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make Table.to_dataframe create real sparse frames #809

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merged 4 commits into from
Mar 7, 2019
Merged

make Table.to_dataframe create real sparse frames #809

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fe40ba5
specify fill value
cdiener Mar 7, 2019
bbf66b3
fix flake8
cdiener Mar 7, 2019
6c11d54
add to changelog
cdiener Mar 7, 2019
f9676d8
fix test for Python 2
cdiener Mar 7, 2019
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9 changes: 5 additions & 4 deletions biom/table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -178,7 +178,7 @@
from copy import deepcopy
from datetime import datetime
from json import dumps
from functools import reduce
from functools import reduce, partial
from operator import itemgetter
from future.builtins import zip
from future.utils import viewitems
Expand Down Expand Up @@ -4045,9 +4045,10 @@ def to_dataframe(self, dense=False):
mat = self.matrix_data.toarray()
constructor = pd.DataFrame
else:
mat = [pd.SparseSeries(r.toarray().squeeze())
for r in self.matrix_data.tocsr()]
constructor = pd.SparseDataFrame
mat = self.matrix_data
constructor = partial(pd.SparseDataFrame,
default_fill_value=0,
copy=True)

return constructor(mat, index=index, columns=columns)

Expand Down
9 changes: 8 additions & 1 deletion biom/tests/test_table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1475,10 +1475,17 @@ def test_add_group_metadata_w_existing_metadata(self):
def test_to_dataframe(self):
exp = pd.SparseDataFrame(np.array([[0.0, 1.0, 2.0], [3.0, 4.0, 5.0]]),
index=['O1', 'O2'],
columns=['S1', 'S2', 'S3'])
columns=['S1', 'S2', 'S3'],
default_fill_value=0.0)
obs = example_table.to_dataframe()
pdt.assert_frame_equal(obs, exp)

def test_to_dataframe_is_sparse(self):
df = example_table.to_dataframe()
density = (example_table.matrix_data.getnnz() /
np.prod(example_table.shape))
assert np.allclose(df.density, density)

def test_to_dataframe_dense(self):
exp = pd.DataFrame(np.array([[0.0, 1.0, 2.0], [3.0, 4.0, 5.0]]),
index=['O1', 'O2'],
Expand Down