# plot_perm_diffs: Calculate permutation p-values and plot group differences In brainGraph: Graph Theory Analysis of Brain MRI Data

## 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 α-level; a red asterisk is added if p < α and a blue asterisk is added if α < p < 0.1 (i.e. a "trend"). You may also choose whether you want a one- or two-sided test.

## Usage

 ```1 2 3``` ```plot_perm_diffs(g1, g2, perm.dt, measure, level = c("graph", "vertex"), auc = FALSE, 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' `auc` Logical indicating whether the data refer to area-under-the-curve (across all densities) (default: FALSE) `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 `ggplot` plotting object `p2` A `ggplot` plotting object

## Author(s)

Christopher G. Watson, [email protected]

`permute.group`
 ```1 2 3 4 5 6 7``` ```## Not run: 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') ## End(Not run) ```