Package: brainGraph 3.0.3
brainGraph: Graph Theory Analysis of Brain MRI Data
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.
Authors:
brainGraph_3.0.3.tar.gz
brainGraph_3.0.3.zip(r-4.5)brainGraph_3.0.3.zip(r-4.4)brainGraph_3.0.3.zip(r-4.3)
brainGraph_3.0.3.tgz(r-4.4-any)brainGraph_3.0.3.tgz(r-4.3-any)
brainGraph_3.0.3.tar.gz(r-4.5-noble)brainGraph_3.0.3.tar.gz(r-4.4-noble)
brainGraph_3.0.3.tgz(r-4.4-emscripten)brainGraph_3.0.3.tgz(r-4.3-emscripten)
brainGraph.pdf |brainGraph.html✨
brainGraph/json (API)
NEWS
| # Install 'brainGraph' in R: |
| install.packages('brainGraph', repos = c('https://cwatson.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cwatson/braingraph/issues
- aal116 - Coordinates for data from brain atlases
- aal2.120 - Coordinates for data from brain atlases
- aal2.94 - Coordinates for data from brain atlases
- aal90 - Coordinates for data from brain atlases
- brainnetome - Coordinates for data from brain atlases
- brainsuite - Coordinates for data from brain atlases
- craddock200 - Coordinates for data from brain atlases
- destrieux - Coordinates for data from brain atlases
- destrieux.scgm - Coordinates for data from brain atlases
- dk - Coordinates for data from brain atlases
- dk.scgm - Coordinates for data from brain atlases
- dkt - Coordinates for data from brain atlases
- dkt.scgm - Coordinates for data from brain atlases
- dosenbach160 - Coordinates for data from brain atlases
- gordon333 - Coordinates for data from brain atlases
- hcp_mmp1.0 - Coordinates for data from brain atlases
- hoa112 - Coordinates for data from brain atlases
- lpba40 - Coordinates for data from brain atlases
- power264 - Coordinates for data from brain atlases
brain-connectivitybrain-imagingcomplex-networksconnectomeconnectomicsfmrigraph-theorymrinetwork-analysisneuroimagingneurosciencestatisticstractography
Last updated 7 months agofrom:a0d13aea83. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 17 2024 |
| R-4.5-win | NOTE | Sep 17 2024 |
| R-4.5-linux | NOTE | Sep 17 2024 |
| R-4.4-win | NOTE | Sep 17 2024 |
| R-4.4-mac | NOTE | Sep 17 2024 |
| R-4.3-win | NOTE | Sep 17 2024 |
| R-4.3-mac | NOTE | Sep 17 2024 |
Exports:analysis_random_graphsaopapply_thresholdsas_atlasas_brainGraphListbg_to_mediatebrainGraph_bootbrainGraph_GLMbrainGraph_GLM_designbrainGraph_mediatebrainGraph_permutecentr_betw_commcentr_levcheck_sIDcoeff_determcoeff_tablecoeff_varcolMaxcolMaxAbscolMincommunicabilitycontract_brainGraphcor.diff.testcorr.matrixcount_homologouscount_intercovratio.bg_GLMcreate_atlascreate_matsdffits.bg_GLMdiag_sqedge_asymmetryedge_spatial_distefficiencyfastLmBGfastLmBG_3dfastLmBG_3dYfastLmBG_3dY_1pfastLmBG_ffastLmBG_tgateway_coeffget_thresholdsget.residgraph_attr_dtguess_atlashubnessimport_scninvis_binaryis.brainGraphis.brainGraphListloomake_auc_brainGraphmake_brainGraphmake_brainGraphListmake_ego_brainGraphmake_empty_brainGraphmake_intersection_brainGraphmean_distance_wtmtpcNBSnregionspad_zerospart_coeffpartitionpinvplot_brainGraph_guiplot_brainGraph_multiplot_globalplot_rich_normplot_vertex_measuresplot_volumetricqr_Q2qr_R2randomiserandomise_3dregion.namesrich_club_allrich_club_attrsrich_club_coeffrich_club_normrich_corerobustnesss_coreset_brainGraph_attrsim.rand.graph.clustsim.rand.graph.hqssim.rand.graph.parslicersmall.worldsymm_meansymmetrizevertex_attr_dtvertex_spatial_distvif.bg_GLMvulnerabilitywithin_module_deg_z_scorewrite_brainnetxfm.weights
Dependencies:abindclicodetoolscpp11data.tabledoParallelforeachglueigraphiteratorslatticelifecyclemagrittrMASSMatrixpermutepkgconfigrlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Threshold additional set of matrices | apply_thresholds |
| Atlas helper functions | as_atlas Atlas Helpers create_atlas guess_atlas |
| Set graph, vertex, and edge attributes common in MRI analyses | Attributes set_brainGraph_attr xfm.weights |
| Bootstrapping for global graph measures | Bootstrapping brainGraph_boot plot.brainGraph_boot summary.brainGraph_boot |
| Coordinates for data from brain atlases | aal116 aal2.120 aal2.94 aal90 Brain Atlases brainnetome brainsuite craddock200 destrieux destrieux.scgm dk dk.scgm dkt dkt.scgm dosenbach160 gordon333 hcp_mmp1.0 hoa112 lpba40 power264 |
| Default options for brainGraph | brainGraph-package brainGraph brainGraph-options |
| Permutation test for group difference of graph measures | brainGraph_permute plot.brainGraph_permute summary.brainGraph_permute |
| brainGraph generic methods | brainGraph-methods groups.brainGraphList groups.corr_mats nregions region.names region.names.data.table |
| Create a list of brainGraph graphs | as_brainGraphList brainGraphList Extract.brainGraphList is.brainGraphList make_brainGraphList make_brainGraphList.array make_brainGraphList.corr_mats nobs.brainGraphList print.brainGraphList [.brainGraphList |
| Calculate communicability betweenness centrality | centr_betw_comm |
| Calculate a vertex's leverage centrality | centr_lev |
| Test if an object is a character vector of numbers | check_sID pad_zeros |
| Calculate coefficient of variation | coeff_var coeff_var.default |
| Calculate communicability | communicability |
| Contract graph vertices based on brain lobe and hemisphere | contract_brainGraph |
| Calculate the p-value for differences in correlation coefficients | cor.diff.test |
| Calculate correlation matrix and threshold | corr.matrix Extract.corr_mats nregions.corr_mats plot.corr_mats region.names.corr_mats [.corr_mats |
| Count number of edges of a brain graph | Count Edges count_homologous count_inter |
| Create connection matrices for tractography or fMRI data | create_mats |
| Create a brainGraph object | Creating_Graphs is.brainGraph make_brainGraph make_brainGraph.bg_mediate make_brainGraph.igraph make_brainGraph.matrix make_empty_brainGraph summary.brainGraph |
| Create a graph list with GLM-specific attributes | Creating_Graphs_GLM make_brainGraphList.bg_GLM make_brainGraphList.mtpc make_brainGraphList.NBS |
| Calculate an asymmetry index based on edge counts | edge_asymmetry |
| Calculate graph global, local, or nodal efficiency | efficiency |
| Fit General Linear Models at each vertex of a graph | brainGraph_GLM GLM plot.bg_GLM print.bg_GLM summary.bg_GLM [.bg_GLM |
| Extract basic information from a bg_GLM object | case.names.bg_GLM formula.bg_GLM GLM basic info labels.bg_GLM nobs.bg_GLM nregions.bg_GLM region.names.bg_GLM terms.bg_GLM variable.names.bg_GLM |
| Create a design matrix for linear model analysis | brainGraph_GLM_design GLM design |
| Fit design matrices to one or multiple outcomes | fastLmBG fastLmBG_3d fastLmBG_3dY fastLmBG_3dY_1p fastLmBG_f fastLmBG_t GLM fits |
| Influence measures for a bg_GLM object | cooks.distance.bg_GLM covratio.bg_GLM dfbeta.bg_GLM dfbetas.bg_GLM dffits.bg_GLM GLM influence measures hatvalues.bg_GLM influence.bg_GLM rstandard.bg_GLM rstudent.bg_GLM |
| Model selection for bg_GLM objects | extractAIC.bg_GLM GLM model selection logLik.bg_GLM |
| Extract model fit statistics from a bg_GLM object | anova.bg_GLM coef.bg_GLM coeff_determ coeff_table confint.bg_GLM deviance.bg_GLM df.residual.bg_GLM fitted.bg_GLM GLM statistics residuals.bg_GLM sigma.bg_GLM vcov.bg_GLM |
| Create a data table with graph global and vertex measures | Graph Data Tables graph_attr_dt vertex_attr_dt |
| Calculate Euclidean distance of edges and vertices | edge_spatial_dist Graph Distances vertex_spatial_dist |
| Calculate vertex hubness | hubness |
| Import data for structural connectivity analysis | import_scn |
| Approaches to estimate individual network contribution | aop IndividualContributions loo plot.IC summary.IC |
| Calculate the inverse of the cross product of a design matrix | inv inv.array inv.list inv.matrix inv.qr Inverse pinv |
| Calculate the AUC across densities of given attributes | make_auc_brainGraph |
| Create a graph of the union of multiple vertex neighborhoods | make_ego_brainGraph |
| Create the intersection of graphs based on a logical condition | make_intersection_brainGraph |
| Matrix/array utility functions | colMax colMaxAbs colMin diag_sq get_thresholds is_binary Matrix utilities qr.array qr_Q2 qr_R2 symmetrize symmetrize.array symmetrize.matrix symm_mean |
| Calculate weighted shortest path lengths | mean_distance_wt |
| Mediation analysis with brain graph measures as mediator variables | bg_to_mediate brainGraph_mediate Mediation summary.bg_mediate |
| Multi-threshold permutation correction | case.names.mtpc df.residual.mtpc formula.mtpc labels.mtpc mtpc nobs.mtpc nregions.mtpc plot.mtpc region.names.mtpc summary.mtpc terms.mtpc variable.names.mtpc |
| Network-based statistic for brain MRI data | case.names.NBS df.residual.NBS formula.NBS labels.NBS NBS nobs.NBS nregions.NBS summary.NBS terms.NBS variable.names.NBS |
| GUI for plotting graphs overlaid on an MNI152 image or in a circle | plot_brainGraph_gui |
| Save PNG of one or three views for all graphs in a brainGraphList | plot_brainGraph_multi slicer |
| Plot global graph measures across densities | plot_global |
| Plot normalized rich club coefficients against degree threshold | plot_rich_norm |
| Plot vertex-level graph measures at a single density or threshold | plot_vertex_measures |
| Plot group distributions of volumetric measures for a given brain region | plot_volumetric |
| Plot a brain graph with a specific spatial layout | plot.brainGraph |
| Plot a brainGraphList and write to PDF | plot.brainGraphList |
| Plot a graph with results from GLM-based analyses | plot.brainGraph_GLM plot.brainGraph_mediate plot.brainGraph_mtpc plot.brainGraph_NBS Plotting GLM graphs |
| Perform an analysis with random graphs for brain MRI data | analysis_random_graphs Random Graphs sim.rand.graph.clust sim.rand.graph.hqs sim.rand.graph.par |
| GLM non-parametric permutation testing | partition randomise randomise_3d |
| Linear model residuals in structural covariance networks | case.names.brainGraph_resids Extract.brainGraph_resids get.resid groups.brainGraph_resids nobs.brainGraph_resids nregions.brainGraph_resids plot.brainGraph_resids region.names.brainGraph_resids Residuals summary.brainGraph_resids [.brainGraph_resids |
| Rich club calculations | Rich Club rich_club_all rich_club_coeff rich_club_norm rich_core |
| Assign graph attributes based on rich-club analysis | rich_club_attrs |
| Analysis of network robustness | robustness |
| Calculate the s-core of a network | s_core |
| Calculate graph small-worldness | small.world |
| Gateway coefficient, participation coefficient, and within-mod degree z-score | gateway_coeff part_coeff Vertex Roles within_module_deg_z_score |
| Variance inflation factors for 'bg_GLM' objects | vif.bg_GLM |
| Calculate graph vulnerability | vulnerability |
| Write files to be used for visualization with BrainNet Viewer | write_brainnet |
