To date, Pyntacle works with unweighted and undirected graphs, which meet the following criteria:
Pyntacle exchanges information with a graph through a series of reserved attributes, embedded in the
igraph.Graph object. The full list of these attributes is available in the table below, along with the level at
which these attributes are stored (graph, vertex or edge) and the default type that is expected by Pyntacle
methods when they are recalled. They can be edited manually and their value can be changed to fit the user's
need. We do recommend, however, to leave the red labeled attributes untouched,
as any unforeseen modification may cause critical errors.
|Attribute name||Element||Data type||Description|
|name||graph||list of strings||If obtained by a set operation, a graph can have multiple names, one for each originating graph.|
|isolates||graph||list of strings||The list of all the isolates that are removed by Pyntacle when importing the graph from any of the supported network file formats. It stores the vertex name attribute of the isolates that are removed.|
|sif_interaction_name||graph||string||The name of the interaction, as specified in the header of the imported SIF file, None if the graph was not imported from a SIF file.|
|implementation||graph||string||Allowed values: cpu, gpu, igraph. These are automatically set by Pyntacle according to topological properties and to the complexity of the graph. They drive Pyntacle to compute complex chunks of code in parallel on multi-core processors or on GPU, if available, through Numba, or on single core relying on the iGraph Python library.|
|name||vertex||string||Unique node name.|
|parent||vertex||list of strings||Useful when performing set operations between two graphs to keep track the source network of each node. Initialized to None by default.|
|module||vertex||string||Used when searching for communities (identified with progressive, positive integers) within a graph. It indicates the non-overlapping presence of the node in one of the found modules.|
|sif_interaction||edge||list of strings||The value stored in the interaction column of a SIF file (the 2nd leftmost column) specifying the nature of the link between two nodes.
Defaults to None if the graph was not imported from a SIF file.
Note: Multiple interactions between nodes are collapsed into a single edge and all the interactions are stored in a list of unique values sorted lexicographically.
|adjacent_nodes||edge||tuple of strings||A tuple containing the vertex name of two adjacent nodes by this edge.|
|weights||edge||float or integer||Weight assigned to an edge by algorithms that work with or make weighted graphs, like the PageRank index.|
|module||edge||string||Used when searching for communities (identified with progressive, positive integers) within a graph. It indicates the non-overlapping presence of the node in one of the found modules.|