# Graph Theory Analysis of Brain MRI Data

## Documentation for package ‘brainGraph’ version 1.0.0

- DESCRIPTION file.

## Help Pages

aal116 | Coordinates for data from the AAl116 atlas
aal2.120 | Coordinates for data from the AAL2 atlas
aal2.94 | Coordinates for data from the AAL2 atlas
aal90 | Coordinates for data from the AAl90 atlas
analysis_random_graphs | Perform an analysis with random graphs for brain MRI data
aop | Approaches to estimate individual network contribution
assign_lobes | Give vertices in a graph a _lobe_ attribute.
auc_diff | Difference in the area-under-the-curve of two vectors
boot_global | Bootstrapping for global graph measures
brainGraph_GLM | Run linear models at each vertex of a graph
brainGraph_GLM_design | Create a design matrix for linear model analysis
brainGraph_GLM_fit | Fit linear models and calculate statistics
brainGraph_init | Initialize variables for further use in brainGraph
brainsuite | Coordinates for data from BrainSuite atlas
centr_lev | Calculate a vertex's leverage centrality
check.resid | Check model residuals for each brain region
choose.edges | Select edges for re-wiring.
contract_brainGraph | Contract graph vertices based on brain lobe and hemisphere
cor.diff.test | Calculate the p-value for differences in correlation coefficients
corr.matrix | Calculate correlation matrix and threshold
CountEdges | Count number of edges of a brain graph
count_homologous | Count number of edges of a brain graph
count_interlobar | Count number of edges of a brain graph
craddock200 | Coordinates for data from the Craddock200 atlas
create_mats | Create connection matrices for tractography or fMRI data
delete_all_attr | Delete all attributes of a graph
destrieux | Coordinates for data from the Destrieux atlas
destrieux.scgm | Coordinates for data from the Destrieux atlas
dk | Coordinates for data from the Desikan-Killiany atlas
dk.scgm | Coordinates for data from the Desikan-Killiany atlas
dkt | Coordinates for data from the Desikan-Killiany-Tourville atlas
dkt.scgm | Coordinates for data from the Desikan-Killiany-Tourville atlas
dosenbach160 | Coordinates for data from the Dosenbach160 atlas
edge_asymmetry | Calculate an asymmetry index based on edge counts
edge_spatial_dist | Calculate Euclidean distance of edges and vertices
efficiency | Calculate graph global, local, or nodal efficiency
gateway_coeff | Gateway coefficient, participation coefficient, and within-mod degree z-score
get.resid | Linear model residuals across brain regions
graph.efficiency | Calculate graph global, local, or nodal efficiency
GraphColors | Color graph vertices and edges
GraphDistances | Calculate Euclidean distance of edges and vertices
graph_attr_dt | Create a data table with graph global measures
hoa112 | Coordinates for data from Harvard-Oxford atlas
IndividualContributions | Approaches to estimate individual network contribution
loo | Approaches to estimate individual network contribution
lpba40 | Coordinates for data from the LONI probabilistic brain atlas
make_ego_brainGraph | Create a graph of the union of multiple vertex neighborhoods
make_empty_brainGraph | Create an empty graph with attributes for brainGraph
NBS | Network-based statistic for brain MRI data
part_coeff | Gateway coefficient, participation coefficient, and within-mod degree z-score
permute.group | Permutation test for group difference of graph measures
plot_boot | Plot global graph measures with shaded regions calculated from bootstrapping
plot_brainGraph | Plot a brain graph with a specific spatial layout
plot_brainGraph_gui | GUI for plotting graphs overlaid on an MNI152 image or in a circle.
plot_brainGraph_list | Write PNG files for a list of graphs
plot_brainGraph_mni | Draw an axial or sagittal slice of the MNI152 T1 image
plot_brainGraph_multi | Save PNG of three views of a brain graph
plot_corr_mat | Plot a correlation matrix
plot_global | Plot global graph measures across densities
plot_group_means | Plot group distributions of volumetric measures for a given brain region
plot_perm_diffs | Calculate permutation p-values and plot group differences
plot_rich_norm | Plot normalized rich club coefficients against degree threshold
plot_vertex_measures | Plot vertex-level graph measures at a single density or threshold
rich_club_attrs | Assign graph attributes based on rich-club analysis
rich_club_coeff | Calculate the rich club of a graph
rich_club_norm | Calculate the normalized rich club coefficient
rich_core | Calculate the rich core of a graph
robustness | Analysis of network robustness
rotation | Apply a rotation matrix to a set of points
set.brainGraph.attributes | Set graph, vertex, and edge attributes common in MRI analyses
set_brainGraph_attr | Set graph, vertex, and edge attributes common in MRI analyses
set_edge_color | Color graph vertices and edges
set_vertex_color | Color graph vertices and edges
sim.rand.graph.clust | Simulate a random graph with given degree sequence and clustering.
sim.rand.graph.par | Simulate N random graphs w/ same clustering and degree sequence as the input.
small.world | Calculate graph small-worldness
update_brainGraph_gui | Function to dynamically plot a graph
vec.transform | Transform a vector to have a different range
VertexRoles | Gateway coefficient, participation coefficient, and within-mod degree z-score
vertex_attr_dt | Create a data table with graph vertex measures
vertex_spatial_dist | Calculate Euclidean distance of edges and vertices
vulnerability | Calculate graph vulnerability
within_module_deg_z_score | Gateway coefficient, participation coefficient, and within-mod degree z-score
write_brainnet | Write files to be used for visualization with BrainNet Viewer