pynets.plotting package

Submodules

pynets.plotting.adjacency module

Created on Tue Nov 7 10:40:07 2017 Copyright (C) 2017

pynets.plotting.adjacency.plot_community_conn_mat(conn_matrix, labels, out_path_fig_comm, community_aff, cmap, dpi_resolution=300)[source]

Plot a community-parcellated connectivity matrix.

Parameters
conn_matrixarray

NxN matrix.

labelslist

List of string labels corresponding to ROI nodes.

out_path_fig_commstr

File path to save the community-parcellated connectivity matrix image as a .png figure.

community_affarray

Community-affiliation vector.

pynets.plotting.adjacency.plot_conn_mat(conn_matrix, labels, out_path_fig, cmap, binarized=False, dpi_resolution=300)[source]

Plot a connectivity matrix.

Parameters
conn_matrixarray

NxN matrix.

labelslist

List of string labels corresponding to ROI nodes.

out_path_figstr

File path to save the connectivity matrix image as a .png figure.

pynets.plotting.adjacency.plot_conn_mat_func(conn_matrix, conn_model, atlas, dir_path, ID, subnet, labels, roi, thr, node_radius, smooth, hpass, signal)[source]

API for selecting among various functional connectivity matrix plotting approaches.

Parameters
conn_matrixarray

NxN matrix.

conn_modelstr

Connectivity estimation model (e.g. corr for correlation, cov for covariance, sps for precision covariance, partcorr for partial correlation). sps type is used by default.

atlasstr

Name of atlas parcellation used.

dir_pathstr

Path to directory containing subject derivative data for given run.

IDstr

A subject id or other unique identifier.

subnetstr

Resting-state subnet based on Yeo-7 and Yeo-17 naming (e.g. ‘Default’) used to filter nodes in the study of brain subgraphs.

labelslist

List of string labels corresponding to ROI nodes.

roistr

File path to binarized/boolean region-of-interest Nifti1Image file.

thrfloat

A value, between 0 and 1, to threshold the graph using any variety of methods triggered through other options.

node_radiusint

Spherical centroid node size in the case that coordinate-based centroids are used as ROI’s.

smoothint

Smoothing width (mm fwhm) to apply to time-series when extracting signal from ROI’s.

hpassbool

High-pass filter values (Hz) to apply to node-extracted time-series.

signalstr

The name of a valid function used to reduce the time-series region extraction.

pynets.plotting.adjacency.plot_conn_mat_struct(conn_matrix, conn_model, atlas, dir_path, ID, subnet, labels, roi, thr, node_radius, track_type, traversal, min_length, error_margin)[source]

API for selecting among various structural connectivity matrix plotting approaches.

Parameters
conn_matrixarray

NxN matrix.

conn_modelstr

Connectivity estimation model (e.g. corr for correlation, cov for covariance, sps for precision covariance, partcorr for partial correlation). sps type is used by default.

atlasstr

Name of atlas parcellation used.

dir_pathstr

Path to directory containing subject derivative data for given run.

IDstr

A subject id or other unique identifier.

subnetstr

Resting-state subnet based on Yeo-7 and Yeo-17 naming (e.g. ‘Default’) used to filter nodes in the study of brain subgraphs.

labelslist

List of string labels corresponding to ROI nodes.

roistr

File path to binarized/boolean region-of-interest Nifti1Image file.

thrfloat

A value, between 0 and 1, to threshold the graph using any variety of methods triggered through other options.

node_radiusint

Spherical centroid node size in the case that coordinate-based centroids are used as ROI’s.

track_typestr

Tracking algorithm used (e.g. ‘local’ or ‘particle’).

traversalstr

The statistical approach to tracking. Options are: det (deterministic), closest (clos), boot (bootstrapped), and prob (probabilistic).

min_lengthint

Minimum fiber length threshold in mm to restrict tracking.

pynets.plotting.brain module

Created on Tue Nov 7 10:40:07 2017 Copyright (C) 2017

pynets.plotting.brain.create_gb_palette(mat, edge_cmap, coords, labels, node_radius='auto', node_cmap=None, prune=True, centrality_type='eig', max_node_radius=None, max_edge_size=2, node_aff_mat=None)[source]

Create connectome color palette based on graph topography.

Parameters
matarray

NxN matrix.

edge_cmap: colormap

colormap used for representing the weight of the edges.

coordslist

List of (x, y, z) tuples corresponding to an a-priori defined set (e.g. a coordinate atlas).

labelslist

List of string labels corresponding to ROI nodes.

node_radiusint

Spherical centroid node size in the case that coordinate-based centroids are used as ROI’s.

node_radius: scalar or array_like

size(s) of the nodes in points^2.

node_cmap: colormap

colormap used for representing the community assignment of the nodes.

pynets.plotting.brain.plot_all_func(conn_matrix, conn_model, atlas, dir_path, ID, subnet, labels, roi, coords, thr, node_radius, edge_threshold, smooth, prune, parcellation, norm, binary, hpass, signal, edge_color_override=False)[source]

Plot adjacency matrix, connectogram, and glass brain for functional connectome.

Parameters
conn_matrixarray

NxN matrix.

conn_modelstr

Connectivity estimation model (e.g. corr for correlation, cov for covariance, sps for precision covariance, partcorr for partial correlation). sps type is used by default.

atlasstr

Name of atlas parcellation used.

dir_pathstr

Path to directory containing subject derivative data for given run.

IDstr

A subject id or other unique identifier.

subnetstr

Resting-state subnet based on Yeo-7 and Yeo-17 naming (e.g. ‘Default’) used to filter nodes in the study of brain subgraphs.

labelslist

List of string labels corresponding to ROI nodes.

roistr

File path to binarized/boolean region-of-interest Nifti1Image file.

coordslist

List of (x, y, z) tuples corresponding to an a-priori defined set (e.g. a coordinate atlas).

thrfloat

A value, between 0 and 1, to threshold the graph using any variety of methods triggered through other options.

node_radiusint

Spherical centroid node size in the case that coordinate-based centroids are used as ROI’s.

edge_thresholdfloat

The actual value, between 0 and 1, that the graph was thresholded (can differ from thr if target was not successfully obtained.

smoothint

Smoothing width (mm fwhm) to apply to time-series when extracting signal from ROI’s.

prunebool

Indicates whether to prune final graph of disconnected nodes/isolates.

parcellationstr

File path to atlas parcellation Nifti1Image.

normint

Indicates method of normalizing resulting graph.

binarybool

Indicates whether to binarize resulting graph edges to form an unweighted graph.

hpassbool

High-pass filter values (Hz) to apply to node-extracted time-series.

signalstr

The name of a valid function used to reduce the time-series region extraction.

edge_color_overridebool

Switch that enables random sequential colormap selection for edges.

pynets.plotting.brain.plot_all_struct(conn_matrix, conn_model, atlas, dir_path, ID, subnet, labels, roi, coords, thr, node_radius, edge_threshold, prune, parcellation, norm, binary, track_type, traversal, min_length, error_margin)[source]

Plot adjacency matrix, connectogram, and glass brain for functional connectome.

Parameters
conn_matrixarray

NxN matrix.

conn_modelstr

Connectivity estimation model (e.g. corr for correlation, cov for covariance, sps for precision covariance, partcorr for partial correlation). sps type is used by default.

atlasstr

Name of atlas parcellation used.

dir_pathstr

Path to directory containing subject derivative data for given run.

IDstr

A subject id or other unique identifier.

subnetstr

Resting-state subnet based on Yeo-7 and Yeo-17 naming (e.g. ‘Default’) used to filter nodes in the study of brain subgraphs.

labelslist

List of string labels corresponding to ROI nodes.

roistr

File path to binarized/boolean region-of-interest Nifti1Image file.

coordslist

List of (x, y, z) tuples corresponding to an a-priori defined set (e.g. a coordinate atlas).

thrfloat

A value, between 0 and 1, to threshold the graph using any variety of methods triggered through other options.

node_radiusint

Spherical centroid node size in the case that coordinate-based centroids are used as ROI’s.

edge_thresholdfloat

The actual value, between 0 and 1, that the graph was thresholded (can differ from thr if target was not successfully obtained.

prunebool

Indicates whether to prune final graph of disconnected nodes/isolates.

parcellationstr

File path to atlas parcellation Nifti1Image.

normint

Indicates method of normalizing resulting graph.

binarybool

Indicates whether to binarize resulting graph edges to form an unweighted graph.

track_typestr

Tracking algorithm used (e.g. ‘local’ or ‘particle’).

traversalstr

The statistical approach to tracking. Options are: det (deterministic), closest (clos), boot (bootstrapped), and prob (probabilistic).

min_lengthint

Minimum fiber length threshold in mm to restrict tracking.

pynets.plotting.brain.plot_all_struct_func(mG_paths, namer_dir, modality_paths)[source]

Plot adjacency matrix and glass brain for structural-functional multiplex connectome.

Parameters
mG_pathstuple

A tuple of two gpickle file paths containing a NetworkX OrderedMultiGraph object and a MultilayerGraph object (See https://github.com/nkoub/multinetx).

namer_dirstr

Path to output directory for multiplex data.

modality_pathstuple

A tuple of filepath strings to the raw structural and raw functional connectome graph files (.npy).

pynets.plotting.brain.plot_graph_measure_hists(csv_all_metrics)[source]

Plot histograms for each graph theoretical measure for a given subject.

Parameters
csv_all_metricsstr

CSV file of concatenated graph measures across ensemble.

pynets.plotting.brain.plot_network_clusters(graph, communities, out_path, figsize=(8, 8), node_radius=50, plot_overlaps=False, plot_labels=False)[source]

Plot a graph with node color coding for communities.

Parameters
graphNetworkX graph
communitiesarray

Community affiliation vector

out_pathstr

Path to save figure.

figsizeTuple of integers

The figure size; it is a pair of float, default (8, 8).

node_radius: int

Default 50.

plot_overlapsbool

Flag to control if multiple algorithms memberships are plotted. Default is False.

plot_labelsbool

Flag to control if node labels are plotted. Default is False.

pynets.plotting.brain.plot_timeseries(time_series, subnet, ID, dir_path, atlas, labels)[source]

Plot time-series.

Parameters
time-seriesarray

2D m x n array consisting of the time-series signal for each ROI node where m = number of scans and n = number of ROI’s.

subnetstr

Resting-state subnet based on Yeo-7 and Yeo-17 naming (e.g. ‘Default’) used to filter nodes in the study of brain subgraphs.

IDstr

A subject id or other unique identifier.

dir_pathstr

Path to directory containing subject derivative data for given run.

atlasstr

Name of atlas parcellation used.

labelslist

List of string labels corresponding to ROI nodes.

pynets.plotting.brain.show_template_bundles(final_streamlines, template_path, fname)[source]
pynets.plotting.brain.view_tractogram(streams, atlas)[source]

Module contents