R/PlotTax.R

In palmid: RdRP Analysis Suite

# PlotTax
#' Plot a taxonomic-classifier based histogram
#' @param pro   data.frame, A diamond-aligned pro file
#' @param html  boolean, include additional parsing for htmlwidget display [TRUE]
#' @return A histogram ggplot2
#' @keywords palmid pro plot
#' @examples
#' data("waxsys.pro.df")
#'
#' proTax <- PlotTax(waxsys.pro.df, html = TRUE)
#'
#' plot(proTax)
#' @import viridisLite
#' @import dplyr ggplot2
#' @export
PlotTax <- function(pro, html = TRUE){

  ranklvl <-  c("phylum",  "family",  "genus",   "species")
  rankcols <- c("#9f62a1", "#00cc07", "#ff9607", "#ff2a24")

  # Taxonomic ranges
  tax <- data.frame(
    rank = factor(
          c("species", "genus", "family", "phylum"),
           levels = ranklvl ),
    llim = c(90,        70,      45,        0),
    ulim = c(101,       90,      70,        45),
    count= c(0, 0, 0, 0) )

  # count each taxonomic rank
  for ( i in 1:4 ){
    tax$count[i] <- length(which( pro$pident <  tax$ulim[i]
                                & pro$pident >= tax$llim[i]))
  }

  if (html){
    add_label <- geom_label(data = tax, aes(x = NULL, y = 5, label = count))
    set.xlab <- "Count/rank"
    set.ylab <- ""
  } else {
    set.xlab <- "Count/rank"
    set.ylab <- ""
    add_label <- geom_label(data = tax, aes(x = rank, y = 5, label = count))

  }
  # Bar plot of ranks
  taxPlot <- ggplot() +
    geom_col(data = tax, aes(x=rank, y=count, fill = rank),
            show.legend = FALSE) +
    scale_fill_manual(values = rankcols) +
    xlab(set.xlab) + ylab(set.ylab) +
    #add_label +
    ggtitle("") + theme_bw() +
    theme(axis.text.x = element_text(angle = 45, vjust = 0.5, hjust=1))

  return(taxPlot)
}