R/plot_diversity_stats.R

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

#' @title Diversity plot with stats
#' @param x \code{\link{phyloseq-class}} object
#' @param index diversity index. Calculated using microbiome::alpha
#' @param group Grouping variable to compare
#' @param group.colors Colors for plotting groups
#' @param dot.opacity for ggplot alpha to determine opacity for points
#' @param box.opacity for ggplot alpha to determine opacity for box
#' @param violin.opacity for ggplot alpha to determine opacity for violin
#' @param group.order Default is NULL. a list specifing order of x-axis.
#' @param label.format For ggpubr::stat_compare_means "p.signif"
#' E.g. c("H","CRC","nonCRC")
#' @param stats Logical TRUE or FALSE. Calls ggpubr::stat_compare_means.
#' @param ... params for ggpubr::stat_compare_means
#' @importFrom ggpubr stat_compare_means rotate_x_text
#' @importFrom gghalves geom_half_violin
#' @examples
#' \dontrun{
#' library(microbiomeutilities)
#' library(ggpubr)
#' data("zackular2014")
#' p0 <- zackular2014
#' mycols <- c("brown3", "steelblue", "grey50")
#' p.m <- plot_diversity_stats(p0,
#'   group = "DiseaseState",
#'   index = "diversity_shannon",
#'   group.order = c("H", "CRC", "nonCRC"),
#'   group.colors = mycols
#' )
#' print(p.m)
#' }
#' @keywords visualization analysis
#' @export
plot_diversity_stats <- function(x, index,
                                 group = NULL,
                                 group.colors = c("brown3", "steelblue"),
                                 dot.opacity = 0.25,
                                 box.opacity = 0.25,
                                 violin.opacity = 0.5,
                                 group.order = NULL,
                                 stats = TRUE,
                                 label.format = "p.format",
                                 ...) {
  if (stats == TRUE) {
    p <- plot_diversity_with_stats(x, index,
      group = group,
      group.colors = group.colors,
      dot.opacity = dot.opacity,
      box.opacity = box.opacity,
      violin.opacity = violin.opacity,
      group.order = group.order,
      label.format = label.format
    )
  } else if (stats == FALSE) {
    p <- plot_diversity_without_stats(x,
      index = index,
      group = group,
      group.colors = group.colors,
      dot.opacity = dot.opacity,
      box.opacity = box.opacity,
      violin.opacity = violin.opacity,
      group.order = group.order,
      label.format = label.format
    )
  }
}