Simple plotting method for R IRanges and GRanges objects

plot-iranges.R

# IRanges plot
# by Aaron Wolen (2016)

plot.GRanges <- function(x, ...) plot(GenomicRanges::ranges(x))

plot.IRanges <-
  function(x,
           xlim = NULL,
           ylim = NULL,
           height = 0.8,
           col = "grey",
           border = NULL,
           add = FALSE,
           xlab = NULL,
           ylab = NULL,
           add.labels = FALSE,
           col.labels = "black",
           ...) {
    if (!requireNamespace("GenomicRanges", quietly = TRUE))
      stop("GenomicRanges package is required.", call. = FALSE)

    if (is.null(xlab))
      xlab <- ""
    if (is.null(ylab))
      ylab <- ""

    xrng  <- range(x)
    group <- GenomicRanges::disjointBins(x)

    if (is.null(xlim))
      xlim <- c(IRanges::start(xrng), IRanges::end(xrng))
    if (is.null(ylim))
      ylim <- c(1 - height / 2, max(group) + height / 2)

    if (!add) {
      plot.default(
        NULL,
        xlim = xlim,
        ylim = ylim,
        axes = FALSE,
        xlab = xlab,
        ylab = ylab
      )
      abline(h = unique(group), col = "grey90")
      axis(1, at = pretty(xlim), tick = TRUE)
    }

    rect(
      xleft = start(x),
      ybottom = group - height / 2,
      xright = end(x) ,
      ytop = group + height / 2,
      col = col,
      border = border
    )

    if (add.labels & !is.null(names(x))) {
      text(
        x = mid(x),
        y = group,
        labels = names(x),
        col = col.labels
      )
    }
  }