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brainGraph (version 3.1.0)

Graph Theory Analysis of Brain MRI Data

Description

A set of tools for performing graph theory analysis of brain MRI data. It works with data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), diffusion tensor tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from DPABI). It contains a graphical user interface for graph visualization and data exploration, along with several functions for generating useful figures.

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Version

Install

install.packages('brainGraph')

Monthly Downloads

608

Version

3.1.0

License

GPL-3

Issues

10

Pull Requests

1

Stars

188

Forks

53

Maintainer

Christopher G Watson

Last Published

April 4th, 2024

Functions in brainGraph (3.1.0)

corr.matrix

Calculate correlation matrix and threshold
cor.diff.test

Calculate the p-value for differences in correlation coefficients
choose.edges

Select edges for re-wiring
brainGraph_permute

Permutation test for group difference of graph measures
Bootstrapping

Bootstrapping for global graph measures
apply_thresholds

Threshold additional set of matrices
communicability

Calculate communicability
coeff_var

Calculate coefficient of variation
auc_diff

Difference in the area-under-the-curve of two vectors
dir2files

Return a vector of filenames based on a directory name or options list
efficiency

Calculate graph global, local, or nodal efficiency
Attributes

Set graph, vertex, and edge attributes common in MRI analyses
Atlas Helpers

Atlas helper functions
Brain Atlases

Coordinates for data from brain atlases
contract_brainGraph

Contract graph vertices based on brain lobe and hemisphere
centr_lev

Calculate a vertex's leverage centrality
GLM influence measures

Influence measures for a bg_GLM object
GLM

Fit General Linear Models at each vertex of a graph
Graph Data Tables

Create a data table with graph global and vertex measures
GLM basic info

Extract basic information from a bg_GLM object
Count Edges

Count number of edges of a brain graph
check_weights

Check for vertex or edge attributes
create_mats

Create connection matrices for tractography or fMRI data
hubness

Calculate vertex hubness
get_rand_attrs

Convenience function to get attributes for lists of random graphs
import_scn

Import data for structural connectivity analysis
centr_betw_comm

Calculate communicability betweenness centrality
Creating_Graphs_GLM

Create a graph list with GLM-specific attributes
GLM statistics

Extract model fit statistics from a bg_GLM object
make_auc_brainGraph

Calculate the AUC across densities of given attributes
GLM model selection

Model selection for bg_GLM objects
edge_asymmetry

Calculate an asymmetry index based on edge counts
delete_all_attr

Delete all attributes of a graph
Inverse

Calculate the inverse of the cross product of a design matrix
IndividualContributions

Approaches to estimate individual network contribution
Matrix utilities

Matrix/array utility functions
make_intersection_brainGraph

Create the intersection of graphs based on a logical condition
mean_distance_wt

Calculate weighted shortest path lengths
Random Graphs

Perform an analysis with random graphs for brain MRI data
Plotting GLM graphs

Plot a graph with results from GLM-based analyses
plot_global

Plot global graph measures across densities
Creating_Graphs

Create a brainGraph object
Mediation

Mediation analysis with brain graph measures as mediator variables
GLM helpers

Helper functions to set-up for GLM analyses
check_sID

Test if an object is a character vector of numbers
plot.brainGraph

Plot a brain graph with a specific spatial layout
make_ego_brainGraph

Create a graph of the union of multiple vertex neighborhoods
plot_vertex_measures

Plot vertex-level graph measures at a single density or threshold
Graph Distances

Calculate Euclidean distance of edges and vertices
randomise

GLM non-parametric permutation testing
plot_rich_norm

Plot normalized rich club coefficients against degree threshold
plot.brainGraphList

Plot a brainGraphList and write to PDF
plot_brainGraph_multi

Save PNG of one or three views for all graphs in a brainGraphList
GLM fits

Fit design matrices to one or multiple outcomes
Rich Club

Rich club calculations
small.world

Calculate graph small-worldness
GLM design

Create a design matrix for linear model analysis
subset_graph

Subset graphs based on a given logical condition
set_graph_colors

Color graph vertices and edges
s_core

Calculate the s-core of a network
Residuals

Linear model residuals in structural covariance networks
plot_volumetric

Plot group distributions of volumetric measures for a given brain region
mtpc

Multi-threshold permutation correction
vulnerability

Calculate graph vulnerability
Vertex Roles

Gateway coefficient, participation coefficient, and within-mod degree z-score
write_brainnet

Write files to be used for visualization with BrainNet Viewer
rich_club_attrs

Assign graph attributes based on rich-club analysis
robustness

Analysis of network robustness
Utility functions

Utility functions
rename_levels

Rename the levels of global metrics in a data.table
vif.bg_GLM

Variance inflation factors for bg_GLM objects
update_fs_names

Update column names in a Freesurfer table
NBS

Network-based statistic for brain MRI data
brainGraph

Default options for brainGraph
brainGraph-methods

brainGraph generic methods
brainGraphList

Create a list of brainGraph graphs