To Graph Database

Date published: 26/09/23

bin.to_db.get_graph(feature_matrix: DataFrame, edge_list: DataFrame, from_col: str, to_col: str) → Graph

Construct a graph from edge list data.

Args:

feature_matrix (pd.DataFrame):

The feature matrix.

edge_list (pd.DataFrame):

The edge list.

from_col (str):

The “from” column name.

to_col (str):

The “to” column name.

Returns:

nx.Graph:

The graph to write to the database.

bin.to_db.log_results(tracking_uri: str, experiment_prefix: str, grn_name: str, feature_matrix: DataFrame, edge_list: DataFrame) → None

Log experiment results to the experiment tracker.

Args:

tracking_uri (str):

The tracking URI.

experiment_prefix (str):

The experiment name prefix.

grn_name (str):

The name of the GRN.

feature_matrix (pd.DataFrame):

The feature matrix.

edge_list (pd.DataFrame):

The edge list.

bin.to_db.main(config: DictConfig) → None

The main entry point for the plotting pipeline.

Args:

config (DictConfig):

The pipeline configuration.

bin.to_db.to_db(db_host: str, db_name: str, db_username: str, db_password: str, collection: str, G: Graph) → None

Write the graph to the database.

Args:

db_host (str):

The database host.

db_name (str):

The database name.

db_username (str):

The database username.

db_password (str):

The database password.

collection (str):

The database collection.

G (nx.Graph):

The graph.