## Functions to merge individual AFLP datasets and convert formats
## 17 February 07
## Andrew Hipp

AFLPmerge = function(sortCols = FALSE) {
## assumes that each file selected has the loci labelled in the header, but no column for the sample names; 
##  sample names are designated as row.names; locus names are the header
## Arguments:
##  sortCols = logical, determines whether the matrix will be sorted by columns (typically locus names) as well as rows. Default = FALSE
## note: leave sortCols = FALSE if any of your column names are non-unique across datasets! otherwise the dataset will not be correct
  filesVector = choose.files(caption = "select all files you want to merge")
  filesList = lapply(filesVector, read.table, header = TRUE)
  namesList = lapply(filesList, row.names)
  namesListSorted = lapply(namesList, sort)
  for(i in namesListSorted) {
    if(!identical(i,namesListSorted[[1]])) {
      print("NOT ALL NAMES ARE IDENTICAL")
      return(namesListSorted)
      stop() }}
  for (i in filesList) {
    i = i[sort(row.names(i)), ] }
  mergedData = filesList[[1]]
  for (i in 2:length(filesList)) mergedData = cbind(mergedData, filesList[[i]])
  if(sortCols) mergedData = mergedData[,sort(names(mergedData))]
  message("To save the merged data file, copy the following and paste into the command line, changing the filename and variable as needed:")
  message("")
  message("write.table(___$mergedData, '___.txt', quote = FALSE)")
  comment(mergedData) = "AFLPmerge"
  return(list(files = filesList, mergedData = mergedData, names = namesList, namesSorted = namesListSorted)) }

structureFormat = 
## Takes a matrix of the form exported by AFLPmerge and converts it to STRUCTURE format
## Arguments:
##  AFLPdata = data matrix in AFLPmerge format (set comment = "AFLPmerge" if the matrix isn't actually coming from AFLPmerge)
##  unknown = value to set all second alleles to. Default = -9, as is standard for STRUCTURE at the time of this writing.
function(AFLPdata, unknown = -9) {
  errorCheck = checkAFLPformat(AFLPdata)
  if(errorCheck[1] == "error") stop(errorCheck[2])

  numberOfIndividuals = dim(AFLPdata)[1]
  numberOfLoci = dim(AFLPdata)[2]
  dummyMatrix = AFLPdata
  row.names(dummyMatrix) = paste(row.names(dummyMatrix),"_unknownAllele",sep = "")
  dummyMatrix[ , ] = unknown
  fullMatrix = rbind(AFLPdata, dummyMatrix)
  fullMatrix = fullMatrix[sort(row.names(fullMatrix)), ]
  message("To save the formated structure file, copy the following and paste into the command line, changing the filename and variable as needed:")
  message("")
  message("write.table(___, '___.txt', quote = FALSE)")
  message("")
  message("Once saved, do a global replace for the string '_unknownAllele', which should be replaced with a NULL.")
  message("Then the file should import into STRUCTURE without modification.")
  message("")
  message(paste("Number of individuals:",numberOfIndividuals))
  message(paste("Number of loci:",numberOfLoci))
  return(fullMatrix) }

delTaxa = 
## Deletes taxa from an AFLPmerge-format data matrix
## Removes all zeros if requested
## Arguments
##  AFLPdata = data matrix in AFLPmerge format (set comment = "AFLPmerge" if the matrix isn't actually coming from AFLPmerge)
##  taxonVector = vector of individual titles to retain; if NULL, then delTaxa calls a dialog box to select taxa
##  delZeros = flag to delete all zeros. Default = TRUE
function(AFLPdata, taxonVector = NULL, delZeros = TRUE) {
  errorCheck = checkAFLPformat(AFLPdata)
  if(errorCheck[1] == "error") stop(errorCheck[2])
  if(identical(taxonVector, NULL)) taxonVector <- select.list(row.names(AFLPdata), preselect = NULL, multiple = TRUE, title =
    "Select individuals to include in the analysis; use shift and ctrl to select multiple names.")
  newData = AFLPdata[taxonVector, ]
  if(delZeros) newData = newData[ ,apply(newData,2,sum) != 0] 
  numberOfIndividuals = dim(newData)[1]
  numberOfLoci = dim(newData)[2]
  message("New dataset dimensions:")
  message(paste("  Number of individuals:",numberOfIndividuals))
  message(paste("  Number of loci:",numberOfLoci))
  return(list(dataMatrix = newData, taxaIncluded = taxonVector)) }
  
checkAFLPformat = 
## Checks whether the comment on a dataset is "AFLPformat"
function(AFLPdata) {
  if(!identical(comment(AFLPdata), "AFLPmerge")) {
    message("This dataset appears not to have been generated by AFLPmerge")
    message("If you are pretty sure your dataset is a matrix in the right format, set comment([NAME_OF_YOUR_DATA_MATRIX]) = 'AFLPmerge' and call this function again")
    message("Note that if you are calling this on an AFLPmerge object, you need to select out only the AFLP dataset (e.g., aflpData$mergedData)")
    message("")
    return(c("error","reformat aborted; try again with another data matrix or after setting the comment for this matrix to 'AFLPmerge'")) }
  return("ok") }
  
## TO SAVE COMMA DELIMITED:

##  write.table(XXX$mergedData,"XXX.txt",sep = ",", quote = FALSE)

pcordConvert = function(AFLPdata, datatype = "C") {
  numberOfIndividuals = dim(AFLPdata)[1]
  numberOfLoci = dim(AFLPdata)[2]
  testHeader = numeric(4*numberOfLoci)
  dim(testHeader) <- c(4,numberOfLoci)
  testHeader = as.data.frame(testHeader)
  names(testHeader) = names(AFLPdata)
  row.names(testHeader)[1] = numberOfIndividuals
  row.names(testHeader)[2] = numberOfLoci
  row.names(testHeader)[3] = ""
  row.names(testHeader)[4] = " "
  testHeader[,] = ""
  testHeader[1,1] = "Trees"
  testHeader[2,1] = "Loci"
  testHeader[3,] = "C"
  testHeader[4,] = names(AFLPdata)
  pcordFile = rbind(testHeader,AFLPdata)
  message("To save this file, copy and paste the following:")
  message("write.table(testPCORDfile,'pcORDtest.csv',sep = ',', quote = FALSE, col.names = FALSE)")
  return(pcordFile) }