R/bartax.R

In escamero/mirlyn: Multiple Iterations of Rarefying for Library Normalization

#Lowabundance_tax clumps low abundance taxa into a "Low abundance" group. Default is set to 1%.
lowabundance_tax <- function(x, taxrank = "Genus", lower_limit = 0.01) {
  otu_table(x) <- otu_table(x)[!is.na(tax_table(x)[, taxrank])]
  x <- microbiome::transform(x, "compositional")
  x <- suppressMessages(phyloseq::tax_glom(x, taxrank = taxrank))
  x <- phyloseq::psmelt(x)
  x[[taxrank]] <- as.character(x[[taxrank]])
  x[[taxrank]][x[["Abundance"]] < lower_limit] <- paste0("<", lower_limit * 100,"% abundance")
  x
}

#If not using low abundance, will just use the raw sequence count values extracted from the phyloseq object using psmelt.
raw_tax <- function(x, taxrank = "Genus"){
  x <- suppressMessages(phyloseq::tax_glom(x, taxrank = taxrank))
  x <- phyloseq::psmelt(x)
  x
}

#' Taxonomic Composition Stacked Barcharts
#'
#' The [bartax()] function will create taxonomic composition barcharts. If desired,
#'low-abundant taxonomic groups will be clustered into a single low abundant group.
#'
#' @param x is a `phyloseq` object.
#' @param lowabun is the cut off value for a low-abundant group. Set to `NULL` to not use.
#' @param xvar is a categorical variable selected from the metadata.
#' @param yvar is the relative abundance of reads.
#' @param taxrank is the specified taxonomic rank.
#' @param cols is a vector containing specified colour values (sufficient number for
#'   number of taxonomic groups).
#'
#' @return A `ggplot` object.
#'
#' @examples
#' library(mirlyn)
#' data(example)
#' cols <- c("black","darkgoldenrod1","dodgerblue","deeppink4","chartreuse3",
#'    "burlywood4","navy","blueviolet", "tan2","lavenderblush3","cyan4")
#' bartax(example, "Sample", lowabun = 0.01, yvar = "Abundance", taxrank = "Phylum", cols)
#'
#' @export
bartax <- function(x, xvar = "Sample", lowabun = 0.01, yvar = "Abundance", taxrank = "Genus", cols = NULL){
  if (!is.null(lowabun)){
    x <- lowabundance_tax(x, taxrank = taxrank, lower_limit = lowabun)
  }else{
    x <- raw_tax(x, taxrank = taxrank)
  }
  taxbar <- ggplot(x, aes_string(x=xvar, y=yvar, fill=taxrank)) +
    geom_bar(stat="identity") +
    theme_bw() +
    scale_y_continuous(labels=function(x) paste0(x*100,"%"),limits=c(0,1.05),expand=c(0,0))
  if(!is.null(cols)){
    taxbar <- taxbar + scale_fill_manual(values = cols)
  }
  taxbar
}

#' Taxonomic Composition Stacked Barcharts - 7 levels
#'
#' The [fullbartax()] function will create taxonomic composition for barcharts for all
#' 7 taxonomic levels.
#' 
#' @param x is a `phyloseq` object.
#' @param lowabun is the cut off value for a low-abundant group.
#' @param xvar is a categorical variable selected from the metadata.
#' @param yvar is the relative abundance of reads.
#' @param cols is a vector containing specified colour values (sufficient number for
#'   number of taxonomic groups found at all levels).
#'
#' @return A `list` of `ggplot` objects.
#'
#' @examples
#' \dontrun{
#' library(mirlyn)
#' data(example)
#' fullbartax(example,"Sample", lowabun = 0.01, yvar="Abundance")
#' }
#'
#' @export
fullbartax <- function(x, xvar = "Sample", lowabun = 0.01, yvar = "Abundance", cols = NULL){
  kingdom_plot <- bartax(x, xvar = xvar, taxrank = "Kingdom", cols = cols)
  phylum_plot <- bartax(x, xvar = xvar, taxrank = "Phylum", cols = cols)
  class_plot <- bartax(x,xvar = xvar, taxrank = "Class", cols = cols)
  order_plot <- bartax(x, xvar = xvar, taxrank = "Order", cols = cols)
  family_plot <- bartax(x, xvar = xvar, taxrank = "Family", cols = cols)
  genus_plot <- bartax(x, xvar = xvar, taxrank = "Genus", cols = cols)
  species_plot <- bartax(x, xvar = xvar, taxrank = "Species", cols = cols)
  list(
    Kingdom = kingdom_plot,
    Phylum = phylum_plot,
    Class = class_plot,
    Order = order_plot,
    Family = family_plot,
    Genus = genus_plot,
    Species = species_plot
  )
}