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https://github.com/chanzuckerberg/cellxgene.git
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546e272a60
* Add user-defined category-label colors Fixes https://github.com/chanzuckerberg/cellxgene/issues/1152 As described in https://github.com/chanzuckerberg/cellxgene/issues/1307 * Respond to feedback from @bkmartinjr in nodejs * Respond to feedback from @bkmartinjr in python * Add tests to the server module * Autoformat python, run linter * Make colors_get error handling specific * Respond to feedback from @bkmartinjr * Respond to feedback from @bkmartinjr * Fix whitespace * Fix python lint errrors * Update documentation * Add --disable-user-colors option to launch and cxgtool.py * Fix python formatting * Rename '--disable-user-colors' to '--disable-custom-colors'
83 lines
3.4 KiB
Python
83 lines
3.4 KiB
Python
import unittest
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from server.data_common.matrix_loader import MatrixDataLoader
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from server.common.app_config import AppConfig
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import server.compute.diffexp_cxg as diffexp_cxg
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import server.compute.diffexp_generic as diffexp_generic
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import numpy as np
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from server.test import PROJECT_ROOT
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class DiffExpTest(unittest.TestCase):
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"""Tests the diffexp returns the expected results for one test case, using different
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adaptor types and different algorithms."""
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def load_dataset(self, path):
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app_config = AppConfig()
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app_config.single_dataset__datapath = path
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app_config.server__verbose = True
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app_config.complete_config()
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loader = MatrixDataLoader(path)
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adaptor = loader.open(app_config)
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return adaptor
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def get_mask(self, adaptor, start, stride):
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"""Simple function to return a mask or rows"""
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rows = adaptor.get_shape()[0]
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sel = list(range(start, rows, stride))
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mask = np.zeros(rows, dtype=bool)
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mask[sel] = True
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return mask
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def check_1_10_2_10(self, results):
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"""Checks the results for a specific set of rows selections"""
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expects = [
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[956, 0.016060986, 0.0008649321884808977, 1.0],
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[1124, 0.96602094, 0.0011717216548271284, 1.0],
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[1809, 1.1110606, 0.0019304405196777848, 1.0],
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[1712, -0.5525154, 0.0051788902660723345, 1.0],
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[1754, 0.5201581, 0.005691734062127954, 1.0],
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[948, 1.6390722, 0.006622111055981219, 1.0],
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[1810, 0.78618884, 0.007055917428377063, 1.0],
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[779, 1.5241305, 0.007202934422407284, 1.0],
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[1575, 1.0317602, 0.007830310753043345, 1.0],
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[576, 0.97873515, 0.008272092578813124, 1.0],
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]
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self.assertEqual(len(results), len(expects))
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for result, expect in zip(results, expects):
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self.assertEqual(result[0], expect[0])
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self.assertAlmostEqual(result[1], expect[1])
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self.assertAlmostEqual(result[2], expect[2])
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self.assertAlmostEqual(result[3], expect[3])
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def test_anndata_default(self):
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"""Test an anndata adaptor with its default diffexp algorithm (diffexp_generic)"""
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adaptor = self.load_dataset(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad")
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maskA = self.get_mask(adaptor, 1, 10)
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maskB = self.get_mask(adaptor, 2, 10)
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results = adaptor.compute_diffexp_ttest(maskA, maskB, 10)
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self.check_1_10_2_10(results)
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def test_cxg_default(self):
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"""Test a cxg adaptor with its default diffexp algorithm (diffexp_cxg)"""
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adaptor = self.load_dataset(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg")
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maskA = self.get_mask(adaptor, 1, 10)
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maskB = self.get_mask(adaptor, 2, 10)
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# run it through the adaptor
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results = adaptor.compute_diffexp_ttest(maskA, maskB, 10)
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self.check_1_10_2_10(results)
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# run it directly
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results = diffexp_cxg.diffexp_ttest(adaptor, maskA, maskB, 10)
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self.check_1_10_2_10(results)
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def test_cxg_generic(self):
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"""Test a cxg adaptor with the generic adaptor"""
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adaptor = self.load_dataset(f"{PROJECT_ROOT}/server/test/test_datasets/pbmc3k.cxg")
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maskA = self.get_mask(adaptor, 1, 10)
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maskB = self.get_mask(adaptor, 2, 10)
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# run it directly
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results = diffexp_generic.diffexp_ttest(adaptor, maskA, maskB, 10)
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self.check_1_10_2_10(results)
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