Utility¶
Transformations¶

graspy.utils.
pass_to_ranks
(graph, method='simplenonzero')[source]¶ Rescales edge weights of an adjacency matrix based on their relative rank in the graph.
Parameters:  graph: Adjacency matrix
 method: {'simplenonzero' (default), 'simpleall', 'zeroboost'} string, optional
 'simplenonzero'
 assigns ranks to all nonzero edges, settling ties using the average. Ranks are then scaled by \(\frac{rank(\text{nonzero edges})}{\text{total nonzero edges} + 1}\)
 'simpleall'
 assigns ranks to all nonzero edges, settling ties using the average. Ranks are then scaled by \(\frac{rank(\text{nonzero edges})}{n^2 + 1}\) where n is the number of nodes
 'zeroboost'
 preserves the edge weight for all 0s, but ranks the other edges as if the ranks of all 0 edges has been assigned. If there are 10 0valued edges, the lowest nonzero edge gets weight 11 / (number of possible edges). Ties settled by the average of the weight that those edges would have received. Number of possible edges is determined by the type of graph (loopless or looped, directed or undirected).
Returns:  graph: numpy.ndarray, shape(n_vertices, n_vertices)
Adjacency matrix of graph after being passed to ranks
See also
scipy.stats.rankdata

graspy.utils.
to_laplace
(graph, form='DAD', regularizer=None)[source]¶ A function to convert graph adjacency matrix to graph laplacian.
Currently supports IDAD, DAD, and RDAD laplacians, where D is the diagonal matrix of degrees of each node raised to the 1/2 power, I is the identity matrix, and A is the adjacency matrix.
RDAD is regularized laplacian: where \(D_t = D + regularizer*I\).
Parameters:  graph: object
Either arraylike, (n_vertices, n_vertices) numpy array, or an object of type networkx.Graph.
 form: {'IDAD' (default), 'DAD', 'RDAD'}, string, optional
 'IDAD'
 Computes \(L = I  D*A*D\)
 'DAD'
 Computes \(L = D*A*D\)
 'RDAD'
 Computes \(L = D_t*A*D_t\) where \(D_t = D + regularizer*I\)
 regularizer: int, float or None, optional (default=None)
Constant to be added to the diagonal of degree matrix. If None, average node degree is added. If int or float, must be >= 0. Only used when
form
== 'RDAD'.
Returns:  L: numpy.ndarray
2D (n_vertices, n_vertices) array representing graph laplacian of specified form
References
[1] Qin, Tai, and Karl Rohe. "Regularized spectral clustering under the degreecorrected stochastic blockmodel." In Advances in Neural Information Processing Systems, pp. 31203128. 2013
Helper Functions¶

graspy.utils.
import_graph
(graph)[source]¶ A function for reading a graph and returning a shared data type.
Parameters:  graph: object
Either arraylike, shape (n_vertices, n_vertices) numpy array, or an object of type networkx.Graph.
Returns:  out: arraylike, shape (n_vertices, n_vertices)
A graph.
See also
networkx.Graph
,numpy.array

graspy.utils.
import_edgelist
(path, extension='edgelist', delimiter=None, nodetype=<class 'int'>, return_vertices=False)[source]¶ Function for reading a single or multiple edgelists. When importing multiple edgelists, the union of vertices from all graphs is computed so that each output graph have matched vertex set. The order of nodes are sorted by node values.
Parameters:  path : str, Path object, or iterable
If
path
is a directory, then the importing order will be sorted in alphabetical order. extension : str, optional
If
path
is a directory, then the function will convert all files with matching extension. delimiter : str or None, default=None, optional
Delimiter of edgelist. If None, the delimiter is whitespace.
 nodetype : int (default), float, str, Python type, optional
Convert node data from strings to specified type.
 return_vertices : bool, default=False, optional
Returns the union of all ind
Returns:  out : list of arraylike, or arraylike, shape (n_vertices, n_vertices)
If
path
is a directory, a list of arrays is returned. Ifpath
is a file, an array is returned. vertices : arraylike, shape (n_vertices, )
If
return_vertices
== True, then returns an array of all vertices that were included in the output graphs.

graspy.utils.
symmetrize
(graph, method='triu')[source]¶ A function for forcing symmetry upon a graph.
Parameters:  graph: object
Either arraylike, (n_vertices, n_vertices) numpy matrix, or an object of type networkx.Graph.
 method: {'triu' (default), 'tril', 'avg'}, optional
An option indicating which half of the edges to retain when symmetrizing.
 'triu'
 Retain the upper right triangle.
 'tril'
 Retain the lower left triangle.
 'avg'
 Retain the average weight between the upper and lower right triangle, of the adjacency matrix.
Returns:  graph: arraylike, shape (n_vertices, n_vertices)
the graph with asymmetries removed.

graspy.utils.
remove_loops
(graph)[source]¶ A function to remove loops from a graph.
Parameters:  graph: object
Either arraylike, (n_vertices, n_vertices) numpy matrix, or an object of type networkx.Graph.
Returns:  graph: arraylike, shape(n_vertices, n_vertices)
the graph with selfloops (edges between the same node) removed.