Add tip colors and round node labels for nexus files produced via APE for use in FigTree

ape_nex_mod.R

#==============================================================================#
#' INSTALLATION
#' 
#' devtools::source_gist("3c3f12926de648431937")
#==============================================================================#
#
#
#==============================================================================#
#' Adds tip colors to tiplabels of an object of class "phylo"
#' 
#' Arguments:    
#'    x          an object of class phylo with tip labels    
#'    tip_colors a vector of the same length as the number of tips in x    
#'               comprised of color designations in hexadecimal format.
#' 
#' Returns:    
#'    an object of class "phylo"
#==============================================================================#
add.tip.color <- function(x, tip_colors){
  tips <- x$tip.label
  colors <- paste0("[&!color=", tip_colors, "]")
  x$tip.label <- paste0(tips, colors)
  return(x)
}

#==============================================================================#
#' Rounds node labels produced via bootstrap.
#' 
#' Arguments:    
#'    x          an object of class phylo with tip labels    
#' 
#' Returns:    
#'    an object of class "phylo" with rounded node labels.
#==============================================================================#
round.nodes <- function(x){
  x$node.label <- round(x$node.label)
  return(x)
}

installation:

devtools::source_gist("3c3f12926de648431937")

Example usage:

library("poppr")
library("ape")
devtools::source_gist("3c3f12926de648431937")
data(microbov)
micpop  <- genind2genpop(microbov)
mictree <- aboot(micpop) # generates tree based off of Nei's distance with 100 bootstrap replicates
cols    <- any2col(micpop@pop.names)
write.nexus(add.tip.color(mictree, cols), file = "myTree.nex") # saves tree in nexus format with tip colors