R/S3plots.R

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

#' @title S3 Plot Methods for \code{\link{EGAnet}}
#'
#' @name EGAnet-plot
#'
#' @description General usage for plots created by \code{\link{EGAnet}}'s S3 methods.
#' Plots across the \code{\link{EGAnet}} package leverage \{\link{GGally}\}'s \code{\link[GGally]{ggnet2}}
#' and \{\link{ggplot2}\}'s \code{\link[ggplot2]{ggplot}}.
#'
#' Most plots allow the full usage of the \code{gg*} series functionality and therefore
#' plotting arguments should be referenced through those packages rather than here in
#' \code{\link{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 \code{\link[GGally]{ggnet2}} and \code{\link[ggplot2]{ggplot}}.
#'
#' There are some constraints placed on certain plots to keep the \code{\link{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 \code{\link{EGAnet}} style
#'
#' @section General Usage:
#'
#' \preformatted{
#' 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, ...)
#' }
#'
#' @section General Arguments:
#'
#' \itemize{
#'
#' \item \code{x} --- \code{\link{EGAnet}} object with available S3 plot method
#' (see full list below)
#'
#' \item \code{color.palette} --- Character (vector). Either a character (length = 1) from the
#' pre-defined palettes in \code{\link[EGAnet]{color_palette_EGA}}
#' or character (length = total number of communities) using
#' HEX codes (see \strong{Color Palettes} and \strong{Examples} sections)
#'
#' \item \code{layout} --- Character (length = 1). Layouts can be set using \code{\link[sna]{gplot.layout}} and the
#' ending layout name; for example, \code{gplot.layout.circle} can be set
#' in these functions using \code{layout = "circle"} or \code{mode = "circle"}
#' (see \strong{Examples})
#'
#' \item \code{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 \code{1} or the first plot
#'
#' \item \code{id} --- Numeric index(es) or character name(s). IDs to use when plotting
#' \code{\link[EGAnet]{dynEGA}} \code{level = "individual"}.
#' Defaults to \code{NULL} or 4 IDs drawn at random
#'
#' \item \code{plot.type} --- Character (length = 1). Whether \code{\link[EGAnet]{hierEGA}}
#' networks should plotted in a stacked, \code{"multilevel"} fashion
#' or as \code{"separate"} plots. Defaults to \code{"multilevel"}
#'
#' \item \code{color.match} --- Boolean (length = 1). Whether lower order community colors in the
#' \code{\link[EGAnet]{hierEGA}} plot should be "matched" and used as
#' the border color for the higher order communities. Defaults to \code{FALSE}
#'
#' \item \code{p_type} --- Character (length = 1). Type of \emph{p}-value when plotting
#' \code{\link[EGAnet]{invariance}}. Defaults to \code{"p"} or
#' uncorrected \emph{p}-value. Set to \code{"p_BH"} for the
#' Benjamini-Hochberg corrected \emph{p}-value
#'
#' \item \code{p_value} --- Numeric (length = 1). The \emph{p}-value to use alongside \code{p_type} when
#' plotting \code{\link[EGAnet]{invariance}}. Defaults to \code{0.05}
#'
#' \item \code{...} --- Additional arguments to pass on to
#' \code{\link[GGally]{ggnet2}} and \code{\link[sna]{gplot.layout}}
#' (see \strong{Examples})
#'
#' }
#'
#' @section \code{*EGA} Plots:
#'
#' \code{\link[EGAnet]{bootEGA}}, \code{\link[EGAnet]{dynEGA}},
#' \code{\link[EGAnet]{EGA}}, \code{\link[EGAnet]{EGA.estimate}},
#' \code{\link[EGAnet]{EGA.fit}}, \code{\link[EGAnet]{hierEGA}},
#' \code{\link[EGAnet]{invariance}}, \code{\link[EGAnet]{riEGA}}
#'
#' @section All Available S3 Plot Methods:
#'
#' \code{\link[EGAnet]{boot.ergoInfo}}, \code{\link[EGAnet]{bootEGA}},
#' \code{\link[EGAnet]{dynEGA}}, \code{dynEGA.Group}, \code{dynEGA.Individual},
#' \code{dynEGA.Population}, \code{\link[EGAnet]{EGA}},
#' \code{\link[EGAnet]{EGA.estimate}}, \code{\link[EGAnet]{EGA.fit}},
#' \code{\link[EGAnet]{hierEGA}}, \code{\link[EGAnet]{infoCluster}},
#' \code{\link[EGAnet]{invariance}}, \code{\link[EGAnet]{itemStability}},
#' \code{\link[EGAnet]{riEGA}}
#'
#' @section Color Palettes:
#'
#' \code{\link[EGAnet]{color_palette_EGA}} will implement some color palettes in
#' \code{\link{EGAnet}}. The main \code{\link{EGAnet}} style palette is \code{"polychrome"}.
#' This palette currently has 40 colors but there will likely be a need to expand it further
#' (e.g., \code{\link[EGAnet]{hierEGA}} demands a lot of colors).
#'
#' The \code{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 \code{color.palette} argument can be used to
#' select color palettes from \code{\link[EGAnet]{color_palette_EGA}} as well
#' as those in the color scheme of \code{\link[RColorBrewer]{RColorBrewer}}
#'
#' \emph{For more worked examples than below, see \href{https://r-ega.net/articles/plotting.html}{Plots in \{EGAnet\}}}
#'
#' @examples
#' \donttest{
#' # 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"
#' )}
#'
#' @aliases plot.EGAnet
#'
#' @rdname EGAnet-plot
#'
# Updated 04.08.2023
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