Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.

meierlab.networks.graph.gen_graph_from_matrix

meierlab.networks.graph.gen_graph_from_matrix(G, atlas, matrix_file, atlas_delim=',', matrix_delim='\t', to_fz=True)

Generate a (weighted, undirected) graph from a matrix file.

Parameters:

atlasstr or file path

Atlas parcellation used to generate the main graph.

matrix_filestr or file path

A text file containing edge weight information (e.g., a correlation matrix).

atlas_delimstr, optional

Delimiter used to read the atlas, by default “,”

matrix_delimstr, optional

Delimiter used to read the matrix_file, by default “t”

to_fzbool, optional

Fisher-Z transform the correlations, default True.

Returns:

networkx.Graph

A graph with additional edge weight attributes.

Examples

>>> from meierlab.networks import graph
>>> atlas = 'schaefer2018/atlas.csv'
>>> sub_file = 'sub-001.tsv'
>>> G = graph.gen_base_graph_from_atlas(atlas)
>>> g = graph.gen_graph_from_matrix(G,atlas,sub_file)
>>> edge_weights = [d[edge_attr] for (_,_,d) in g.edges(data=True)]
>>> edge_weights[0:10]
[1.0, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2]