scripts/plotRanges.R

In tobiasko/posprot: Positional Proteomics in R

plotRanges <- function(x, xlim = x, main = deparse(substitute(x)),
                       col = "black", sep = 0.5, ...) 
{
  height <- 1
  if (is(xlim, "Ranges"))
    xlim <- c(min(start(xlim)), max(end(xlim)))
  bins <- disjointBins(IRanges(start(x), end(x) + 1))
  plot.new()
  plot.window(xlim, c(0, max(bins)*(height + sep)))
  ybottom <- bins * (sep + height) - height
  rect(start(x)-0.5, ybottom, end(x)+0.5, ybottom + height, col = col, ...)
  title(main)
  axis(1)
}

plotRanges <- function(x, xlim = x, main = deparse(substitute(x)),
                       col = "black", sep = 0.5, ...) 
{
  pep.colors <- data.frame(key = c("free", "label", "acetylated"), value = c("black", "blue", "green"))
  height <- 1
  if (is(xlim, "Ranges"))
    xlim <- c(min(start(xlim)), max(end(xlim)))
  bins <- disjointBins(IRanges(start(x), end(x) + 1))
  plot.new()
  plot.window(xlim, c(0, max(bins)*(height + sep)))
  ybottom <- bins * (sep + height) - height
  rect(start(x)-0.5, ybottom, end(x)+0.5, ybottom + height, col = pep.colors[match(elementMetadata(x)$nterm.label, pep.colors$key),2], ...)
  title(main)
  axis(1)
}