glm_graph_plots: Plot a graph with results from GLM-based analyses

In brainGraph: Graph Theory Analysis of Brain MRI Data

Plot a graph with results from GLM-based analyses

Description

These methods are convenience functions for plotting a graph based on results from GLM-based analyses (i.e., brainGraph_GLM, brainGraph_mediate, mtpc, NBS). There are several default arguments which differ depending on the input object.

Usage

## S3 method for class 'brainGraph_NBS'
plot(x, alpha = 0.05,
  subgraph = paste("p.nbs >", 1 - alpha), vertex.label = NA,
  vertex.color = "color.comp", edge.color = "color.comp",
  subtitle = NULL, main = paste0("NBS: ", x$name), cex.main = 2, ...)

## S3 method for class 'brainGraph_GLM'
plot(x, p.sig = c("p", "p.fdr", "p.perm"),
  subgraph = NULL, main = paste0(x$outcome, ": ", x$name),
  subtitle = NULL, cex.main = 2, ...)

## S3 method for class 'brainGraph_mtpc'
plot(x, subgraph = "sig == 1",
  main = paste0(x$outcome, ": ", x$name), subtitle = NULL,
  cex.main = 2, ...)

## S3 method for class 'brainGraph_mediate'
plot(x, subgraph = "p.acme > 0.95",
  main = sprintf("Effect of \"%s\" on\n\"%s\"\nmediated by \"%s\"",
  x$treat, x$outcome, x$mediator), subtitle = NULL, cex.main = 1, ...)

Arguments

x	A brainGraph_GLM, brainGraph_mtpc, brainGraph_mediate, or brainGraph_NBS object
alpha	Numeric; the significance level. Default: 0.05
subgraph	Character string specifying the condition for subsetting the graph.
vertex.label	Character vector of the vertex labels to be displayed.
vertex.color	Character string specifying the vertex attribute to color the vertices by.
edge.color	Character string specifying the edge attribute to color the edges by.
subtitle	Character string; the subtitle. Default: 'default'
main	Character string; the main title. Default: NULL
cex.main	Numeric; the scaling factor for text size; see par
...	Other arguments passed to plot.brainGraph
p.sig	Character string indicating which p-value to use for determining significance (default: p)

Details

The default arguments are specified so that the user only needs to type plot(x) at the console, if desired. For all methods, the plot's subtitle will be omitted.

NBS

By default, a subgraph will be plotted consisting of only those vertices which are part of a significant connected component. Vertex/edge colors will correspond to connected component membership. Vertex names will be omitted. Finally, the plot title will contain the contrast name.

brainGraph_GLM

By default, a subgraph will be plotted consisting of only those vertices for which p < \alpha. It will also include a plot title with the outcome measure and contrast name.

mtpc

By default, a subgraph will be plotted consisting of only those vertices for which A_{mtpc} > A_{crit}. It will also include a plot title with the outcome measure and contrast name.

brainGraph_mediate

By default, a subgraph will be plotted consisting of only those vertices for which P_{acme} < \alpha. It will also include a plot title with the treatment, mediator, and outcome variable names.

See Also

Other Plotting functions: plot.brainGraphList, plot.brainGraph, plot_brainGraph_multi

brainGraph documentation built on June 22, 2024, 7:36 p.m.