def test_get_shortest_paths_graph(self):
"""Test method to get shortest paths graph."""
shortest_path_graph = self.mapped_network.copy()
shortest_path_graph.delete_vertices([2, 6, 7, 8])
shortest_path_graph.simplify(combine_edges=max)
shortest_path_graph.delete_vertices(
shortest_path_graph.vs.select(_degree_eq=0))
eid = shortest_path_graph.get_eid("0", "3")
shortest_path_graph.delete_edges(eid)
weights = list(1 - np.array(shortest_path_graph.es['weight']))
shortest_path_graph.es['weight'] = weights
n = Network(
self.interact_network,
max_adj_p=0.05,
max_l2fc=-1,
min_l2fc=1,
)
n.set_up_network(self.protein_list)
fn = FilteredNetwork(n)
shortest_path_graph_to_test = fn.get_shortest_paths_graph()
self.__check_for_graph_eq(shortest_path_graph,
shortest_path_graph_to_test)
def test_init(self):
"""Test the constructor and set_up methods."""
n = Network(
self.interact_network,
max_adj_p=0.05,
max_l2fc=-1,
min_l2fc=1,
)
n.set_up_network(self.protein_list, gene_filter=True)
self.__check_for_graph_eq(n.graph, self.mapped_network)
def test_get_downregulated_genes_network(self):
"""Test the method to get downregulated genes network."""
de_down = self.mapped_network.copy()
de_down.delete_vertices([0, 1, 2, 3, 4, 6, 7, 8])
de_down.delete_vertices(de_down.vs.select(_degree_eq=0))
n = Network(
self.interact_network,
max_adj_p=0.05,
max_l2fc=-1,
min_l2fc=1,
)
n.set_up_network(self.protein_list)
fn = FilteredNetwork(n)
de_down_to_test = fn.get_downregulated_genes_network()
self.__check_for_graph_eq(de_down, de_down_to_test)