brainGraph: Graph Theory Analysis of Brain MRI Data
Version 1.0.0

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

Browse man pages Browse package API and functions Browse package files

AuthorChristopher G. Watson <cgwatson@bu.edu>
Date of publication2017-04-10 13:06:14 UTC
MaintainerChristopher G. Watson <cgwatson@bu.edu>
LicenseGPL-3
Version1.0.0
URL https://github.com/cwatson/brainGraph
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("brainGraph")

Man 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
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.
color_vertices_edges: Color graph vertices and edges
contract_brainGraph: Contract graph vertices based on brain lobe and hemisphere
cor.diff.test: Calculate the p-value for differences in correlation...
corr.matrix: Calculate correlation matrix and threshold
count_edges: 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...
dkt.scgm: Coordinates for data from the Desikan-Killiany-Tourville...
dosenbach160: Coordinates for data from the Dosenbach160 atlas
edge_asymmetry: Calculate an asymmetry index based on edge counts
efficiency: Calculate graph global, local, or nodal efficiency
get.resid: Linear model residuals across brain regions
graph_attr_dt: Create a data table with graph global measures
hoa112: Coordinates for data from Harvard-Oxford atlas
individ_contrib: 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
permute.group: Permutation test for group difference of graph measures
plot_boot: Plot global graph measures with shaded regions calculated...
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...
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...
plot_perm_diffs: Calculate permutation p-values and plot group differences
plot_rich_norm: Plot normalized rich club coefficients against degree...
plot_vertex_measures: Plot vertex-level graph measures at a single density or...
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_attr: Set graph, vertex, and edge attributes common in MRI analyses
sim.rand.graph.clust: Simulate a random graph with given degree sequence and...
sim.rand.graph.par: Simulate N random graphs w/ same clustering and degree...
small.world: Calculate graph small-worldness
spatial_dist: Calculate Euclidean distance of edges and vertices
update_brainGraph_gui: Function to dynamically plot a graph
vec.transform: Transform a vector to have a different range
vertex_attr_dt: Create a data table with graph vertex measures
vertex_roles: Gateway coefficient, participation coefficient, and...
vulnerability: Calculate graph vulnerability
write_brainnet: Write files to be used for visualization with BrainNet Viewer

Functions

CountEdges Man page
GraphColors Man page
GraphDistances Man page
IndividualContributions Man page
NBS Man page Source code
VertexRoles Man page
aal116 Man page
aal2.120 Man page
aal2.94 Man page
aal90 Man page
analysis_random_graphs Man page Source code
aop Man page Source code
assign_lobes Man page Source code
auc_diff Man page Source code
boot_global Man page Source code
brainGraph_GLM Man page Source code
brainGraph_GLM_design Man page Source code
brainGraph_GLM_fit Man page Source code
brainGraph_init Man page Source code
brainsuite Man page
centr_lev Man page Source code
check.resid Man page Source code
choose.edges Man page Source code
contract_brainGraph Man page Source code
cor.diff.test Man page Source code
corr.matrix Man page Source code
count_homologous Man page Source code
count_interlobar Man page Source code
craddock200 Man page
create_mats Man page Source code
delete_all_attr Man page Source code
destrieux Man page
destrieux.scgm Man page
dk Man page
dk.scgm Man page
dkt Man page
dkt.scgm Man page
dosenbach160 Man page
edge_asymmetry Man page Source code
edge_spatial_dist Man page Source code
efficiency Man page Source code
gateway_coeff Man page Source code
get.resid Man page Source code
graph.efficiency Man page Source code
graph_attr_dt Man page Source code
hoa112 Man page
loo Man page Source code
lpba40 Man page
make_ego_brainGraph Man page Source code
make_empty_brainGraph Man page Source code
normalize_mats_det Source code
normalize_mats_prob Source code
part_coeff Man page Source code
permute.group Man page Source code
plot_boot Man page Source code
plot_brainGraph Man page Source code
plot_brainGraph_gui Man page Source code
plot_brainGraph_list Man page Source code
plot_brainGraph_mni Man page Source code
plot_brainGraph_multi Man page Source code
plot_corr_mat Man page Source code
plot_global Man page Source code
plot_group_means Man page Source code
plot_perm_diffs Man page Source code
plot_rich_norm Man page Source code
plot_vertex_measures Man page Source code
rich_club_attrs Man page Source code
rich_club_coeff Man page Source code
rich_club_norm Man page Source code
rich_core Man page Source code
robustness Man page Source code
rotation Man page Source code
set.brainGraph.attributes Man page Source code
set_brainGraph_attr Man page Source code
set_edge_color Man page Source code
set_vertex_color Man page Source code
sim.rand.graph.clust Man page Source code
sim.rand.graph.par Man page Source code
small.world Man page Source code
update_brainGraph_gui Man page Source code
vec.transform Man page Source code
vertex_attr_dt Man page Source code
vertex_spatial_dist Man page Source code
vulnerability Man page Source code
within_module_deg_z_score Man page Source code
write_brainnet Man page Source code

Files

inst
inst/extdata
inst/extdata/brainGraph_icon.png
NAMESPACE
NEWS.md
data
data/dosenbach160.rda
data/dk.rda
data/destrieux.rda
data/craddock200.rda
data/dk.scgm.rda
data/brainsuite.rda
data/aal116.rda
data/lpba40.rda
data/hoa112.rda
data/aal2.94.rda
data/aal2.120.rda
data/dkt.scgm.rda
data/aal90.rda
data/dkt.rda
data/destrieux.scgm.rda
R
R/plot_brainGraph_multi.R
R/cor_diff_test.R
R/choose_edges.R
R/utils.R
R/plot_brainGraph_list.R
R/robustness.R
R/plot_brainGraph_gui.R
R/create_mats.R
R/plot_group_means.R
R/plot_rich_norm.R
R/centr_lev.R
R/update_brainGraph_gui.R
R/sim_rand_graph_par.R
R/set_brainGraph_attributes.R
R/brainGraph_GLM.R
R/check_resid.R
R/sysdata.rda
R/small_world.R
R/contract_brainGraph.R
R/sim_rand_graph_clust.R
R/get_resid.R
R/plot_global.R
R/make_ego_brainGraph.R
R/rich_club.R
R/NBS.R
R/plot_brainGraph.R
R/boot_global.R
R/vertex_attr_dt.R
R/graph_efficiency.R
R/plot_vertex_measures.R
R/corr_matrix.R
R/permute_group.R
R/plot_boot.R
R/graph_attr_dt.R
R/count_edges.R
R/vertex_roles.R
R/write_brainnet.R
R/brainGraph_init.R
R/plot_brainGraph_mni.R
R/analysis_random_graphs.R
R/plot_perm_diffs.R
R/vulnerability.R
R/make_empty_brainGraph.R
R/edge_asymmetry.R
R/individ_contrib.R
R/assign_lobes.R
R/plot_corr_mat.R
R/color_vertices_edges.R
R/spatial_dist.R
MD5
DESCRIPTION
man
man/create_mats.Rd
man/brainGraph_GLM_fit.Rd
man/boot_global.Rd
man/contract_brainGraph.Rd
man/aal2.94.Rd
man/lpba40.Rd
man/rich_core.Rd
man/assign_lobes.Rd
man/centr_lev.Rd
man/cor.diff.test.Rd
man/aal90.Rd
man/plot_global.Rd
man/plot_boot.Rd
man/brainGraph_GLM_design.Rd
man/update_brainGraph_gui.Rd
man/get.resid.Rd
man/aal116.Rd
man/destrieux.scgm.Rd
man/auc_diff.Rd
man/delete_all_attr.Rd
man/craddock200.Rd
man/dosenbach160.Rd
man/vertex_attr_dt.Rd
man/make_ego_brainGraph.Rd
man/plot_vertex_measures.Rd
man/count_edges.Rd
man/set_brainGraph_attr.Rd
man/plot_group_means.Rd
man/plot_brainGraph_list.Rd
man/permute.group.Rd
man/plot_corr_mat.Rd
man/brainGraph_init.Rd
man/check.resid.Rd
man/dk.Rd
man/make_empty_brainGraph.Rd
man/plot_brainGraph_multi.Rd
man/robustness.Rd
man/dkt.scgm.Rd
man/rich_club_attrs.Rd
man/destrieux.Rd
man/vertex_roles.Rd
man/corr.matrix.Rd
man/plot_brainGraph_mni.Rd
man/rich_club_norm.Rd
man/aal2.120.Rd
man/edge_asymmetry.Rd
man/choose.edges.Rd
man/hoa112.Rd
man/write_brainnet.Rd
man/plot_perm_diffs.Rd
man/sim.rand.graph.par.Rd
man/small.world.Rd
man/color_vertices_edges.Rd
man/sim.rand.graph.clust.Rd
man/efficiency.Rd
man/vec.transform.Rd
man/vulnerability.Rd
man/dkt.Rd
man/rich_club_coeff.Rd
man/spatial_dist.Rd
man/NBS.Rd
man/brainsuite.Rd
man/plot_rich_norm.Rd
man/rotation.Rd
man/brainGraph_GLM.Rd
man/analysis_random_graphs.Rd
man/individ_contrib.Rd
man/graph_attr_dt.Rd
man/dk.scgm.Rd
man/plot_brainGraph.Rd
man/plot_brainGraph_gui.Rd
brainGraph documentation built on May 30, 2017, 1:34 a.m.