Minimum Graph Requirements

Pyntacle version 1.0


To date, Pyntacle works with unweighted and undirected graphs, which meet the following criteria:




Reserved Graph Attributes

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.