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BUGFIX for sparse expression matrices #20

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Feb 8, 2021
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BUGFIX for sparse expression matrices #20

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15 changes: 13 additions & 2 deletions arboreto/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@
import pandas as pd
import logging

import scipy
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_delayed
Expand Down Expand Up @@ -119,7 +120,12 @@ def fit_model(regressor_type,
"""
regressor_type = regressor_type.upper()

assert tf_matrix.shape[0] == len(target_gene_expression)

if isinstance(target_gene_expression, scipy.sparse.spmatrix):
target_gene_expression = target_gene_expression.A.flatten()

assert tf_matrix.shape[0] == target_gene_expression.shape[0]


def do_sklearn_regression():
regressor = SKLEARN_REGRESSOR_FACTORY[regressor_type](random_state=seed, **regressor_kwargs)
Expand Down Expand Up @@ -226,7 +232,12 @@ def clean(tf_matrix,
if target_gene_name not in tf_matrix_gene_names:
clean_tf_matrix = tf_matrix
else:
clean_tf_matrix = np.delete(tf_matrix, tf_matrix_gene_names.index(target_gene_name), 1)
ix = tf_matrix_gene_names.index(target_gene_name)
if isinstance(tf_matrix, scipy.sparse.spmatrix):
clean_tf_matrix = scipy.sparse.hstack([tf_matrix[:, :ix],
tf_matrix[:, ix+1:]])
else:
clean_tf_matrix = np.delete(tf_matrix, ix, 1)

clean_tf_names = [tf for tf in tf_matrix_gene_names if tf != target_gene_name]

Expand Down