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Change metadata merge logic #7

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Change metadata merge logic #7

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3f77c7d
Added version that respects index for metadata merging
timtreis Oct 31, 2022
b19f4b0
reintroduced old functionality
timtreis Oct 31, 2022
1131cfb
Fixed typo to make my unit test happy
timtreis Oct 31, 2022
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6 changes: 3 additions & 3 deletions mofax/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1330,9 +1330,9 @@ def get_sample_r2(
views: Optional[Union[str, int, List[str], List[int]]] = None,
df: bool = True,
) -> pd.DataFrame:
findices, factors = self.__check_factors(factors, unique=True)
groups = self.__check_groups(groups)
views = self.__check_views(views)
findices, factors = self._check_factors(factors, unique=True)
groups = self._check_groups(groups)
views = self._check_views(views)

r2s = []
for view in views:
Expand Down
48 changes: 31 additions & 17 deletions mofax/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ def _load_samples_metadata(model):
],
columns=["sample", "group"],
)

if "samples_metadata" in model.model:
if len(list(model.model["samples_metadata"][model.groups[0]].keys())) > 0:
_samples_metadata = pd.concat(
Expand All @@ -41,23 +42,36 @@ def _load_samples_metadata(model):
if "sample" in _samples_metadata.columns:
del _samples_metadata["sample"]

samples_metadata = pd.concat(
[
samples_metadata.reset_index(drop=True),
_samples_metadata.reset_index(drop=True),
],
axis=1,
)

# Decode objects as UTF-8 strings
for column in samples_metadata.columns:
if samples_metadata[column].dtype == "object":
try:
samples_metadata[column] = [
i.decode() for i in samples_metadata[column].values
]
except (UnicodeDecodeError, AttributeError):
pass
for df in [samples_metadata, _samples_metadata]:
for column in df.columns:
if df[column].dtype == "object":
try:
df[column] = [i.decode() for i in df[column].values]
except (UnicodeDecodeError, AttributeError):
pass

if "sample" in _samples_metadata.columns:

samples_metadata = pd.merge(
left=samples_metadata,
left_on="sample",
right=_samples_metadata,
right_on="index",
)

if "index" in samples_metadata.columns:
del samples_metadata["index"]

else:

samples_metadata = pd.concat(
[
samples_metadata.reset_index(drop=True),
_samples_metadata.reset_index(drop=True),
],
axis=1,
)

samples_metadata = samples_metadata.set_index("sample")
return samples_metadata
Expand Down Expand Up @@ -230,7 +244,7 @@ def _make_iterable(x):

def calculate_r2(Z, W, Y):
a = np.nansum((Y - Z.T.dot(W)) ** 2.0)
b = np.nansum(Y ** 2)
b = np.nansum(Y**2)
r2 = (1.0 - a / b) * 100
return r2

Expand Down