library(ggplot2)

qtl.trans = read.table('./translocations.perms.3000.100samples-old.txt', h = T)
qtl.trans = qtl.trans[qtl.trans$qtl_type == 'trans',]
pval = ifelse(qtl.trans$total_number_of_trans_reads > 5, 0, 1)

#chr.from and transloc.from correspond to the coordinates of the repeated segment
#chr.to and transloc.to correspond to the coordinates of the qtl
plot.transloc <- function(chr.from, transloc.from, chr.to, transloc.to, p.value, pdffile = './transloc.qtls.map.pdf'){
  chr.lengths = c(30427671, 19698289, 23459830, 18585056, 26975502)
  names(chr.lengths) = c('Chr1', 'Chr2', 'Chr3', 'Chr4', 'Chr5')
  chr.offset <- c(0, cumsum(chr.lengths[-5]))
  names(chr.offset) = names(chr.lengths)
  from = transloc.from + chr.offset[chr.from]
  to = transloc.to + chr.offset[chr.to]
  dfr <- data.frame(from = from/1000000, to = to/1000000, p.value = p.value <= 0.05)
  p <- ggplot(dfr) + geom_point(aes(x = from, y = to, fill = p.value, colour = p.value, alpha = 0.5)) + scale_fill_manual(values = c('black', 'firebrick')) + scale_colour_manual(values = c('black', 'firebrick')) + xlab('Position of heterozygous, short segment (Mb)') + ylab('QTL (Mb)') + theme(legend.position = 'none')
  p <- p + geom_vline(xintercept = chr.offset/1000000) + geom_hline(yintercept = chr.offset/1000000)
  dfr.transonly <- dfr[which(dfr$p.value),]
  p.transonly <- ggplot(dfr.transonly) + geom_point(aes(x = from, y = to, fill = p.value, colour = p.value, alpha = 0.5)) + scale_colour_manual(values = c( 'firebrick')) + xlab('Position of heterozygous, short segment (Mb)') + ylab('QTL (Mb)') + theme(legend.position = 'none')
  p.transonly <- p.transonly + geom_vline(xintercept = chr.offset/1000000) + geom_hline(yintercept = chr.offset/1000000)
  pdf(pdffile)
  print(p)
  print(p.transonly)
  dev.off()
}

plot.transloc(qtl.trans$chr.segment, qtl.trans$start.segment, qtl.trans$chr.full_qtl, qtl.trans$start.full_qtl, pval, './transloc.qtls.map.pdf')