def test_difference(self):
genes = ["G1"]
conditions = ["T1", "T2", "T3", "T4"]
expression = np.zeros((1, 4))
expression[0] = [10, 11, 65, 109]
pvalues = np.zeros((1, 3))
pvalues[0] = [0.02, 0.048, 0.0012]
profile = ExpressionProfile(genes, conditions, expression, pvalues)
self.assertEqual(profile.differences(), {"G1": [0, 0, 1]})
def test_difference(self):
genes = ["G1"]
conditions = ["T1", "T2", "T3", "T4"]
expression = np.zeros((1, 4))
expression[0] = [10, 11, 65, 109]
pvalues = np.zeros((1, 3))
pvalues[0] = [0.02, 0.048, 0.0012]
profile = ExpressionProfile(genes, conditions, expression, pvalues)
self.assertEqual(profile.differences(), {"G1": [0, 0, 1]})
def test_export_import(self):
genes = ["G1"]
conditions = ["T1", "T2", "T3", "T4"]
expression = np.zeros((1, 4))
expression[0] = [10, 11, 65, 109]
profile = ExpressionProfile(genes, conditions, expression)
data_frame = profile.data_frame
new_profile = ExpressionProfile.from_data_frame(data_frame)
self.assertEqual(profile, new_profile)
def test_export_import(self):
genes = ["G1"]
conditions = ["T1", "T2", "T3", "T4"]
expression = np.zeros((1, 4))
expression[0] = [10, 11, 65, 109]
profile = ExpressionProfile(genes, conditions, expression)
data_frame = profile.data_frame
new_profile = ExpressionProfile.from_data_frame(data_frame)
self.assertEqual(profile, new_profile)
def build_expression_profile():
warn(
"The profile is not correct because the picture is black and white (do not use this profile for testing)"
)
expression = np.zeros((7, 1))
expression[0, 0] = .0
expression[1, 0] = .0
expression[2, 0] = .0
expression[3, 0] = .0
expression[4, 0] = .0
expression[5, 0] = .0
expression[6, 0] = .0
genes = ["G1", "G2", "G3", "G4", "G5", "G6", "G7"]
conditions = ["Exp"]
return ExpressionProfile(genes, conditions, expression)
def build_expression_profile():
expression = np.zeros((4, 3))
expression[0, 0] = 0.17
expression[0, 1] = 0.20
expression[0, 2] = 0.93
expression[1, 0] = 0.36
expression[1, 1] = 0.83
expression[1, 2] = 0.77
expression[2, 0] = 0.87
expression[2, 1] = 0.65
expression[2, 2] = 0.07
expression[3, 0] = 0.55
expression[3, 1] = 0.49
expression[3, 2] = 0.52
genes = ["Gene2", "Gene3", "Gene6", "Gene7"]
conditions = ["Exp#1", "Exp#2", "Exp#3"]
return ExpressionProfile(genes, conditions, expression)