R/phy_plotTaxon_boxplot.R

In g-antonello/gautils: An R package for quick microbiome data wrangle and visualization

#' Boxplot of a taxon
#'
#' Simply a wrapping function to quickly plot a taxon and fill the boxes by a variable
#'
#' @param physeq a phyloseq object
#' @param y the name of the taxon you want to plot (y axis)
#' @param x the name of the trait you want to plot (x axis)
#' @param fill another variable you may want to fill your boxes by
#' @param transform a transformation, all those in the phy_transform are allowed
#'
#' @return a ggplot2 object
#' @export
#'
#' @examples
#' data("enterotype")
#'
#' phy_plotTaxon_boxplot(physeq = enterotype,
#'                      y = "Rikenella",
#'                      x = "Enterotype",
#'                      fill = "SeqTech",
#'                      transform = "clr")
#'

phy_plotTaxon_boxplot <- function(physeq,
                                  y,
                                  x,
                                  fill,
                                  transform = NULL){

  real_name <- y
  easier_name <- make.names(real_name)

  # transform otu counts
  if(!is.null(transform)){
    physeq_transf <- phy_transform(physeq, transform = transform)
    taxa_names(physeq_transf) <- make.names(taxa_names(physeq_transf))
  }else{
    physeq_transf <- physeq
  }

  data_merged <- phy_OtuMetaTable(physeq_transf)

  boxpl <- ggplot(data = data_merged, aes_string(x = x, y = easier_name, fill = fill))+
    geom_boxplot()+
    labs(title = sapply(strsplit(real_name, "(\\.|_|-)"), paste, collapse = " "),
         caption = paste0("transformation: ", transform),
         y = "Taxon Abundance"
    )


  return(boxpl)
}