diff options
| -rw-r--r-- | gn3/computations/partial_correlations.py | 27 | ||||
| -rw-r--r-- | tests/unit/computations/test_partial_correlations.py (renamed from tests/unit/test_partial_correlations.py) | 57 |
2 files changed, 79 insertions, 5 deletions
diff --git a/gn3/computations/partial_correlations.py b/gn3/computations/partial_correlations.py index b3de31c..e73edfd 100644 --- a/gn3/computations/partial_correlations.py +++ b/gn3/computations/partial_correlations.py @@ -7,6 +7,7 @@ GeneNetwork1. from functools import reduce from typing import Any, Tuple, Sequence +from scipy.stats import pearsonr, spearmanr def control_samples(controls: Sequence[dict], sampleslist: Sequence[str]): """ @@ -123,6 +124,32 @@ def find_identical_traits( if len(item[1]) > 1), tuple())) +def tissue_correlation( + primary_trait_values: Tuple[float, ...], + target_trait_values: Tuple[float, ...], + method: str) -> Tuple[float, float]: + """ + Compute the correlation between the primary trait values, and the values of + a single target value. + + This migrates the `cal_tissue_corr` function embedded in the larger + `web.webqtl.correlation.correlationFunction.batchCalTissueCorr` function in + GeneNetwork1. + """ + def spearman_corr(*args): + result = spearmanr(*args) + return (result.correlation, result.pvalue) + + method_fns = {"pearson": pearsonr, "spearman": spearman_corr} + + assert len(primary_trait_values) == len(target_trait_values), ( + "The lengths of the `primary_trait_values` and `target_trait_values` " + "must be equal") + assert method in method_fns.keys(), ( + "Method must be one of: {}".format(",".join(method_fns.keys()))) + + return method_fns[method](primary_trait_values, target_trait_values) + def batch_computed_tissue_correlation( trait_value: str, symbol_value_dict: dict, method: str = "pearson") -> Tuple[dict, dict]: diff --git a/tests/unit/test_partial_correlations.py b/tests/unit/computations/test_partial_correlations.py index 60e54c1..7ff8b80 100644 --- a/tests/unit/test_partial_correlations.py +++ b/tests/unit/computations/test_partial_correlations.py @@ -1,11 +1,7 @@ """Module contains tests for gn3.partial_correlations""" from unittest import TestCase -from gn3.partial_correlations import ( - fix_samples, - control_samples, - dictify_by_samples, - find_identical_traits) +from gn3.computations.partial_correlations import * sampleslist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] control_traits = ( @@ -209,3 +205,54 @@ class TestPartialCorrelations(TestCase): control_names=contn, control_values=contv): self.assertEqual( find_identical_traits(primn, primv, contn, contv), expected) + + def test_tissue_correlation_error(self): + """ + Test that `tissue_correlation` raises specific exceptions for particular + error conditions. + """ + for primary, target, method, error, error_msg in ( + ((1,2,3), (4,5,6,7), "pearson", + AssertionError, + ( + "The lengths of the `primary_trait_values` and " + "`target_trait_values` must be equal")), + ((1,2,3), (4,5,6,7), "spearman", + AssertionError, + ( + "The lengths of the `primary_trait_values` and " + "`target_trait_values` must be equal")), + ((1,2,3,4), (5,6,7), "pearson", + AssertionError, + ( + "The lengths of the `primary_trait_values` and " + "`target_trait_values` must be equal")), + ((1,2,3,4), (5,6,7), "spearman", + AssertionError, + ( + "The lengths of the `primary_trait_values` and " + "`target_trait_values` must be equal")), + ((1,2,3), (4,5,6), "nonexistentmethod", + AssertionError, + ( + "Method must be one of: pearson, spearman"))): + with self.subTest(primary=primary, target=target, method=method): + with self.assertRaises(error, msg=error_msg): + tissue_correlation(primary, target, method) + + def test_tissue_correlation(self): + """ + Test that the correct correlation values are computed for the given: + - primary trait + - target trait + - method + """ + for primary, target, method, expected in ( + ((12.34, 18.36, 42.51), (37.25, 46.25, 46.56), "pearson", + (0.6761779252651052, 0.5272701133657985)), + ((1, 2, 3, 4, 5), (5, 6, 7, 8, 7), "spearman", + (0.8207826816681233, 0.08858700531354381)) + ): + with self.subTest(primary=primary, target=target, method=method): + self.assertEqual( + tissue_correlation(primary, target, method), expected) |