R/stamppPhylip.R

In StAMPP: Statistical Analysis of Mixed Ploidy Populations

#' Export to Phylip Format
#'
#' Converts the genetic distance matrix generated with stamppNeisD into Phylip format and exports it as a text file
#'
#' @param distance.mat the matrix containing the genetic distances generated from stamppNeisD to be converted into Phylip format
#' @param file the file path and name to save the Phylip format matrix as
#' @details The exported Phylip formated text file can be easily imported into sofware packages such as DARWin (Perrier & Jacquemound-Collet 2006) to be used to generate neighbour joining trees
#' @examples
#' # import genotype data and convert to allele frequecies
#' data(potato.mini, package="StAMPP")
#' potato.freq <- stamppConvert(potato.mini, "r")
#' # Calculate genetic distance between populations
#' potato.D.pop <- stamppNeisD(potato.freq, TRUE)
#' # Export the genetic distance matrix in Phylip format
#' \dontrun{stamppPhylip(potato.D.pop, file="potato_distance.txt")}
#' @references Perrier X, Jacquemound-Collet JP (2006) DARWin - Dissimilarity Analysis and Representation for Windows. Agricultural Research for Development
#' @author Luke Pembleton <luke.pembleton at agriculture.vic.gov.au>
#' @importFrom utils write.table
#' @export
stamppPhylip <-function(distance.mat, file=""){

  rnames <- row.names(distance.mat) #individual or population names from Neis genetic distance matrix

  for(x in 1:(length(rnames))){ #if name is longer than 11 characters, truncate to 11 characters

    if(nchar(rnames[x])>11) rnames[x]=substr(rnames[x], 1, 11)

  }

  max.id <- max(nchar(rnames)) #length of the longest name

  for(i in 1:(length(rnames))){ #add spaces to the end of each name so that all names are the length of the longest name plus 4 spaces

    short <- (max.id+4)-nchar(rnames[i])

    for(c in 1:short){

      rnames[i] <- paste(rnames[i], "")

    }

  }

  rnames <- c(paste("  ",length(distance.mat[1,])), rnames) #insert the number of individuals or populations at the top of the PHYLIP file

  phylip.mat <- rbind("", distance.mat)

  row.names(phylip.mat) <- rnames #add the fomrated names to the PHYLIP file

  for (i in 1:(length(distance.mat[1,]))){

    c=i+1

    vec <- distance.mat[i,]

    vec <- sprintf("%.5f", vec) #format all genetic distances to 5 decimal places

    phylip.mat[c,]=vec

  }

  phylip.mat[phylip.mat=="-0.00000"]="0.00000"

  write.table(phylip.mat, file=file, sep="\t", row.names=TRUE, col.names=FALSE, quote=FALSE) #save the PHYLIP format distane matrix as a text file

}