Interactions¶
-
class
openomics.database.interaction.
Interactions
(path, file_resources, source_col_name=None, target_col_name=None, source_index=None, target_index=None, edge_attr=None, filters=None, directed=True, relabel_nodes=None, verbose=False)[source][source]¶ Bases:
openomics.database.base.Database
Methods Summary
filter_values
(df, filters[, case])get_interactions
([nodelist, data, inclusive])- param nodelist
A list of nodes to fetch edges from
info
()load_network
(file_resources, …)Handles data processing from file_resources to a Pandas DataFrame which contain edgelist data, then constructs and return a NetworkX Graph.
name
()Methods Documentation
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get_interactions
(nodelist=None, data=False, inclusive=True)[source][source]¶ - Parameters
nodelist (list) – A list of nodes to fetch edges from
data (bool) – default False Whether to include edge attributes
inclusive (bool) – default False Whether to only retrieve edges from nodes inclusive in nodelist.
- Returns
a NetworkX edgelist
- Return type
edges (OutEdgeView)
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abstract
load_network
(file_resources, source_col_name, target_col_name, edge_attr, directed, filters)[source][source]¶ Handles data processing from file_resources to a Pandas DataFrame which contain edgelist data, then constructs and return a NetworkX Graph. :param file_resources: a dict of file name and file path/object :param source_col_name: column name of the dataframe for source in the edge :type source_col_name: str :param target_col_name: column name of the dataframe for target in the edge :type target_col_name: str :param edge_attr: list of str for column data to include in each edge :type edge_attr: list :param directed: True to return a DiGraph(), else Graph() :type directed: bool :param filters: A dict of {column name: column values} to filter the dataframe
- Returns
a NetworkX Graph or DiGraph
- Return type
network