def load_pairsinfo(self, pairs_filename):
row_count, table_data = ming_fileio_library.parse_table_with_headers(
pairs_filename)
if "CLUSTERID1" in table_data:
for i in range(row_count):
node1 = table_data["CLUSTERID1"][i]
node2 = table_data["CLUSTERID2"][i]
cosine = table_data["Cosine"][i]
deltamz = table_data["DeltaMZ"][i]
pair = NetworkPair(node1, node2, cosine, deltamz)
self.pairs.append(pair)
else:
row_count, table_data = ming_fileio_library.parse_table_without_headers(
pairs_filename)
for i in range(row_count):
node1 = table_data[0][i]
node2 = table_data[1][i]
cosine = table_data[4][i]
deltamz = table_data[2][i]
pair = NetworkPair(node1, node2, cosine, deltamz)
self.pairs.append(pair)
#Make stuff consistent, specifically adding adjacency list
for pair in self.pairs:
node1 = pair.node1
node2 = pair.node2
if not (node1 in self.index_to_neighbors):
self.index_to_neighbors[node1] = []
if not (node2 in self.index_to_neighbors):
self.index_to_neighbors[node2] = []
self.index_to_neighbors[node1].append(node2)
self.index_to_neighbors[node2].append(node1)
def load_pairsinfo(self, pairs_filename): row_count, table_data = ming_fileio_library.parse_table_with_headers(pairs_filename) if "CLUSTERID1" in table_data: for i in range(row_count): node1 = table_data["CLUSTERID1"][i] node2 = table_data["CLUSTERID2"][i] cosine = table_data["Cosine"][i] deltamz = table_data["DeltaMZ"][i] pair = NetworkPair(node1, node2, cosine, deltamz) self.pairs.append(pair) else: row_count, table_data = ming_fileio_library.parse_table_without_headers(pairs_filename) for i in range(row_count): node1 = table_data[0][i] node2 = table_data[1][i] cosine = table_data[4][i] deltamz = table_data[2][i] pair = NetworkPair(node1, node2, cosine, deltamz) self.pairs.append(pair) #Make stuff consistent, specifically adding adjacency list for pair in self.pairs: node1 = pair.node1 node2 = pair.node2 if not(node1 in self.index_to_neighbors): self.index_to_neighbors[node1] = [] if not(node2 in self.index_to_neighbors): self.index_to_neighbors[node2] = [] self.index_to_neighbors[node1].append(node2) self.index_to_neighbors[node2].append(node1)
def loading_network(filename, hasHeaders=False, edgetype="Cosine"):
node1_list = []
node2_list = []
mass_difference = []
property1 = []
cosine_score = []
explained_intensity = []
edge_annotation = []
if hasHeaders == True:
row_count, table_data = ming_fileio_library.parse_table_with_headers(filename)
if row_count == -1:
return nx.MultiGraph()
node1_list = table_data["CLUSTERID1"]
node2_list = table_data["CLUSTERID2"]
mass_difference = table_data["DeltaMZ"]
property1 = table_data["MEH"]
cosine_score = None
if "Cosine" in table_data:
cosine_score = table_data["Cosine"]
if "COSINE" in table_data:
cosine_score = table_data["COSINE"]
if "OtherScore" in table_data:
explained_intensity = table_data["OtherScore"]
if len(property1) != len(node1_list):
property1 = node1_list
if len(explained_intensity) != len(node1_list):
explained_intensity = node1_list
if "EdgeAnnotation" in table_data:
edge_annotation = table_data["EdgeAnnotation"]
else:
edge_annotation = [" "] * len(node1_list)
else:
row_count, table_data = ming_fileio_library.parse_table_without_headers(filename)
if row_count == -1:
return nx.MultiGraph()
node1_list = table_data[0]
node2_list = table_data[1]
mass_difference = table_data[2]
property1 = table_data[3]
cosine_score = table_data[4]
explained_intensity = table_data[5]
edge_annotation = [" "] * len(node1_list)
edge_property_map = {}
edge_object_list = []
intermediate_graph_nodes = set()
intermediate_edges_to_add = []
for i in range(row_count):
edge_object = {}
edge_object["node1"] = node1_list[i]
edge_object["node2"] = node2_list[i]
edge_object["mass_difference"] = mass_difference[i]
edge_object["property1"] = property1[i]
edge_object["cosine_score"] = float(cosine_score[i])
edge_object["explained_intensity"] = float(explained_intensity[i])
edge_object["component"] = -1
edge_object["EdgeType"] = edgetype
edge_object["EdgeAnnotation"] = edge_annotation[i].rstrip()
edge_object["EdgeScore"] = float(cosine_score[i])
edge_key = node1_list[i] + "-" + node2_list[i]
edge_property_map[edge_key] = edge_object
intermediate_graph_nodes.add(edge_object["node1"])
intermediate_graph_nodes.add(edge_object["node2"])
# set key to edgetype for options to remove edge later in case multiple edges are present
edge_key_for_dict = CONST.EDGE.COSINE_TYPE
intermediate_edges_to_add.append((edge_object["node1"], edge_object["node2"], edge_key_for_dict, edge_object))
G=nx.MultiGraph()
G.add_nodes_from(intermediate_graph_nodes)
G.add_edges_from(intermediate_edges_to_add)
return G
def loading_network(filename, hasHeaders=False):
node1_list = []
node2_list = []
mass_difference = []
property1 = []
cosine_score = []
explained_intensity = []
edge_annotation = []
if hasHeaders == True:
row_count, table_data = ming_fileio_library.parse_table_with_headers(filename)
if row_count == -1:
return nx.MultiGraph()
node1_list = table_data["CLUSTERID1"]
node2_list = table_data["CLUSTERID2"]
mass_difference = table_data["DeltaMZ"]
property1 = table_data["MEH"]
cosine_score = None
if "Cosine" in table_data:
cosine_score = table_data["Cosine"]
if "COSINE" in table_data:
cosine_score = table_data["COSINE"]
explained_intensity = table_data["OtherScore"]
if len(property1) != len(node1_list):
property1 = node1_list
if len(explained_intensity) != len(node1_list):
explained_intensity = node1_list
if "EdgeAnnotation" in table_data:
edge_annotation = table_data["EdgeAnnotation"]
else:
edge_annotation = [" "] * len(node1_list)
else:
row_count, table_data = ming_fileio_library.parse_table_without_headers(filename)
if row_count == -1:
return nx.MultiGraph()
node1_list = table_data[0]
node2_list = table_data[1]
mass_difference = table_data[2]
property1 = table_data[3]
cosine_score = table_data[4]
explained_intensity = table_data[5]
edge_annotation = [" "] * len(node1_list)
edge_property_map = {}
edge_object_list = []
intermediate_graph_nodes = set()
intermediate_edges_to_add = []
for i in range(row_count):
edge_object = {}
edge_object["node1"] = node1_list[i]
edge_object["node2"] = node2_list[i]
edge_object["mass_difference"] = mass_difference[i]
edge_object["property1"] = property1[i]
edge_object["cosine_score"] = float(cosine_score[i])
edge_object["explained_intensity"] = float(explained_intensity[i])
edge_object["component"] = -1
edge_object["EdgeType"] = "Cosine"
edge_object["EdgeAnnotation"] = edge_annotation[i].rstrip()
edge_object["EdgeScore"] = float(cosine_score[i])
edge_key = node1_list[i] + "-" + node2_list[i]
edge_property_map[edge_key] = edge_object
intermediate_graph_nodes.add(edge_object["node1"])
intermediate_graph_nodes.add(edge_object["node2"])
intermediate_edges_to_add.append((edge_object["node1"], edge_object["node2"], edge_object))
G=nx.MultiGraph()
G.add_nodes_from(intermediate_graph_nodes)
G.add_edges_from(intermediate_edges_to_add)
return G
def loading_network(filename, hasHeaders=False):
node1_list = []
node2_list = []
mass_difference = []
property1 = []
cosine_score = []
explained_intensity = []
if hasHeaders == True:
row_count, table_data = ming_fileio_library.parse_table_with_headers(
filename)
if row_count == -1:
return nx.Graph()
node1_list = table_data["CLUSTERID1"]
node2_list = table_data["CLUSTERID2"]
mass_difference = table_data["DeltaMZ"]
property1 = table_data["MEH"]
cosine_score = None
if "Cosine" in table_data:
cosine_score = table_data["Cosine"]
if "COSINE" in table_data:
cosine_score = table_data["COSINE"]
explained_intensity = table_data["OtherScore"]
if len(property1) != len(node1_list):
property1 = node1_list
if len(explained_intensity) != len(node1_list):
explained_intensity = node1_list
else:
row_count, table_data = ming_fileio_library.parse_table_without_headers(
filename)
if row_count == -1:
return nx.Graph()
node1_list = table_data[0]
node2_list = table_data[1]
mass_difference = table_data[2]
property1 = table_data[3]
cosine_score = table_data[4]
explained_intensity = table_data[5]
edge_property_map = {}
edge_object_list = []
intermediate_graph_nodes = set()
intermediate_edges_to_add = []
for i in range(row_count):
edge_object = {}
edge_object["node1"] = node1_list[i]
edge_object["node2"] = node2_list[i]
edge_object["mass_difference"] = mass_difference[i]
edge_object["property1"] = property1[i]
edge_object["cosine_score"] = float(cosine_score[i])
edge_object["explained_intensity"] = float(explained_intensity[i])
edge_object["component"] = -1
edge_key = node1_list[i] + "-" + node2_list[i]
edge_property_map[edge_key] = edge_object
intermediate_graph_nodes.add(edge_object["node1"])
intermediate_graph_nodes.add(edge_object["node2"])
intermediate_edges_to_add.append(
(edge_object["node1"], edge_object["node2"], edge_object))
G = nx.Graph()
G.add_nodes_from(intermediate_graph_nodes)
G.add_edges_from(intermediate_edges_to_add)
return G