R/gg_species_dnds_blast_tbl.R

In HajkD/metablastr: Perform Massive Local BLAST Searches

#' @title Plot pairwise dN, dS, or dN/dS distributions of orthologous genes
#' @description This function enables users to plot pairwise dN, dS, or dN/dS distributions of orthologous genes.
#' @param blast_tbl a \code{blast_tbl}.
#' @param type type of sustitution rate quantification that shall be visualized on the y-axis. Options are:
#' \itemize{
#' \item \code{type = "dN"}
#' \item \code{type = "dS"}
#' \item \code{type = "dN/dS"}
#' \item \code{type = "dN+dS"}
#' }
#' @param order a character vector specifying the order of the species using their scientific names (which have to match the species names stored in the \code{subject_species}
#' column of the input \code{blast_tbl}). 
#' @param xlab label of x-axis.
#' @param ylab label of y-axis.
#' @param title title label.
#' @author Hajk-Georg Drost
#' @export

gg_species_dnds_blast_tbl <- function(blast_tbl, type, order, xlab = "", ylab = "", title = "") {
  
  if (!is.element(type, c("dN", "dS", "dN/dS", "dN+dS")))
    stop("Please specify a type that is supported by this function. E.g. dN, dS, dN+dS, or dN/dS.", call. = FALSE)
  
  subject_species <- dN <- dS <- dNdS <- dN_plus_dS <- ..density.. <- NULL
  
  if (type == "dN/dS") {
    p <-
      ggplot2::ggplot(
        blast_tbl,
        ggplot2::aes(
          x = dNdS,
          y = factor(subject_species, levels = rev(order)),
          fill = subject_species,
          colour = subject_species,
          height = ..density..
        )
      )
  }
  
  if (type == "dN+dS") {
    blast_tbl <- dplyr::mutate(blast_tbl, dN_plus_dS = dN + dS)
    p <-
      ggplot2::ggplot(
        blast_tbl,
        ggplot2::aes(
          x = dN_plus_dS,
          y = factor(subject_species, levels = rev(order)),
          fill = subject_species,
          colour = subject_species,
          height = ..density..
        )
      )
  }
  
  if (type == "dN") {
    p <-
      ggplot2::ggplot(
        blast_tbl,
        ggplot2::aes(
          x = dN,
          y = factor(subject_species, levels = rev(order)),
          fill = subject_species,
          colour = subject_species,
          height = ..density..
        )
      )
  }
  
  if (type == "dS") {
    p <-
      ggplot2::ggplot(
        blast_tbl,
        ggplot2::aes(
          x = dS,
          y = factor(subject_species, levels = rev(order)),
          fill = subject_species,
          colour = subject_species,
          height = ..density..
        )
      )
  }
  p <- p +
    ggridges::geom_density_ridges(
      scale = 5,
      show.legend = FALSE,
      alpha = 0.4,
      size = 1.5,
      stat = "density", trim = TRUE
    ) + ggridges::theme_ridges() + ggsci::scale_colour_lancet() + ggsci::scale_fill_lancet() + ggplot2::labs(x = xlab,
                                                                                                             y = ylab) +
    ggplot2::theme(legend.text = ggplot2::element_text(size = 18)) +
    ggplot2::theme(
      axis.title  = ggplot2::element_text(size = 18, face = "bold"),
      axis.text.y = ggplot2::element_text(size = 18, face = "bold"),
      axis.text.x = ggplot2::element_text(size = 18, face = "bold"),
      panel.background = ggplot2::element_blank(),
      plot.title = ggplot2::element_text(
        size = 18,
        colour = "black",
        face = "bold"
      )
    ) + ggplot2::ggtitle(title) + ggplot2::scale_x_continuous(breaks = scales::pretty_breaks(n = 8))
  
  return(p)
}