R/plot_alpha_diversities.R

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

#' @title Creat a plot for alpha diversities calculated using the \code{\link{microbiome}} package
#' @description Utility plot function for diversity measures calcualted by \code{\link{microbiome}} package.
#' @details Uses the \code{\link{microbiome}} package global function to calculate diversities and then returns
#' a plot.
#' @param x \code{\link{phyloseq-class}} object.
#' @param type Either alpha (Diversity Index) or dominance	(Dominance Index) or evenness	(Evenness Index)
#' @param index.val see global function in \code{\link{microbiome}} package
#' @param variableA Variable of interested to be checked. This will also be used to color the plot
#' @param palette Any of the \code{\link{RColorBrewer}} plettes
#' @param plot.type Three optons c("stripchart", "boxplot", "violin")
#' @return  \code{\link{ggplot}} object. This can be further modified using ggpubr
#' @importFrom ggpubr ggstripchart ggboxplot ggviolin facet
#' @export
#' @examples
#' library(microbiome)
#' library(microbiomeutilities)
#' data("zackular2014")
#' p0 <- zackular2014
#' p <- plot_alpha_diversities(p0,
#'   type = "dominance",
#'   index.val = "all",
#'   plot.type = "stripchart",
#'   variableA = "DiseaseState",
#'   palette = "jco"
#' )
#'
#' print(p)
#' @keywords visualization analysis
#' index.val <- c("shannon, simpson")
plot_alpha_diversities <- function(x, type, index.val = "all", plot.type, variableA, palette) {
  x1 <- x
  meta_df <- meta(x1)
  meta_df$sam_rep_nw <- rownames(meta_df)
  if (type == "diversities") {
    adiv <- alpha(x, index = index.val)
    adiv$sam_rep_nw <- rownames(adiv)
  }
  else if (type == "dominance") {
    adiv <- dominance(x, index = index.val)
    adiv$sam_rep_nw <- rownames(adiv)
  }
  else if (type == "evenness") {
    message("This will take some time")
    adiv <- evenness(x, index = index.val)
    adiv$sam_rep_nw <- rownames(adiv)
  } else if (type == "global") {
    adiv <- microbiome::alpha(x, index = index.val)
    adiv$sam_rep_nw <- rownames(adiv)
  }
  adiv.nw <- reshape2::melt(adiv)
  colnames(adiv.nw) <- c("sam_rep_nw", "Diversity", "div.val")
  meta_df_nw <- reshape2::melt(meta_df)
  meta_adiv <- merge.data.frame(meta_df_nw, adiv.nw, by = "sam_rep_nw")

  if (plot.type == "boxplot") {
    p <- ggboxplot(meta_adiv,
      x = variableA, y = "div.val",
      facet.by = "Diversity", add = "jitter",
      fill = variableA,
      palette = palette
    )

    p2 <- facet(p + theme_bw(),
      facet.by = "Diversity",
      short.panel.labs = FALSE,
      scales = "free", # Allow long labels in panels
      panel.labs.background = list(fill = "white")
    )
  } else if (plot.type == "stripchart") {
    p <- ggstripchart(meta_adiv,
      x = variableA, y = "div.val",
      facet.by = "Diversity",
      color = variableA,
      palette = palette
    )

    p2 <- facet(p + theme_bw(),
      facet.by = "Diversity",
      short.panel.labs = FALSE,
      scales = "free", # Allow long labels in panels
      panel.labs.background = list(fill = "white")
    )
  } else if (plot.type == "violin") {
    p <- ggviolin(meta_adiv,
      x = variableA, y = "div.val",
      facet.by = "Diversity", add = "jitter",
      fill = variableA,
      palette = palette
    )

    p2 <- facet(p + theme_bw(),
      facet.by = "Diversity",
      short.panel.labs = FALSE,
      scales = "free", # Allow long labels in panels
      panel.labs.background = list(fill = "white")
    )
  }

  return(p2)
}