R/plotSegmentsId.r

In genostats/FEstim: Genetic Data Analyses in Presence of Inbreeding

plotSegmentsId <- function (byROHfile = FALSE, fileOrSubmaps, unit = "cM",
            regions, color2 = "green4", main, build) {
    # chose which unit to use for the plot
    l <- unitPlotId(file = fileOrSubmaps, unit = unit, byROHfile)
    ecart <- l$ecart
    larg  <- l$larg
    pos1  <- l$pos1
    pos2  <- l$pos2
    
    #empty plot
    if (missing(main))
      main = NULL
    plot( x = c(larg * 0.5, larg * 11.5),
          y = c( 0,
            lengthChromosome(1, unit, build) + lengthChromosome(12, unit, build) + 1.25 * ecart),
          type = "n", xaxt = "n", yaxt = "n", xlab = "", ylab = "", main = main, cex.main = 1.5)
    
    
    #chromosome loop
    for (i in seq_len(22)) {
      if (i < 12) {
        i2 <- i
        offset_y <- lengthChromosome(12, unit, build) + ecart
      } else {
        i2 <- i - 11
        offset_y <- 0
      }
      
      #dessiner le chromosome
      paintCytobands( i, units = unit,
        pos = c(larg * i2, offset_y + lengthChromosome(i, unit, build) + ecart / 4),
        orientation = "v", legend = FALSE, build = build)
      
      text(larg * i2, offset_y - 0.25 * ecart, i)
      
      #traitement de l'options regions
      if (!is.null(regions)) {
        regions_chr <- regions[regions$chr == i,]
        if (nrow(regions_chr) > 0) {
          for (k in seq_len(nrow(regions_chr))) {
            xx <- c(rep(larg * i2, 2), rep(larg * (i2 + 0.5), 2))
            
            yy <- c( 0.25 * ecart + abs( lengthChromosome(i, unit, build) - c(regions_chr$start[k], regions_chr$end[k])),
                     0.25 * ecart + abs( lengthChromosome(i, unit, build) - c(regions_chr$end[k], regions_chr$start[k])))
            
            polygon( x = xx, y = yy + offset_y, col = color2, border = color2, lwd = 1.5)
          }
        }
      }
      
      #recuperer les lignes pour un individus et un chromosome specifique
      if (byROHfile) {
        seg_chr <- fileOrSubmaps[fileOrSubmaps$CHR == i, ]
      } else {
        seg_chr <- fileOrSubmaps[fileOrSubmaps$chromosome == i, ]
      }
      
      if (nrow(seg_chr) > 0) {
        for (k in seq_len(nrow(seg_chr))) {
          xx <- c(rep(larg * i2, 2), rep(larg * (i2 + 0.5), 2))
          
          yy <- c( 0.25 * ecart + abs( lengthChromosome(i, unit, build) - c(seg_chr[k, pos1], seg_chr[k, pos2])),
                   0.25 * ecart + abs( lengthChromosome(i, unit, build) - c(seg_chr[k, pos2], seg_chr[k, pos1])))
          
          polygon( x = xx, y = yy + offset_y, col = ifelse(byROHfile, color(seg_chr$PHE[k]), color(seg_chr$pheno[k])),
            border = ifelse( byROHfile, color(seg_chr$PHE[k]), color(seg_chr$pheno[k])),
            lwd    = 1)
        }
      }
    }
  }