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Diffstat (limited to 'gn3/computations/partial_correlations.py')
| -rw-r--r-- | gn3/computations/partial_correlations.py | 16 |
1 files changed, 16 insertions, 0 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index 07dc16d..ffdf0c5 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -10,6 +10,8 @@ from typing import Any, Tuple, Sequence from scipy.stats import pearsonr, spearmanr from gn3.settings import TEXTDIR +import pandas + from gn3.data_helpers import parse_csv_line def control_samples(controls: Sequence[dict], sampleslist: Sequence[str]): @@ -258,6 +260,20 @@ def compute_partial_correlations_fast(# pylint: disable=[R0913, R0914] else fetched_correlations[corr[0]][0:2]) for idx, corr in enumerate(all_correlations)) +def build_data_frame( + xdata: Tuple[float, ...], ydata: Tuple[float, ...], + zdata: Union[ + Tuple[float, ...], + Tuple[Tuple[float, ...], ...]]) -> pandas.DataFrame: + """ + Build a pandas DataFrame object from xdata, ydata and zdata + """ + x_y_df = pandas.DataFrame({"x": xdata, "y": ydata}) + if isinstance(zdata[0], float): + return x_y_df.join(pandas.DataFrame({"z": zdata})) + return x_y_df.join(pandas.DataFrame( + {"z{}".format(i): val for i, val in enumerate(row)} for row in zdata)) + def partial_correlation_matrix( xdata: Tuple[float, ...], ydata: Tuple[float, ...], zdata: Tuple[float, ...], method: str = "pearsons", |