Source code for graphein.grn.edges

# %%
# Graphein
# Author: Arian Jamasb <>, Ramon Vinas
# License: MIT
# Project Website:
# Code Repository:
import logging
from typing import Callable, List, Optional

import networkx as nx
import pandas as pd

from graphein.grn.parse_regnetwork import RegNetwork_df
from graphein.grn.parse_trrust import TRRUST_df

log = logging.getLogger(__name__)

[docs]def add_trrust_edges( G: nx.Graph, trrust_filtering_funcs: Optional[List[Callable]] = None ) -> nx.Graph: """ Adds edges from TRRUST to GRNGraph :param G: Graph to edges to (populated with gene_id nodes) :type G: nx.Graph :param trrust_filtering_funcs: List of functions to apply to TRRUST dataframe as pre-processing prior to graph constructions. Defaults to None. :type trrust_filtering_funcs: List[Callable], optional :return: nx.Graph GRNGraph with TRRUST regulatory interactions added as edges :rtype: nx.Graph """ G.graph["sources"].append("trrust") G.graph["trrust_df"] = TRRUST_df( G.graph["gene_list"], filtering_funcs=trrust_filtering_funcs, ) add_interacting_genes(G, df=G.graph["trrust_df"], kind="trrust") return G
[docs]def add_regnetwork_edges( G: nx.Graph, regnetwork_filtering_funcs: Optional[List[Callable]] = None ) -> nx.Graph: """ Adds edges from RegNetwork to GRNGraph :param G: Graph to edges to (populated with gene_id nodes) :param kwargs: Additional parameters to pass to RegNetwork :return: nx.Graph GRNGraph with RegNetwork regulatory interactions added as edges """ G.graph["sources"].append("regnetwork") G.graph["regnetwork_df"] = RegNetwork_df( G.graph["gene_list"], filtering_funcs=regnetwork_filtering_funcs, ) add_interacting_genes(G, df=G.graph["regnetwork_df"], kind="regnetwork") return G
[docs]def add_interacting_genes( G: nx.Graph, df: pd.DataFrame, kind: str ) -> nx.Graph: """ Generic function for adding interaction edges to GRNGraph :param G: GRNGraph to populate with edges :type G: nx.Graph :param df: DataFrame containing edgelist :type df: pd.DataFrame :param kind: name of interaction type :type kind: str :returns: Graph with edges added :rtype: nx.Graph """ gene_1 = df["g1"].values gene_2 = df["g2"].values reg_type = df["regtype"].values interacting_genes = set(list(zip(gene_1, gene_2, reg_type))) for g1, g2, r in interacting_genes: if G.has_edge(g1, g2): G.edges[g1, g2]["kind"].add(kind) G.edges[g1, g2]["regtype"].add(r) else: G.add_edge(g1, g2, kind={kind}, regtype={r}) log.debug(f"Added {len(df)} {kind} interaction edges") return G