neurostatx.cli.CompareGraphs

Attributes

Name	Description
app	Cyclopts application for the CompareGraphs command-line tool.

Functions

Name	Description
CompareGraphs	Extract high-percentile nodes from one graph and color them on another.

appattributemodule attribute#

View source

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

Cyclopts application for the CompareGraphs command-line tool.

CompareGraphsfunction#

View source

def CompareGraphs(in_graph1: Annotated[str, Parameter(show_default=False, group='Essential Files Options')], weight: Annotated[str, Parameter(show_default=False, group='Essential Files Options')], percentile: Annotated[float, Parameter(show_default=False, group='Essential Files Options')], in_graph2: Annotated[str, Parameter(show_default=False, group='Essential Files Options')], out_folder: Annotated[str, Parameter(group='Essential Files Options')] = './comparison_results/', verbose: Annotated[bool, Parameter(-v, --verbose, group='Optional parameters')] = False, overwrite: Annotated[bool, Parameter(-f, --overwrite, group='Optional parameters')] = False, label_centroids: Annotated[bool, Parameter(show_default=True, group='Network Visualization Options')] = True, label_subjects: Annotated[bool, Parameter(show_default=True, group='Network Visualization Options')] = False, centroids_size: Annotated[int, Parameter(show_default=True, group='Network Visualization Options')] = 500, centroid_alpha: Annotated[float, Parameter(show_default=True, group='Network Visualization Options')] = 1, centroid_node_color: Annotated[str, Parameter(show_default=True, group='Network Visualization Options')] = 'white', centroid_edge_color: Annotated[str, Parameter(show_default=True, group='Network Visualization Options')] = 'black', subject_node_size: Annotated[int, Parameter(show_default=True, group='Network Visualization Options')] = 5, background_alpha: Annotated[bool, Parameter(show_default=True, group='Network Visualization Options')] = True, subject_edge_color: Annotated[str, Parameter(show_default=True, group='Network Visualization Options')] = None, colormap: Annotated[str, Parameter(show_default=True, group='Network Visualization Options')] = 'gray', legend_title: Annotated[str, Parameter(show_default=False, group='Network Visualization Options')] = 'Membership values')

Extract high-percentile nodes from one graph and color them on another.

CompareGraphs compares two undirected weighted graph networks by extracting the Xth-percentile nodes from –in-graph1 and labelling those nodes on –in-graph2. The percentile is set by –percentile.

Notes

Graph appearance

Graph appearance can be customized with the visualization parameters below. Using subjects labelling will crowd the network if it contains a high number of nodes. Centroids are labelled by default c1, c2, ... and subjects s1, s2, ....

Parameters

Name	Type	Default	Description
in_graph1	str	required	First graph from which subjects above –percentile will be extracted and colored.
weight	str	required	Edge weight to use for the graph.
percentile	float	required	Percentile value used to extract subjects.
in_graph2	str	required	Second graph to color extracted subjects on.
out_folder	str	'./comparison_results/'	Path of the folder in which the results will be written. If not specified, current folder and default name will be used. Defaults to ./comparison_results/.
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.
label_centroids	bool	True	If true, centroids will be labelled. Defaults to True.
label_subjects	bool	False	If true, will label subjects nodes. Defaults to False.
centroids_size	int	500	Size of the centroids nodes. Defaults to 500.
centroid_alpha	float	1	Alpha value representing the transparency of the centroids nodes. Defaults to 1.
centroid_node_color	str	'white'	Centroids nodes color to use. Defaults to white.
centroid_edge_color	str	'black'	Assign a color to the edge of the centroids nodes. Defaults to black.
subject_node_size	int	5	Assign the size of the subjects nodes. Defaults to 5.
background_alpha	bool	True	If true, will plot the background nodes with alpha = 0.2. Defaults to True.
subject_edge_color	str	None	Assign a color to the edge of the subjects nodes. Defaults to None.
colormap	str	'gray'	Colormap to use when coloring the edges of the network based on the membership values of each cluster. Available colormaps are those from Matplotlib (https://matplotlib.org/stable/tutorials/colors/colormaps.html). Defaults to gray.
legend_title	str	'Membership values'	Legend title (colormap). Defaults to Membership values.

Examples

CompareGraphs --in-graph1 graph1.gml --in-matrix membership_mat.npy
--percentile 80 --in-graph2 graph2.gml