Utilities

Graph Utils

rhodonite.utils.graph.add_dict_edge_list(g, prop_dict, prop_name, eval_type, **eprop_kwargs)

Converts a dictionary to graph edges with an edge property map.

Parameters:

• g (graph_tool.Graph) – A graph.
• prop_dict (dict) – A dictionary where keys are tuples of source target vertices or indices, and values are the value of a property or weight assigned to the edge. vertices and values are the values to be inserted into the property map.
• val_type (str) – The type of the property. See graph_tool.PropertyMap.
• eprop_kwargs – See graph_tool.PropertyMap.

rhodonite.utils.graph.dict_to_edge_prop(g, prop_dict, val_type, edge_index_dict=None)

Maps dictionary values to an edge property using keys.

Parameters:

• g (graph_tool.Graph) – A graph.
• prop_dict (dict) – A dictionary where keys are tuples of source target vertices or indices, and values are the value of a property or weight assigned to the edge.
• val_type (str) – See graph_tool.PropertyMap.
• eprop_kwargs – Other edge property map kwargs. See graph_tool.PropertyMap

Returns

eprop : graph_tool.PropertyMap

An edge property map.

rhodonite.utils.graph.dict_to_vertex_prop(g, prop_dict, val_type)

Maps dictionary values to a vertex property using keys.

Parameters:

• g (graph_tool.Graph) – A graph.
• prop_dict (dict) – A dictionary where vertices or vertex indices, and values are the value of a property or weight assigned to the vertex.
• vprop_kwargs – See graph_tool.PropertyMap.

Returns

vprop : graph_tool.PropertyMap

rhodonite.utils.graph.internalize_prop_dict(g, prop_dict, prop_tag='{}')

internalize_props_from_dict Internalises property maps contained in a dictionary and that correspond to graph, g, to that graph itself.

Parameters:

• g (graph_tool.Graph) – A graph.
• prop_dict (dict of graph_tool.PropertyMap) – A dictionary of graph_tool.PropertyMap for a graph, g, its vertices or edges.
• prop_tag (str, optional) – A common name to apply to the keys of internalized properties. Curly braces should be included to indicate where the unique key for each property map should be included. e.g. my_graph_prop_{} Defaults to key for each property map in prop_dict.

rhodonite.utils.graph.subgraph_eprop_agg(g, vertices, eprop, aggfuncs)

Retrieves the edge property values of all edges in a subgraph and returns a list of user-provided aggregations.

Parameters:

• g (graph_tool.Graph) – The original graph.
• vertices (iter) – Vertices of the subgraph.
• eprop (graph_tool.PropertyMap) – An edge property of graph, g.
• aggfuncs (iter) – A series of aggregation functions that can be applied to an array of values from the property map. e.g. aggfuncs=[np.mean, np.median] will return the mean and the median, only retrieving the actual values from g once.

Returns:

agg (list A list of aggregated values.)

rhodonite.utils.graph.subgraph_eprop_values(g, vertices, eprop)

get_subgraph_eprop Retrieves the edge property values of all edges in a subgraph.

Parameters:

• g (graph_tool.Graph) – The original graph.
• vertices (iter) – Vertices of the subgraph.
• eprop (graph_tool.EdgePropertyMap) – An edge property for graph, g.

Returns:

vals (array Edge property values from the subgraph.)

Math Utils

Misc Utils

Tabular Utils