R/plotabif.R

In seqinr: Biological Sequences Retrieval and Analysis

plotabif <- function(abifdata, 
  chanel = 1, 
  tmin = 1/tscale, 
  tmax = abifdata$Data[["SCAN.1"]]/tscale, 
  tscale = 1000, 
  yscale = 1000, type = "l", las = 1, 
  xlab = paste("Time", tscale, sep = "/"),
  ylab = paste("RFU", yscale, sep = "/"), 
  irange = (tmin*tscale):(tmax*tscale),
  x = irange/tscale,
  xlim = c(tmin, tmax),
  chanel.names = c(1:4,105),
  DATA = paste("DATA", chanel.names[chanel], sep = "."),
  y = abifdata$Data[[DATA]][irange]/yscale,
  ylim = c(min(y), max(y)),
  dyn = abifdata$Data[[paste("DyeN", chanel, sep = ".")]],
  main = paste(deparse(substitute(abifdata)), chanel, dyn, sep = " ; "),
  calibr = NULL,
  ladder.bp = NULL,
  allele.names = "identifiler",
  ladder.lab = TRUE,
  ...){

  old.par <- par(no.readonly = TRUE)
  on.exit(par(old.par))
  if(is.null(calibr)){
    plot(x, y, type = type, las = las, 
      xlab = xlab, ylab = ylab, xlim = xlim, ylim = ylim, main = main, ...)
  } else {
    x <- calibr(irange)
    xlim <- range(x)
    plot(x, y, type = type, las = las, 
      xlab = "Size [bp]", ylab = ylab, xlim = xlim, ylim = ylim, main = main, ...)
    tps <- pretty(irange)
    par(cex=0.5)
    axis(1, at = calibr(tps), tps/tscale, line = 0.4, col = grey(0.5))
    par(cex=1)
    if(!is.null(ladder.bp)){ # Allelic ladder add
      data(list = allele.names,envir=environment())
      tmp <- get(allele.names)[chanel]
      n <- length(ladder.bp)
      labels <- unlist(tmp)
      col <-  rep("black", n)
      col[grep("\\.", labels)] <- "red"
      abline(v = ladder.bp, col = col)
      if(ladder.lab){
        text(ladder.bp, y = par("usr")[4], labels, xpd = NA, 
             pos = 3, srt = 45, col = col, cex = 0.8)
      }
    }
  }
  locpar <- par(no.readonly = TRUE)
  invisible(locpar)
}