brainGraph (version 0.48.0)

plot_perm_diffs: Calculate permutation p-values and plot group differences

Description

For a given (global- or vertex-level) graph measure, determine the permutation p-value and create a plot showing group differences, either across densities or regions. You may specify the $\alpha$-level; a red asterisk is added if $p < \alpha$ and a blue asterisk is added if $\alpha < p < 0.1$ (i.e. a "trend"). You may also choose whether you want a one- or two-sided test.

Usage

plot_perm_diffs(g1, g2, perm.dt, measure, level = c("graph", "vertex"),
  alternative = c("two.sided", "less", "greater"), alpha = 0.05,
  groups = NULL, ylabel = NULL)

Arguments

g1

List of igraph graph objects for group 1

g2

List of igraph graph objects for group 2

perm.dt

Data table with the permutation results

measure

Character string for the graph measure of interest

level

Character string, either 'graph' or 'vertex'

alternative

Character string, whether to do a two- or one-sided test (default: 'two.sided')

alpha

Significance level (default: 0.05)

groups

Character vector of group names (default: NULL)

ylabel

Character string for y-axis label (default: NULL)

Value

• A list with three elements:
• dt
  A data table with p-values for each density/region
• p1
  A ggplot2 plotting object
• p2
  A ggplot2 plotting object

See Also

permute.group

Examples

perms.mod.sig <- perms.sig(g[[1]], g[[2]], perms.all, 'mod', level='graph',
  'less', groups, ylabel='Modularity')
perms.mod.btwn <- perms.sig(g[[1]], g[[2]], perms.btwn, 'btwn.cent',
  level='vertex')