# Genepop reorder
#' @title Return a genepop file with populatons in specified order.
#' @description Function to subset loci and populations
#' @param genepop the genepop data to be manipulated. This can be either a file path
#' or a dataframe read in with tab separation, header=FALSE , quote="", and stringsAsFactors=FALSE.
#' This will be the standard genepop format with the first n+1 rows corresponding to the n loci names,
#' or a single comma delimited row of loci names followed by the locus data. Populations are
#' separated by "Pop". Each individual ID is linked to the locus data by " , " (space,space space) and is read in as
#' as a single row (character).
#' @param reorder vector of the population names in the order required. Note all population names must be included and can be
#' determined using genepop_detective().
#' @param path the filepath and filename of output.
#' @rdname genepop_reorder
#' @importFrom data.table fread as.data.table
#' @importFrom utils write.table
#' @export
##
genepop_reorder <- function(genepop,reorder,path)
{
#Check to see if genepop is a data.frame from the workspace and convert to data.table
if(is.data.frame(genepop)){genepop <- data.table::as.data.table(genepop)}
#Check to see if genepop is a file path or dataframe
if(is.character(genepop)){
genepop <- data.table::fread(genepop,
header = FALSE, sep = "\t",
stringsAsFactors = FALSE)
}
## check if loci names are read in as one large character vector (1 row)
header <- genepop[1,]
if(length(gregexpr(',', header, fixed=F)[[1]])>1){
lociheader <- strsplit(header,",")
lociheader <- gsub(" ","",unlist(lociheader))
#remove the first column of loci names
genepop <- as.vector(genepop)
genepop <- genepop[-1,]
genepop <- c(lociheader,genepop)
genepop <- data.table::as.data.table(genepop,stringsAsFactors = FALSE)
}
## Stacks version information
stacks.version <- genepop[1,] #this could be blank or any other source. First row is ignored by genepop
#Remove first label of the stacks version
genepop <- genepop[-1,]
colnames(genepop) <- "data"
#ID the rows which flag the Populations
Pops <- which(genepop$data == "Pop" | genepop$data =="pop" | genepop$data == "POP")
npops <- 1:length(Pops)
## separate the data into the column headers and the rest
ColumnData <- genepop$data[1:(Pops[1]-1)]
ColumnData <- gsub("\r","",ColumnData)#remove any hidden carriage returns
snpData <- genepop[Pops[1]:NROW(genepop),]
#Get a datafile with just the snp data no pops
tempPops <- which(snpData$data=="Pop"| snpData$data =="pop" | snpData$data == "POP") ## Changed because we allowed
snpData <- snpData[-tempPops,]
#separate the snpdata
temp <- as.data.frame(do.call(rbind, strsplit(snpData$data," ")))
#data format check
if(unique(temp[,2])!="," | !length(which(temp[,3]==""))>1){
stop("Genepop sampleID delimiter not in proper format. Ensure sampleIDs are separated from loci by ' , ' (space comma space space). Function stopped.",call. = FALSE)
}
temp2 <- temp[,4:length(temp)] #split characters by spaces
#Contingency to see if R read in the top line as the "stacks version"
if (length(temp2)!=length(ColumnData)){colnames(temp2) <- c(stacks.version,ColumnData)}
if (length(temp2)==length(ColumnData)){colnames(temp2) <- ColumnData}
if (length(temp2)!=length(ColumnData)){stacks.version="No STACKS version specified"}
#stacks version character
stacks.version <- as.character(stacks.version)
## Get the population names (prior to the _ in the Sample ID)
NamePops <- temp[,1] # Sample names of each
NameExtract <- substr(NamePops,1,regexpr("_",NamePops)-1)
## Re order according to the reorder vector
NameExtract <- factor(NameExtract,levels=reorder)
temp2 <- temp2[order(NameExtract),] # reorder
NamePops <- NamePops[order(NameExtract)]#reorder
NameExtract=as.character(NameExtract[order(NameExtract)]) #reorder
## Now add the population tags using npops (number of populations and Pops for the inter differences)
tPops <- c(Pops,NROW(genepop))
PopIDs <- NULL
for (i in 2:length(tPops)){
hold <- tPops[i]-tPops[i-1]-1
if(i==length(tPops)){hold=hold+1}
pophold <- rep(npops[i-1],hold)
PopIDs <- c(PopIDs,pophold)
}
temp2$Pop <- PopIDs;rm(hold,pophold,tPops,PopIDs)
## Now subset out the the data according to the specified loci and whether or not you want to keep them.
reqCols <- temp2[,-length(temp2)]
#Now recompile the GenePop format
#the number of individuals for all populations but the last (Pop tagged to the end)
if(length(table(temp2$Pop))>1){PopLengths <- table(NameExtract)[reorder[-length(reorder)]]} else {PopLengths=1}
if(length(table(temp2$Pop))==2){PopPosition = PopLengths+1}
if(length(table(temp2$Pop))>2){
PopPosition <- c(PopLengths[1]+1,rep(NA,(length(PopLengths)-1)))
for (i in 2:length(PopLengths)){
PopPosition[i] <- PopLengths[i]+PopPosition[i-1]
}
}
# paste together the Loci as one long integer separated for each loci by a space
Loci <- do.call(paste,c(reqCols[,], sep=" "))
#Grab the Population tags that each invididual had following the format ID_,__
PopVec <- paste0(NamePops," , ")
#Paste these to the Loci
Loci <- paste(PopVec,Loci,sep="")
#Insert the value of "Pop" which partitions the data among populations #only if more than one population
if(length(table(temp2$Pop))!=1){Loci <- insert_vals(Vec=Loci,breaks=PopPosition,newVal="Pop")}
#Add the first "Pop" label
Loci <- c("Pop",Loci)
## Add the column labels and the stacks version
Output <- c(stacks.version,names(reqCols),Loci)
# Save the file
utils::write.table(Output,path,col.names=FALSE,row.names=FALSE,quote=FALSE)
} #End function
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