neurostatx.cli.GraphMetrics

Attributes

Name	Description
OPERATIONS	Mapping of metric names to NetworkX functions GraphMetrics can run.
app	Cyclopts application for the GraphMetrics command-line tool.

Functions

Name	Description
GraphMetrics	Compute NetworkX metrics on an existing undirected weighted graph.

OPERATIONSattributemodule attribute#

View source

OPERATIONS = get_metrics_ops()

Mapping of metric names to NetworkX functions GraphMetrics can run.

appattributemodule attribute#

View source

app = App(default_parameter=Parameter(negative=()))

Cyclopts application for the GraphMetrics command-line tool.

GraphMetricsfunction#

View source

def GraphMetrics(operation: Annotated[List[str], Parameter(show_choices=True, show_default=False, group=Group(Arguments))], out_file: Annotated[str, Parameter(show_default=False, group='Essential Files Options')] = None, verbose: Annotated[bool, Parameter(-v, --verbose, group='Optional parameters')] = False, overwrite: Annotated[bool, Parameter(-f, --overwrite, group='Optional parameters')] = False)

Compute NetworkX metrics on an existing undirected weighted graph.

Runtime depends on hardware and the chosen metric; a large graph (~10 000 nodes) can take about 10 minutes.

Notes

Available metrics

Available metrics come from NetworkX algorithms that can handle undirected weighted graphs (see the operation argument) [1]. If NODE is required, provide a single node label (such as c1). If NODES is required, provide multiple nodes within quotation marks (such as "c1 c2 c3").

• eigencentrality: GRAPH WEIGHT — eigenvector centrality for all nodes.
• closenesscentrality: GRAPH WEIGHT — closeness centrality for all nodes.
• betweennesscentrality: GRAPH WEIGHT — betweenness centrality for all nodes.
• informationcentrality: GRAPH WEIGHT — information centrality for all nodes.
• currentflowbc: GRAPH WEIGHT — current flow betweenness centrality for all nodes.
• loadcentrality: GRAPH WEIGHT — load centrality for all nodes.
• harmoniccentrality: GRAPH WEIGHT — harmonic centrality for all nodes.
• eccentricity: GRAPH WEIGHT — eccentricity for all nodes.
• clustering: GRAPH WEIGHT — clustering coefficient for all nodes.
• constraint: GRAPH NODES WEIGHT — constraint for all specified nodes.
• effectivesize: GRAPH NODES WEIGHT — effective size for all specified nodes.
• closenessvitality: GRAPH NODE WEIGHT — closeness vitality for a single node.
• degree: GRAPH WEIGHT — degree of the specified node.

References

[1] NetworkX algorithms

Parameters

Name	Type	Default	Description
operation	List[str]	required	List of arguments to provide to the script. The first argument is the operation to perform. The second argument is the input graph file. The rest of the arguments are the arguments required by the operation (see above).
out_file	str	None	Path and name of the file containing the metrics for each node. Defaults to ./operation_name.xlsx.
verbose	bool	False	If true, produce verbose output. Defaults to False.
overwrite	bool	False	If true, force overwriting of existing output files. Defaults to False.

Examples

GraphMetrics --out-folder output/ eigencentrality graph.gexf membership