def test__subset_and_standardize(self, expression_data_no_na, standardize,
feature_ids, sample_ids):
from flotilla.data_model.base import BaseData
base_data = BaseData(expression_data_no_na)
base_data.subset, base_data.means = \
base_data._subset_and_standardize(base_data.data,
sample_ids=sample_ids,
feature_ids=feature_ids,
return_means=True,
standardize=standardize)
subset = base_data._subset(base_data.data,
sample_ids=sample_ids,
feature_ids=feature_ids)
means = subset.mean().rename_axis(base_data.feature_renamer)
subset = subset.fillna(means).fillna(0)
subset = subset.rename_axis(base_data.feature_renamer, 1)
if standardize:
data = StandardScaler().fit_transform(subset)
else:
data = subset
subset_standardized = pd.DataFrame(data,
index=subset.index,
columns=subset.columns)
pdt.assert_frame_equal(subset_standardized, base_data.subset)
pdt.assert_series_equal(means, base_data.means)
def test__subset_and_standardize(self, expression_data_no_na,
standardize, feature_ids,
sample_ids):
from flotilla.data_model.base import BaseData
base_data = BaseData(expression_data_no_na)
base_data.subset, base_data.means = \
base_data._subset_and_standardize(base_data.data,
sample_ids=sample_ids,
feature_ids=feature_ids,
return_means=True,
standardize=standardize)
subset = base_data._subset(base_data.data, sample_ids=sample_ids,
feature_ids=feature_ids)
means = subset.mean().rename_axis(base_data.feature_renamer)
subset = subset.fillna(means).fillna(0)
subset = subset.rename_axis(base_data.feature_renamer, 1)
if standardize:
data = StandardScaler().fit_transform(subset)
else:
data = subset
subset_standardized = pd.DataFrame(data, index=subset.index,
columns=subset.columns)
pdt.assert_frame_equal(subset_standardized, base_data.subset)
pdt.assert_series_equal(means, base_data.means)
def test__subset(self, expression_data_no_na, sample_ids, feature_ids):
from flotilla.data_model.base import BaseData
base_data = BaseData(expression_data_no_na)
subset = base_data._subset(base_data.data, sample_ids=sample_ids,
feature_ids=feature_ids)
data = base_data.data
if feature_ids is None:
feature_ids = data.columns
else:
feature_ids = pd.Index(set(feature_ids).intersection(data.columns))
if sample_ids is None:
sample_ids = data.index
else:
sample_ids = pd.Index(set(sample_ids).intersection(data.index))
true_subset = data.ix[sample_ids, feature_ids]
pdt.assert_frame_equal(subset, true_subset)
def test__subset(self, expression_data_no_na, sample_ids, feature_ids):
from flotilla.data_model.base import BaseData
base_data = BaseData(expression_data_no_na)
subset = base_data._subset(base_data.data,
sample_ids=sample_ids,
feature_ids=feature_ids)
data = base_data.data
if feature_ids is None:
feature_ids = data.columns
else:
feature_ids = pd.Index(set(feature_ids).intersection(data.columns))
if sample_ids is None:
sample_ids = data.index
else:
sample_ids = pd.Index(set(sample_ids).intersection(data.index))
true_subset = data.ix[sample_ids, feature_ids]
pdt.assert_frame_equal(subset, true_subset)
