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add --obs-names and --var-names CLI params (#371)

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* add --obs-names and --var-names CLI params

* fix lint

* performance improvements in scanpy engine

* fix lint

* fix typo

* correctly handle sparse formats in diffexp

* fix diffexp and 1d slicing

* diffexp uses t-stat, not pval; clean up arg handling

* make _slice a static method

* revise scanpy tests to match new API
This commit is contained in:
Bruce Martin
2018-10-30 14:07:38 -07:00
committed by GitHub
parent 01369801fc
commit b181751493
7 changed files with 133 additions and 88 deletions
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server/test/test_scanpy_engine.py
+18 -10
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@@ -3,6 +3,7 @@ from os import path
import pytest
import time
import unittest
import argparse
import numpy as np
from pandas import Series
@@ -12,7 +13,14 @@ from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
class UtilTest(unittest.TestCase):
def setUp(self):
self.data = ScanpyEngine("example-dataset/pbmc3k.h5ad", layout_method="umap", diffexp_method="ttest")
args = argparse.Namespace()
args.layout = "umap"
args.diffexp = "ttest"
args.max_category_items = 100
args.obs_names = None
args.var_names = None
self.data = ScanpyEngine("example-dataset/pbmc3k.h5ad", args)
self.data._create_schema()
def test_init(self):
@@ -30,7 +38,7 @@ class UtilTest(unittest.TestCase):
@pytest.mark.filterwarnings("ignore:Scanpy data matrix")
def test_data_type(self):
self.data.data.X = self.data.data.X.astype("float64")
self.assertWarns(UserWarning, self.data._validatate_data_types())
self.assertWarns(UserWarning, self.data._validate_data_types())
def test_filter_idx(self):
filter_ = {
@@ -130,10 +138,10 @@ class UtilTest(unittest.TestCase):
def test_annotations(self):
annotations = self.data.annotation(None, "obs")
self.assertEqual(annotations["names"], ["n_genes", "percent_mito", "n_counts", "louvain", "name"])
self.assertEqual(annotations["names"], ["name", "n_genes", "percent_mito", "n_counts", "louvain"])
self.assertEqual(len(annotations["data"]), 2638)
annotations = self.data.annotation(None, "var")
self.assertEqual(annotations["names"], ["n_cells", "name"])
self.assertEqual(annotations["names"], ["name", "n_cells"])
self.assertEqual(len(annotations["data"]), 1838)
def test_annotation_fields(self):
@@ -160,10 +168,10 @@ class UtilTest(unittest.TestCase):
}
}
annotations = self.data.annotation(filter_["filter"], "obs")
self.assertEqual(annotations["names"], ["n_genes", "percent_mito", "n_counts", "louvain", "name"])
self.assertEqual(annotations["names"], ["name", "n_genes", "percent_mito", "n_counts", "louvain"])
self.assertEqual(len(annotations["data"]), 497)
annotations = self.data.annotation(filter_["filter"], "var")
self.assertEqual(annotations["names"], ["n_cells", "name"])
self.assertEqual(annotations["names"], ["name", "n_cells"])
self.assertEqual(len(annotations["data"]), 2)
def test_filtered_layout(self):
@@ -222,12 +230,12 @@ class UtilTest(unittest.TestCase):
data_frame_obs = self.data.data_frame(filter_["filter"], "obs")
self.assertEqual(len(data_frame_obs["var"]), 1838)
self.assertEqual(len(data_frame_obs["obs"]), 497)
self.assertEqual(type(data_frame_obs["obs"][0]), list)
self.assertIsInstance(data_frame_obs["obs"][0], (list, tuple))
self.assertEqual(type(data_frame_obs["var"][0]), int)
data_frame_var = self.data.data_frame(filter_["filter"], "var")
self.assertEqual(len(data_frame_var["var"]), 1838)
self.assertEqual(len(data_frame_var["obs"]), 497)
self.assertEqual(type(data_frame_var["var"][0]), list)
self.assertIsInstance(data_frame_var["var"][0], (list, tuple))
self.assertEqual(type(data_frame_var["obs"][0]), int)
def test_data_single_gene(self):
@@ -244,10 +252,10 @@ class UtilTest(unittest.TestCase):
data_frame_var = self.data.data_frame(filter_["filter"], axis)
if axis == "obs":
self.assertEqual(type(data_frame_var["var"][0]), int)
self.assertEqual(type(data_frame_var["obs"][0]), list)
self.assertIsInstance(data_frame_var["obs"][0], (list, tuple))
elif axis == "var":
self.assertEqual(type(data_frame_var["obs"][0]), int)
self.assertEqual(type(data_frame_var["var"][0]), list)
self.assertIsInstance(data_frame_var["var"][0], (list, tuple))
if __name__ == '__main__':
unittest.main()