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fix for incorrect stats computation in diff exp t-test (#2318)

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* 2211 fixes

* lint

* lint

* add missing test and bug found by test

* change terminology for count distribution

* update scanpy requirement

* update scanpy requirement
This commit is contained in:
Bruce Martin
2021-07-23 11:36:26 -07:00
committed by GitHub
parent 1ebde2213d
commit 1ea2b7fe80
28 changed files with 336 additions and 90 deletions
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backend/czi_hosted/data_cxg/cxg_adaptor.py
+9 -1
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@@ -8,7 +8,7 @@ import pandas as pd
import tiledb
from server_timing import Timing as ServerTiming
from backend.common.constants import Axis
from backend.common.constants import Axis, XApproxDistribution
from backend.common.errors import DatasetAccessError, ConfigurationError
from backend.czi_hosted.common.immutable_kvcache import ImmutableKVCache
from backend.common.utils.type_conversion_utils import get_schema_type_hint_from_dtype
@@ -37,6 +37,7 @@ class CxgAdaptor(DataAdaptor):
self.lsuri_results = ImmutableKVCache(lambda key: self._lsuri(uri=key, tiledb_ctx=self.tiledb_ctx))
self.arrays = ImmutableKVCache(lambda key: self._open_array(uri=key, tiledb_ctx=self.tiledb_ctx))
self.schema = None
self.X_approx_distribution = None
self._validate_and_initialize()
@@ -175,6 +176,10 @@ class CxgAdaptor(DataAdaptor):
if cxg_version not in ["0.0", "0.1", "0.2.0"]:
raise DatasetAccessError(f"cxg matrix is not valid: {self.url}")
if self.dataset_config.X_approx_distribution == "auto":
raise ConfigurationError("X-approx-distribution 'auto' mode unsupported.")
self.X_approx_distribution = self.dataset_config.X_approx_distribution
self.title = title
self.about = about
self.cxg_version = cxg_version
@@ -281,6 +286,9 @@ class CxgAdaptor(DataAdaptor):
data = X.multi_index[obs_items, var_items][""]
return data
def get_X_approx_distribution(self) -> XApproxDistribution:
return self.X_approx_distribution
def get_shape(self):
X = self.open_array("X")
return X.shape