R/plot.R

In dinaIssakova/rgenesconverged: A Package for Estimating Probability of Convergent Evolution from Genomic Data

#' rgenesconvergedPlot
#'
#'
#' @description Plot tree associated with the given gene, accentuating convergent lineages.
#'
#' @param tree A phylogenetic tree
#' @param phydat An object of class phydat
#' @param spe The name of the species to compare to
#' @param pos The position of interest
#' @param th threshold
#' @param type Type of analysis: 'abs' for basic model or 'score' for by convergence score model
#'
#' @return None
#'
#' @examples
#' \dontrun{
#' rgenesconvergedPlot(tree, primates, "Human", pos=1, th=5, type="score")
#' }
#'
#' @importFrom ggtree ggtree
#' @importFrom ggtree groupOTU
#' @importFrom ggtree geom_tiplab
#' @importFrom ggtree geom_text2
#' @importFrom ggtree aes
#' @import ggplot2
#' @export
rgenesconvergedPlot <- function(tree, phydat, spe, pos, th, type=c("abs", "score")) {

  convNodes <- getConvergent(tree, phydat, spe, pos, th, type=type)
  convNodes <- c(convNodes, spe)
  groupInfo <- split(tree$tip.label, tree$tip.label%in%convNodes)
  ptree <- ggtree::groupOTU(tree, groupInfo)

  # Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.
  # ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates
  # and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
  plottree <- ggtree::ggtree(ptree, branch.length = tree$edge.length, aes(color=group)) +
   geom_text2(aes(subset=!isTip, label=node), hjust=-.3) +
   geom_tiplab()

  plottree
}