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Update core.py #18

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Update core.py #18

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41 changes: 23 additions & 18 deletions mofax/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1015,14 +1015,13 @@ def calculate_variance_explained(
),
Y=np.array(self.data[view][group]),
)
r2_df = r2_df.append(
{
r2_df = pd.concat([r2_df, pd.DataFrame(
[{
"View": view,
"Group": group,
"R2": r2,
"Factor": factor_name,
},
ignore_index=True,
}])], ignore_index=True
)
else:
r2 = calculate_r2(
Expand All @@ -1032,9 +1031,13 @@ def calculate_variance_explained(
W=np.array(self.expectations["W"][view][factor_indices, :]),
Y=np.array(self.data[view][group]),
)
r2_df = r2_df.append(
{"View": view, "Group": group, "R2": r2}, ignore_index=True
)
r2_df = pd.concat([r2_df, pd.DataFrame(
[{
"View": view,
"Group": group,
"R2": r2
}])], ignore_index=True
)

# use custom groups
# note that when calculating for a custom set of groups,
Expand Down Expand Up @@ -1073,24 +1076,27 @@ def calculate_variance_explained(
),
Y=np.array(data_view[group]),
)
r2_df = r2_df.append(
{
r2_df = pd.concat([r2_df, pd.DataFrame(
[{
"View": view,
"Group": group,
"R2": r2,
"Factor": factor_name,
},
ignore_index=True,
}])], ignore_index=True
)
else:
r2 = calculate_r2(
Z=np.array(z_custom[group][factor_indices, :]),
W=np.array(self.expectations["W"][view][factor_indices, :]),
Y=np.array(data_view[group]),
)
r2_df = r2_df.append(
{"View": view, "Group": group, "R2": r2}, ignore_index=True
)
r2_df = pd.concat([r2_df, pd.DataFrame(
[{
"View": view,
"Group": group,
"R2": r2
}])], ignore_index=True
)
return r2_df

def get_variance_explained(
Expand Down Expand Up @@ -1256,15 +1262,14 @@ def _get_factor_r2_null(
y = np.array(data_view[group])
a = np.sum((y - crossprod) ** 2)
b = np.sum(y ** 2)
r2_df = r2_df.append(
{
r2_df = pd.concat([r2_df, pd.DataFrame(
[{
"View": view,
"Group": group,
"Factor": f"Factor{factor_index+1}",
"R2": 1 - a / b,
"Iteration": i,
},
ignore_index=True,
}])], ignore_index=True
)

if return_full:
Expand Down