EGAnet-plot: S3 Plot Methods for 'EGAnet'

In EGAnet: Exploratory Graph Analysis – a Framework for Estimating the Number of Dimensions in Multivariate Data using Network Psychometrics

S3 Plot Methods for EGAnet

Description

General usage for plots created by EGAnet's S3 methods. Plots across the EGAnet package leverage GGally's ggnet2 and ggplot2's ggplot.

Most plots allow the full usage of the gg* series functionality and therefore plotting arguments should be referenced through those packages rather than here in EGAnet.

The sections below list the functions and their usage for the S3 plot methods. The plot methods are intended to be generic and without many arguments so that nearly all arguments are passed to ggnet2 and ggplot.

There are some constraints placed on certain plots to keep the EGAnet style throughout the (network) plots in the package, so be aware that if some settings are not changing your plot output, then these settings might be fixed to maintain the EGAnet style

General Usage

plot(x, ...)

plot.dynEGA(x, base = 1, id = NULL, ...)

plot.dynEGA.Group(x, base = 1, ...)

plot.dynEGA.Individual(x, base = 1, id = NULL, ...)

plot.hierEGA(
  x, plot.type = c("multilevel", "separate"),
  color.match = FALSE, ...
)

plot.invariance(x, p_type = c("p", "p_BH"), p_value = 0.05, ...)

General Arguments

• x — EGAnet object with available S3 plot method (see full list below)

• color.palette — Character (vector). Either a character (length = 1) from the pre-defined palettes in color_palette_EGA or character (length = total number of communities) using HEX codes (see Color Palettes and Examples sections)

• layout — Character (length = 1). Layouts can be set using gplot.layout and the ending layout name; for example, gplot.layout.circle can be set in these functions using layout = "circle" or mode = "circle" (see Examples)

• base — Numeric (length = 1). Plot to be used as the base for the configuration of the networks. Uses the number of the order in which the plots are input. Defaults to 1 or the first plot

• id — Numeric index(es) or character name(s). IDs to use when plotting dynEGA level = "individual". Defaults to NULL or 4 IDs drawn at random

• plot.type — Character (length = 1). Whether hierEGA networks should plotted in a stacked, "multilevel" fashion or as "separate" plots. Defaults to "multilevel"

• color.match — Boolean (length = 1). Whether lower order community colors in the hierEGA plot should be "matched" and used as the border color for the higher order communities. Defaults to FALSE

• p_type — Character (length = 1). Type of p-value when plotting invariance. Defaults to "p" or uncorrected p-value. Set to "p_BH" for the Benjamini-Hochberg corrected p-value

• p_value — Numeric (length = 1). The p-value to use alongside p_type when plotting invariance. Defaults to 0.05

• ... — Additional arguments to pass on to ggnet2 and gplot.layout (see Examples)

*EGA Plots

bootEGA, dynEGA, EGA, EGA.estimate, EGA.fit, hierEGA, invariance, riEGA

All Available S3 Plot Methods

boot.ergoInfo, bootEGA, dynEGA, dynEGA.Group, dynEGA.Individual, dynEGA.Population, EGA, EGA.estimate, EGA.fit, hierEGA, infoCluster, invariance, itemStability, riEGA

Color Palettes

color_palette_EGA will implement some color palettes in EGAnet. The main EGAnet style palette is "polychrome". This palette currently has 40 colors but there will likely be a need to expand it further (e.g., hierEGA demands a lot of colors).

The color.palette argument will also accept HEX code colors that are the same length as the number of communities in the plot.

In any network plots, the color.palette argument can be used to select color palettes from color_palette_EGA as well as those in the color scheme of RColorBrewer

For more worked examples than below, see Plots in {EGAnet}

Examples

# Using different arguments in {GGally}'s `ggnet2`
plot(ega.wmt, node.size = 6, edge.size = 4)

# Using a different layout in {sna}'s `gplot.layout`
plot(ega.wmt, layout = "circle") # 'layout' argument
plot(ega.wmt, mode = "circle") # 'mode' argument

# Using different color palettes with `color_palette_EGA`

## Pre-defined palette
plot(ega.wmt, color.palette = "blue.ridge2")

## University of Virginia colors
plot(ega.wmt, color.palette = c("#232D4B", "#F84C1E"))

## Vanderbilt University colors
## (with additional {GGally} `ggnet2` argument)
plot(
  ega.wmt, color.palette = c("#FFFFFF", "#866D4B"),
  label.color = "#000000"
)

EGAnet documentation built on Sept. 28, 2024, 9:06 a.m.