R/autoplot.anosim.R

In ggvegan: 'ggplot2' Plots for the 'vegan' Package

#' @title ggplot-based plot for objects of class `"anosim"`
#'
#' @description
#' Produces a multi-layer ggplot object representing the output of objects
#'   produced by [vegan::anosim()].
#'
#' @param object an object of class `"anosim"`, the result of a call to
#'   [vegan::anosim()].
#' @param notch logical; make notched (default) or standard box plot?
#' @param varwidth logical; make box width proportional to the square-root of
#'   the number of observations in the group (default)?
#' @param xlab character; label for the x-axis.
#' @param ylab character; label for the y-axis.
#' @param title character; title for the plot.
#' @param subtitle character; subtitle for the plot.
#' @param caption character; caption for the plot.
#' @param ... additional arguments passed to other methods.
#' @return A ggplot object.
#'
#' @author Didzis Elferts. Modifications by Gavin L. Simpson.
#'
#' @export
#'
#' @importFrom ggplot2 ggplot autoplot geom_boxplot aes labs fortify
#'
#' @examples
#'
#' library("vegan")
#'
#' data(dune)
#' data(dune.env)
#' dune.dist <- vegdist(dune)
#' dune.ano <- with(dune.env, anosim(dune.dist, Management))
#'
#' autoplot(dune.ano, notch = FALSE)

`autoplot.anosim` <- function(
  object,
  notch = TRUE,
  varwidth = TRUE,
  xlab = NULL,
  ylab = NULL,
  title = "Analysis of similarities",
  subtitle = NULL,
  caption = bquote(R == .(r) * "," ~ P == .(p)),
  ...
) {
  df <- fortify(object)

  plt <- ggplot(
    df,
    aes(x = .data[["class"]], y = .data[["rank"]])
  ) +
    geom_boxplot(notch = notch, varwidth = varwidth)

  ## prepare stats for caption --- may not be used
  p <- if (is.null(object$permutations)) {
    "not assessed"
  } else {
    format.pval(object$signif)
  }
  r <- round(object$statistic, 3)

  ## add on labels here, not earlier due to lazy evaluation of caption default
  plt <- plt +
    labs(
      x = xlab,
      y = ylab,
      title = title,
      subtitle = subtitle,
      caption = caption
    )
  plt
}