_names

# export posterior distribution summary for all parameters and
Expand All @@ -423,6 +441,7 @@ def export_posterior(
].values()
)[i]
)
print(f"level {i}", categories)
for k in add_to_varm:
sample_df = pd.DataFrame(
self.samples[f"post_sample_{k}"].get(f"weight_level_{i}", None),
Expand Down