## install pophelper package
#install.packages("devtools")
#devtools::install_github('royfrancis/pophelper')
# load packages
library(pophelper)
# set working directory
setwd("/to/work/directory")
# avoid to output scientific notation
options(scipen=100)
## make a folder called "original" and put all admixture *.Q results into it
# list all files in original folder
file_list_admix <- list.files("original/", pattern = ".Q$", full.names = T)
# exclude K = 1
file_list_admix <- grep(file_list_admix, pattern='\\.1\\.Q$', inv=T, value=T)

# put all grouping information to a tsv file called "group.xls", file format is like following
# 1st column is the fixed orders of each sample
# 2nd and 3rd column are sample ids, the order of sample MUST BE the same as those in *.Q files
# 4th column is the group names which samples belong to
#order id1 id2  group
#110 1  1  Pop8
#119  10 10  Pop8
# read group.xls file
info <- read.table("group.xls", header = T, stringsAsFactors = F, row.names = 3, comment.char = "")
# read *.Q into a list
qlist_admix <- readQ(file_list_admix)
# reorder samples in *.Q files according to 1st column and put them in a new list
qlist_admix1 <- list()
for(i in 1:length(qlist_admix)){
  tmpdf <- qlist_admix[[i]]
  row.names(tmpdf) <- row.names(info)
  tmpnew <- cbind(info, tmpdf)
  tmpnew <- tmpnew[order(tmpnew$order),]
  qlist_admix1[[i]] <- tmpnew[,5:ncol(tmpnew)]
  row.names(qlist_admix1[[i]]) <- row.names(tmpnew)
  write.table(qlist_admix1[[i]], file = paste0("snp", ".K", ncol(qlist_admix[[i]]), ".qmatrix.xls"), row.names = T, col.names = NA, sep = "\t", quote = F)
}
qlist_admix <- qlist_admix1

# reorder Ks to avoid 1 10 11 ... 2 ...
k_order <- vector()
mink <- 2
maxk <- 10
if(maxk < 10){
  k_order <- 1:length(qlist_admix)
} else if (maxk < 20) {
  end1 <- maxk - 10 + 1
  start2 <- end1 + 1
  k_order <- c(start2:length(qlist_admix), 1:end1)
}
# create K labels (2 3 4 ... maxK)
klab <- vector()
if(mink == 1){
  klab <- 1:maxk
} else {
  klab <- mink:maxk
}
# rename Ks in list using K labels
names(qlist_admix) <- klab
print(length(qlist_admix))
print(klab)
## plot join plot
prefix <- "snp.admix"
height <- 2
width <- 18
plotQ(qlist_admix[k_order], imgoutput="join",showindlab=T, showlegend=F, sortind = NA,
      indlabsize=2.5,indlabheight=0,indlabspacer=0.05,barbordersize=NA,
      outputfilename=prefix,imgtype="pdf", sharedindlab = F,
      useindlab = T, showyaxis = T, basesize = 10, sppos = "right", showticks = T,
      splab = paste0("K = ", klab), splabsize = 6, splabface = "bold",
      width = width, height = height, panelspacer = 0.02, dpi = 600, barbordercolour = NA)

plotQ(qlist_admix[k_order], imgoutput="join",showindlab=T, showlegend=F, sortind = NA,
      indlabsize=2.5,indlabheight=0,indlabspacer=0.05,barbordersize=NA,
      outputfilename=prefix,imgtype="png", sharedindlab = F,
      useindlab = T, showyaxis = T, basesize = 10, sppos = "right", showticks = T,
      splab = paste0("K = ", klab), splabsize = 6, splabface = "bold",
      width = width, height = height, panelspacer = 0.02, dpi = 600, barbordercolour = NA)
## plot seperated plot (per K per file)
names(qlist_admix) <- paste0("admix.K", klab)
prefix_sep <- paste0("snp.K", klab)
plotQ(qlist_admix[k_order], imgoutput="sep",showindlab=T, showlegend=F, sortind = NA,
      indlabsize=2.5,indlabheight=0,indlabspacer=0.05,barbordersize=NA, indlabhjust = 0,
      outputfilename=prefix_sep,imgtype="pdf", sharedindlab = F, splab = paste0("K = ", klab),
      useindlab = T, showyaxis = T, basesize = 10, sppos = "right", showticks = T,
      splabsize = 4, splabface = "bold",
      width = width, height = height * 1.5, panelspacer = 0.02, dpi = 600, barbordercolour = NA)

plotQ(qlist_admix[k_order], imgoutput="sep",showindlab=T, showlegend=F, sortind = NA,
      indlabsize=2.5,indlabheight=0,indlabspacer=0.05,barbordersize=NA, indlabhjust = 0,
      outputfilename=prefix_sep,imgtype="png", sharedindlab = F, splab = paste0("K = ", klab),
      useindlab = T, showyaxis = T, basesize = 10, sppos = "right", showticks = T,
      splabsize = 4, splabface = "bold",
      width = width, height = height * 1.5, panelspacer = 0.02, dpi = 600, barbordercolour = NA)