brainGraph (version 2.7.3)

make_brainGraph: Create a brainGraph object

Description

Create a brainGraph graph object, which is an igraph graph object with additional attributes (at all levels). The values are dependent on the specified brain atlas.

Usage

make_brainGraph(g, atlas, rand = FALSE, modality = NULL,
  weighting = NULL, threshold = NULL, subject = NULL, group = NULL)
# S3 method for brainGraph
summary(object, print.attrs = c("all", "none"), ...)

Arguments

g

An igraph graph object.

atlas

Character string specifying the brain atlas

rand

A character string indicating whether this function is being run for a random graph. Default: FALSE

modality

Character vector indicating imaging modality (e.g. 'dti'). Default: NULL

weighting

Character string indicating how the edges are weighted (e.g., 'fa', 'pearson', etc.). Default: NULL

threshold

Numeric indicating the level at which the matrices were thresholded (if at all). Default: NULL

subject

Character vector indicating subject ID. Default: NULL

group

Character vector indicating group membership. Default: NULL

object

A brainGraph object

print.attrs

Character string indicating whether or not to list the object's attributes (default: all)

...

Unused

Value

A brainGraph graph object with additional attributes:

version

(graph-level) The current version of brainGraph

atlas

(graph-level)

lobe

(vertex-leve) Character vector of lobe names

hemi

(vertex-leve) Character vector of hemispheres ('L', 'R', or 'B')

lobe.hemi

Integer vector indicating the lobe and hemisphere

class

(vertex-leve) Character vector of class names (if applicable)

network

(vertex-leve) Character vector of network names (if applicable)

modality

(graph-level)

weighting

(graph-level)

threshold

(graph-level)

name

(graph-level) The subject ID (if specified by subject)

Group

(graph-level) only if group is specified

x, y, z, x.mni, y.mni, z.mni

Spatial coordinates

color.lobe

(vertex- and edge-level) Colors based on lobe

color.class,color.network

(vertex- and edge-level) If applicable

circle.layout

Integer vector for ordering the vertices for circle plots

Details

For the modality argument, you can choose anything you like, but the summary.brainGraph knows about dti, fmri, thickness, area, and volume.

For the weighting argument, you can choose anything you like, but summary.brainGraph knows about fa, sld (streamline density, tractography), pearson, spearman, kendall, and partial (partial correlation coefficient).

See Also

Other Graph creation functions: make_ego_brainGraph, make_empty_brainGraph, make_glm_brainGraph, make_mediate_brainGraph, make_nbs_brainGraph