def setUp(self):
wkf = FakeWorkflow()
wkf.output_dir = TEMP_DIR
self.cv = crossvalidation_workflow.CrossValidationManager(wkf)
self.cv._csv_writer_object = FakeWriter
self.cv._open_csv_handle = types.MethodType(fake_class_method, self.cv)
self.cv._create_output_path = types.MethodType(fake_class_method,
self.cv)
def set_up_cv_seeds(wkf):
cv = crossvalidation_workflow.CrossValidationManager(wkf)
cv.add_gridsearch_parameter('random_seed', list(range(42, 52)))
return cv
wkf = inferelator_workflow("stars", VelocityWorkflow)
wkf.set_file_paths(input_dir=INPUT_DIR,
output_dir=os.path.join(OUTPUT_PATH, "tau43"),
gold_standard_file='gold_standard.tsv',
priors_file=YEASTRACT_PRIOR,
tf_names_file=YEASTRACT_TF_NAMES)
wkf.set_expression_file(h5ad=DATA_FILE, h5_layer="smooth_count")
wkf.set_velocity_parameters(velocity_file_name=DATA_FILE, velocity_file_type="h5ad", velocity_file_layer="pv")
wkf.set_crossvalidation_parameters(split_gold_standard_for_crossvalidation=True,
cv_split_ratio=0.5)
wkf.set_run_parameters(num_bootstraps=5)
wkf.set_count_minimum(0.05)
wkf.add_preprocess_step(single_cell.log2_data)
wkf.tau = 43.28
cv_wrap = crossvalidation_workflow.CrossValidationManager(wkf)
cv_wrap.add_gridsearch_parameter('random_seed', list(range(42, 52)))
cv_wrap.run()
del cv_wrap
wkf = inferelator_workflow("stars", VelocityWorkflow)
wkf.set_file_paths(input_dir=INPUT_DIR,
output_dir=os.path.join(OUTPUT_PATH, "tau43_shuffle"),
gold_standard_file='gold_standard.tsv',
priors_file=YEASTRACT_PRIOR,
tf_names_file=YEASTRACT_TF_NAMES)
wkf.set_expression_file(h5ad=DATA_FILE, h5_layer="smooth_count")
wkf.set_velocity_parameters(velocity_file_name=DATA_FILE, velocity_file_type="h5ad", velocity_file_layer="pv")
wkf.set_crossvalidation_parameters(split_gold_standard_for_crossvalidation=True,
cv_split_ratio=0.5)
def set_up_fig5b(wkf):
cv_wrap = crossvalidation_workflow.CrossValidationManager(wkf)
cv_wrap.add_gridsearch_parameter('random_seed', list(range(42, 52)))
cv_wrap.add_size_subsampling([0.01, 0.025, 0.05, 0.1, 0.25, 0.5, 0.75, 1],
seed=86)
return cv_wrap
