def test_get_gate_from_template(self):
fks = Session(fcs_samples=data1_sample)
fks.add_gate(poly1_gate)
template_gate = fks.get_gate('default', 'Polygon1')
self.assertEqual(template_gate.gate_name, 'Polygon1')
def test_load_samples_from_list_of_paths(self):
fks = Session(fcs_samples=fcs_file_paths)
self.assertEqual(len(fks.sample_lut.keys()), 3)
self.assertIsInstance(fks.get_sample('100715.fcs'), Sample)
sample_ids = ["100715.fcs", "109567.fcs", "113548.fcs"]
self.assertListEqual(fks.get_sample_ids(), sample_ids)
def test_get_group_transforms(self):
wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp"
sample_grp = 'DEN'
fks = Session(copy.deepcopy(test_samples_8c_full_set))
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
xforms = fks.get_group_transforms(sample_grp)
self.assertEqual(len(xforms), 23)
for cm in xforms:
self.assertIsInstance(cm, Transform)
def test_get_sample_comp_matrices(self):
wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp"
sample_grp = 'DEN'
sample_id = '101_DEN084Y5_15_E01_008_clean.fcs'
fks = Session(copy.deepcopy(test_samples_8c_full_set))
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
comp_matrices = fks.get_sample_comp_matrices(sample_grp, sample_id)
self.assertEqual(len(comp_matrices), 1)
for cm in comp_matrices:
self.assertIsInstance(cm, Matrix)
def test_load_wsp_single_quad(self):
wsp_path = "examples/data/simple_diamond_example/simple_diamond_example_quad_gate.wsp"
fcs_path = "examples/data/simple_diamond_example/test_data_diamond_01.fcs"
fks = Session(fcs_samples=fcs_path)
fks.import_flowjo_workspace(wsp_path)
# FlowJo quadrant gates are not true quadrant gates, rather a collection of rectangle gates
self.assertIsInstance(
fks.get_gate('All Samples',
'Q1: channel_A- , channel_B+',
sample_id='test_data_diamond_01.fcs'),
gates.RectangleGate)
fks.analyze_samples(group_name='All Samples')
results = fks.get_gating_results('All Samples',
'test_data_diamond_01.fcs')
gate_count_q1 = results.get_gate_count('Q1: channel_A- , channel_B+')
gate_count_q2 = results.get_gate_count('Q2: channel_A+ , channel_B+')
gate_count_q3 = results.get_gate_count('Q3: channel_A+ , channel_B-')
gate_count_q4 = results.get_gate_count('Q4: channel_A- , channel_B-')
self.assertEqual(gate_count_q1, 49671)
self.assertEqual(gate_count_q2, 50596)
self.assertEqual(gate_count_q3, 50330)
self.assertEqual(gate_count_q4, 49403)
def test_get_sample_gate_events(self):
wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp"
sample_grp = 'DEN'
sample_id = '101_DEN084Y5_15_E01_008_clean.fcs'
gate_name = 'CD3+'
fks = Session(copy.deepcopy(test_samples_8c_full_set))
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
fks.analyze_samples(sample_grp, sample_id)
sample_comp = fks.get_sample_comp_matrices(sample_grp, sample_id)[0]
sample_xform = transforms.LogicleTransform('my_logicle',
param_t=262144.0,
param_w=1.0,
param_m=4.418539922,
param_a=0.0)
df_gated_events = fks.get_gate_events(sample_grp,
sample_id,
gate_name,
matrix=sample_comp,
transform=sample_xform)
self.assertIsInstance(df_gated_events, pd.DataFrame)
self.assertEqual(len(df_gated_events), 133670)
def test_get_parent_quadrant_gate(self):
gml_path = 'examples/gate_ref/gml/gml_parent_quadrant_rect_gate.xml'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_sample(data1_sample.original_filename, group_name)
parent_id = s.get_parent_gate_id(group_name, 'ParRectangle1')
self.assertEqual(parent_id, 'FL2P-FL4P')
parent_gate = s.get_gate(group_name, data1_sample.original_filename, parent_id)
self.assertIsInstance(parent_gate, gates.Quadrant)
def test_get_parent_rect_gate(self):
gml_path = 'examples/data/gate_ref/gml/gml_parent_rect1_rect_par1_gate.xml'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_samples(data1_sample.original_filename, group_name)
parent_gate_name = s.get_parent_gate_name(group_name, 'ScalePar1')
self.assertEqual(parent_gate_name, 'ScaleRect1')
parent_gate = s.get_gate(group_name,
parent_gate_name,
sample_id=data1_sample.original_filename)
self.assertIsInstance(parent_gate, gates.RectangleGate)
def test_parse_wsp_reused_gate_with_child(self):
wsp_path = "examples/data/8_color_data_set/reused_quad_gate_with_child.wsp"
fks = Session(copy.deepcopy(test_samples_8c_full_set))
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
group_name = 'All Samples'
gate_name = 'some_child_gate'
gate_ids = fks.get_gate_ids(group_name)
gate_id_1 = (gate_name, ('root', 'good cells', 'cd4+',
'Q2: CD107a+, IL2+'))
gate_id_2 = (gate_name, ('root', 'good cells', 'cd8+',
'Q2: CD107a+, IL2+'))
self.assertIn(gate_id_1, gate_ids)
self.assertIn(gate_id_2, gate_ids)
def test_analyze_single_sample(self):
wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp"
sample_id = '101_DEN084Y5_15_E01_008_clean.fcs'
sample_grp = 'DEN'
fks = Session(copy.deepcopy(test_samples_8c_full_set))
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
sample_ids = fks.get_group_sample_ids(sample_grp)
self.assertEqual(len(sample_ids), 3)
fks.analyze_samples(sample_grp, sample_id=sample_id)
report = fks.get_group_report(sample_grp)
self.assertEqual(report['sample'].nunique(), 1)
def test_new_group_membership_is_empty(self):
s = Session()
group_name = 'new_group'
s.add_sample_group(group_name)
s.add_samples(copy.deepcopy(
test_samples_base_set)) # load without assigning a group
s_sample_ids = sorted(s.get_group_sample_ids(group_name))
self.assertListEqual(s_sample_ids, [])
def test_analyze_single_sample(self):
wsp_path = "examples/8_color_data_set/8_color_ICS_simple.wsp"
fcs_path = "examples/8_color_data_set/fcs_files"
sample_id = '101_DEN084Y5_15_E01_008_clean.fcs'
sample_grp = 'DEN'
fks = Session(fcs_samples=fcs_path)
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
sample_ids = fks.get_group_sample_ids(sample_grp)
self.assertEqual(len(sample_ids), 3)
fks.analyze_samples(sample_grp, sample_id=sample_id)
report = fks.get_group_report(sample_grp)
self.assertEqual(report.index.get_level_values('sample').nunique(), 1)
def test_load_wsp_single_ellipse(self):
wsp_path = "examples/simple_line_example/single_ellipse_51_events.wsp"
fcs_path = "examples/simple_line_example/data_set_simple_line_100.fcs"
fks = Session(fcs_samples=fcs_path)
fks.import_flowjo_workspace(wsp_path)
self.assertIsInstance(
fks.get_gate('All Samples', 'data_set_simple_line_100.fcs',
'ellipse1'), gates.EllipsoidGate)
fks.analyze_samples(sample_group='All Samples')
results = fks.get_gating_results('All Samples',
'data_set_simple_line_100.fcs')
gate_count = results.get_gate_count('ellipse1')
self.assertEqual(gate_count, 48)
def test_add_samples_with_group(self):
sample_ids = ["100715.fcs", "109567.fcs", "113548.fcs"]
s = Session()
group_name = 'gml'
s.add_sample_group(group_name)
s.add_samples(copy.deepcopy(test_samples_base_set), group_name)
s_sample_ids = sorted(s.get_group_sample_ids(group_name))
self.assertListEqual(sample_ids, s_sample_ids)
def test_add_poly1_gate():
fks = Session(fcs_samples=data1_sample)
fks.add_gate(poly1_gate)
fks.analyze_samples()
result = fks.get_gating_results('default',
data1_sample.original_filename)
res_path = 'examples/gate_ref/truth/Results_Polygon1.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
np.testing.assert_array_equal(truth,
result.get_gate_indices('Polygon1'))
def test_get_sample_groups(self):
wsp_path = "examples/simple_line_example/simple_poly_and_rect.wsp"
fcs_path = "examples/simple_line_example/data_set_simple_line_100.fcs"
fks = Session(fcs_samples=fcs_path)
fks.import_flowjo_workspace(wsp_path)
groups = fks.get_sample_groups()
groups_truth = ['default', 'my_group']
self.assertListEqual(groups, groups_truth)
fks.add_sample_group('group2')
groups_truth.append('group2')
groups = fks.get_sample_groups()
self.assertListEqual(groups, groups_truth)
def test_wsp_fasinh_transform(self):
wsp_path = "examples/data/simple_diamond_example/test_data_diamond_asinh_rect.wsp"
fcs_path = "examples/data/simple_diamond_example/test_data_diamond_01.fcs"
fks = Session(fcs_samples=fcs_path)
fks.import_flowjo_workspace(wsp_path)
self.assertIsInstance(
fks.get_gate('All Samples',
'upper_right',
sample_id='test_data_diamond_01.fcs'),
gates.RectangleGate)
fks.analyze_samples(group_name='All Samples')
results = fks.get_gating_results('All Samples',
'test_data_diamond_01.fcs')
gate_count = results.get_gate_count('upper_right')
self.assertEqual(gate_count, 50559)
def test_add_matrix_poly4_gate():
fks = Session(fcs_samples=data1_sample)
fks.add_comp_matrix(comp_matrix_01)
dim1 = Dimension('PE', compensation_ref='MySpill')
dim2 = Dimension('PerCP', compensation_ref='MySpill')
dims = [dim1, dim2]
poly_gate = gates.PolygonGate('Polygon4', None, dims, poly1_vertices)
fks.add_gate(poly_gate)
res_path = 'examples/gate_ref/truth/Results_Polygon4.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
fks.analyze_samples()
result = fks.get_gating_results('default',
data1_sample.original_filename)
np.testing.assert_array_equal(truth,
result.get_gate_indices('Polygon4'))
def test_analyze_samples_multiproc(self):
wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp"
sample_grp = 'DEN'
sample_id = '101_DEN084Y5_15_E01_008_clean.fcs'
gate_name = 'CD3+'
fks = Session(copy.deepcopy(test_samples_8c_full_set))
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
fks.analyze_samples(sample_grp)
gate_membership = fks.get_gate_membership(sample_grp, sample_id,
gate_name)
self.assertEqual(gate_membership.sum(), 133670)
def test_get_wsp_gated_events(self):
wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp"
sample_grp = 'DEN'
sample_id = '101_DEN084Y5_15_E01_008_clean.fcs'
gate_name = 'CD3+'
fks = Session(copy.deepcopy(test_samples_8c_full_set))
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
fks.analyze_samples(sample_grp, sample_id)
df_gated_events = fks.get_wsp_gated_events(sample_grp, [sample_id],
gate_name)
self.assertIsInstance(df_gated_events, list)
self.assertEqual(len(df_gated_events[0]), 133670)
def test_load_wsp_single_poly(self):
wsp_path = "examples/simple_line_example/simple_poly_and_rect.wsp"
fcs_path = "examples/simple_line_example/data_set_simple_line_100.fcs"
fks = Session(fcs_samples=fcs_path)
fks.import_flowjo_workspace(wsp_path)
self.assertIsInstance(
fks.get_gate('my_group', 'data_set_simple_line_100.fcs', 'poly1'),
gates.PolygonGate)
gate_ids = {'rect1', 'poly1'}
self.assertSetEqual(set(fks.get_gate_ids('my_group')), gate_ids)
def test_add_transform_asinh_range1_gate():
fks = Session(fcs_samples=data1_sample)
fks.add_transform(asinh_xform1)
dim1 = Dimension('FL1-H',
'uncompensated',
'AsinH_10000_4_1',
range_min=0.37,
range_max=0.63)
dims = [dim1]
rect_gate = gates.RectangleGate('ScaleRange1', None, dims)
fks.add_gate(rect_gate)
res_path = 'examples/gate_ref/truth/Results_ScaleRange1.txt'
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
fks.analyze_samples()
result = fks.get_gating_results('default',
data1_sample.original_filename)
np.testing.assert_array_equal(truth,
result.get_gate_indices('ScaleRange1'))
def test_get_ambiguous_gate_objects(self):
wsp_path = "examples/8_color_data_set/8_color_ICS.wsp"
fcs_path = "examples/8_color_data_set/fcs_files/101_DEN084Y5_15_E01_008_clean.fcs"
sample_id = '101_DEN084Y5_15_E01_008_clean.fcs'
sample_grp = 'DEN'
gate_id = 'TNFa+'
gate_path = ['root', 'Time', 'Singlets', 'aAmine-', 'CD3+', 'CD4+']
fks = Session(fcs_samples=fcs_path)
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
fks.analyze_samples(sample_grp)
gate_indices = fks.get_gate_indices(sample_grp,
sample_id,
gate_id,
gate_path=gate_path)
self.assertIsInstance(gate_indices, np.ndarray)
self.assertEqual(np.sum(gate_indices), 21)
def test_parse_wsp_with_ellipse(self):
wsp_path = "examples/data/8_color_data_set/8_color_ICS_with_ellipse.wsp"
fcs_path = "examples/data/8_color_data_set/fcs_files/101_DEN084Y5_15_E01_008_clean.fcs"
sample_id = '101_DEN084Y5_15_E01_008_clean.fcs'
sample_grp = 'DEN'
gate_name = 'ellipse1'
gate_path = ('root', 'Time', 'Singlets', 'aAmine-', 'CD3+')
fks = Session(fcs_samples=fcs_path)
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
fks.analyze_samples(sample_grp, sample_id=sample_id)
gate_indices = fks.get_gate_membership(sample_grp,
sample_id,
gate_name,
gate_path=gate_path)
self.assertIsInstance(gate_indices, np.ndarray)
self.assertEqual(np.sum(gate_indices), 7018)
def test_load_wsp_single_poly(self):
wsp_path = "examples/data/simple_line_example/simple_poly_and_rect.wsp"
fcs_path = "examples/data/simple_line_example/data_set_simple_line_100.fcs"
fks = Session(fcs_samples=fcs_path)
fks.import_flowjo_workspace(wsp_path)
self.assertIsInstance(
fks.get_gate('my_group',
'poly1',
sample_id='data_set_simple_line_100.fcs'),
gates.PolygonGate)
gate_names = {'rect1', 'poly1'}
wsp_gates_tuple = fks.get_gate_ids('my_group')
wsp_gate_names = set([g[0] for g in wsp_gates_tuple])
self.assertSetEqual(wsp_gate_names, gate_names)
def test_parent_quadrant_rect_gate():
gml_path = 'examples/data/gate_ref/gml/gml_parent_quadrant_rect_gate.xml'
res_path = 'examples/data/gate_ref/truth/Results_ParQuadRect.txt'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_samples(data1_sample.original_filename, group_name)
s.analyze_samples(group_name=group_name)
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = s.get_gate_membership(group_name,
data1_sample.original_filename,
'ParRectangle1')
np.testing.assert_array_equal(truth, result)
def test_matrix_transform_logicle_range8c_gate():
gml_path = 'examples/data/gate_ref/gml/gml_matrix_transform_logicle_range8c_gate.xml'
res_path = 'examples/data/gate_ref/truth/Results_ScaleRange8c.txt'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_samples(data1_sample.original_filename, group_name)
s.analyze_samples(group_name=group_name)
truth = pd.read_csv(res_path, header=None, squeeze=True,
dtype='bool').values
result = s.get_gate_membership(group_name,
data1_sample.original_filename,
'ScaleRange8c')
np.testing.assert_array_equal(truth, result)
def test_quadrant2_gate():
gml_path = 'examples/data/gate_ref/gml/gml_quadrant2_gate.xml'
res1_path = 'examples/data/gate_ref/truth/Results_FSCN-SSCN.txt'
res2_path = 'examples/data/gate_ref/truth/Results_FSCD-SSCN-FL1N.txt'
res3_path = 'examples/data/gate_ref/truth/Results_FSCP-SSCN-FL1N.txt'
res4_path = 'examples/data/gate_ref/truth/Results_FSCD-FL1P.txt'
res5_path = 'examples/data/gate_ref/truth/Results_FSCN-SSCP-FL1P.txt'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_samples(data1_sample.original_filename, group_name)
s.analyze_samples(group_name=group_name)
truth1 = pd.read_csv(res1_path,
header=None,
squeeze=True,
dtype='bool').values
truth2 = pd.read_csv(res2_path,
header=None,
squeeze=True,
dtype='bool').values
truth3 = pd.read_csv(res3_path,
header=None,
squeeze=True,
dtype='bool').values
truth4 = pd.read_csv(res4_path,
header=None,
squeeze=True,
dtype='bool').values
truth5 = pd.read_csv(res5_path,
header=None,
squeeze=True,
dtype='bool').values
result = s.get_gating_results(group_name,
data1_sample.original_filename)
np.testing.assert_array_equal(truth1,
result.get_gate_membership('FSCN-SSCN'))
np.testing.assert_array_equal(
truth2, result.get_gate_membership('FSCD-SSCN-FL1N'))
np.testing.assert_array_equal(
truth3, result.get_gate_membership('FSCP-SSCN-FL1N'))
np.testing.assert_array_equal(truth4,
result.get_gate_membership('FSCD-FL1P'))
np.testing.assert_array_equal(
truth5, result.get_gate_membership('FSCN-SSCP-FL1P'))
def test_quadrant_gate_relative_percent(self):
gml_path = 'examples/data/gate_ref/gml/gml_quadrant1_gate.xml'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_samples(data1_sample.original_filename, group_name)
s.analyze_samples(group_name=group_name)
result = s.get_gating_results(group_name,
data1_sample.original_filename)
total_percent = result.get_gate_relative_percent('FL2N-FL4N') + \
result.get_gate_relative_percent('FL2N-FL4P') + \
result.get_gate_relative_percent('FL2P-FL4N') + \
result.get_gate_relative_percent('FL2P-FL4P')
self.assertEqual(100.0, total_percent)
def test_quadrant1_gate():
gml_path = 'examples/data/gate_ref/gml/gml_quadrant1_gate.xml'
res1_path = 'examples/data/gate_ref/truth/Results_FL2N-FL4N.txt'
res2_path = 'examples/data/gate_ref/truth/Results_FL2N-FL4P.txt'
res3_path = 'examples/data/gate_ref/truth/Results_FL2P-FL4N.txt'
res4_path = 'examples/data/gate_ref/truth/Results_FL2P-FL4P.txt'
s = Session()
group_name = 'gml'
s.add_sample_group(group_name, gating_strategy=gml_path)
s.add_samples(data1_sample)
s.assign_samples(data1_sample.original_filename, group_name)
truth1 = pd.read_csv(res1_path,
header=None,
squeeze=True,
dtype='bool').values
truth2 = pd.read_csv(res2_path,
header=None,
squeeze=True,
dtype='bool').values
truth3 = pd.read_csv(res3_path,
header=None,
squeeze=True,
dtype='bool').values
truth4 = pd.read_csv(res4_path,
header=None,
squeeze=True,
dtype='bool').values
s.analyze_samples(group_name)
results = s.get_gating_results(group_name,
data1_sample.original_filename)
result1 = results.get_gate_membership('FL2N-FL4N')
result2 = results.get_gate_membership('FL2N-FL4P')
result3 = results.get_gate_membership('FL2P-FL4N')
result4 = results.get_gate_membership('FL2P-FL4P')
np.testing.assert_array_equal(truth1, result1)
np.testing.assert_array_equal(truth2, result2)
np.testing.assert_array_equal(truth3, result3)
np.testing.assert_array_equal(truth4, result4)
