GroupBootPlot: Create a plot of bootstrapped confidence intervals for all...

Description Usage Arguments Details Value Author(s) References See Also

View source: R/GroupBootPlot.R

Description

This function plots output from bootstrapped networks computed with GroupNetworkBoot.

Usage

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GroupBootPlot(BootOut, GroupNames, edges.x, edges.y, 
labels = TRUE, transparency = 0.15, point.size = 1.5, line.size = 1, 
legend.position = "none", GroupNamesCheck = FALSE)

Arguments

BootOut

The output from GroupNetworkBoot.

GroupNames

A vector of optional group names that will be printed as facet labels in plot. By default, names of the networks are taken. If specified, GroupNames should match the alphabetical order of names of network groups. If unsure, you can check the matching of names by setting GroupNamesCheck = TRUE.

edges.x

If only a subset of edge combinations is of interest for the plot, this subset can be specified by setting edges.x and edges.y. Specifically, node names can be specified as vectors for edges.x and edges.y and all unique combinations of edges.x and edges.y will be plotted. For example, edges.x = c("a", "b") and edges.y = "c" will plot edges a-c and b-c but not a-b.

edges.y

See edges.x.

labels

Logical, should edge labels be included in plots. Default is labels = TRUE.

transparency

Set ggplot2 alpha channel (transparency) for confidence interval ribbon in plot.

point.size

Set point size.

line.size

Set line size.

legend.position

Define legend position to indicate colour for sample and bootstrap means. See ?theme in ggplot2.

GroupNamesCheck

Option to print match of indicated GroupNames to console. Only prints if GroupNames is specified. See GroupNames for details.

Details

The code for the Joint Graphical Lasso procedure was adapted from the R package JGL. Some of the code for the cross-validation procedure was adapted from package parcor. Some of the code was inspired by package qgraph. GroupBootPlot automatically calls BootTable to format GroupNetworkBoot output, so see BootTable for completely independent plotting.

Value

The output of GroupBootPlot returns a plot based on ggplot2 with the bootstrapped confidence intervals of edges across groups.

Author(s)

Nils Kappelmann <n.kappelmann@gmail.com>, Giulio Costantini

References

Danaher, P., Wang, P., and Witten, D. M. (2014). The joint graphical lasso for inverse covariance estimation across multiple classes. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 76(2), 373-397. http://doi.org/10.1111/rssb.12033

See Also

JGL, qgraph, parcor


EstimateGroupNetwork documentation built on Jan. 8, 2020, 9:07 a.m.