R/methods_image.R

In robinweide/GENOVA: GENOVA: expore the Hi-C

#' Display a part of a Hi-C matrix
#'
#' @name  GENOVA_image
#' @param x A \code{contacts_matrix} object, as returned by
#'   \code{\link[GENOVA]{select_subset}()}.
#' @param col a list of colors such as that generated by
#'   \code{\link[grDevices]{hcl.colors}}, \code{\link[grDevices]{gray.colors}}
#'   or similar functions. Defaults to GENOVA palette.
#' @param zlim the minimum and maximum z values for which colors should be
#'   plotted, defaulting to the range of finite values of off-diagonal elements
#'   of \code{x}.
#' @param xlab,ylab each a character string giving the labels for the x and y
#'   axis. Default is to use the chromosome name as axis title.
#' @inheritDotParams graphics::image.default -y -z
#' @export
#'
#' @examples
#' \dontrun{
#' x <- select_subset(exp, "chr1", 50e6, 60e6)
#' image(x)
#' }
image.contacts_matrix <- function(
  x,
  col = NULL, zlim = NULL,
  xlab = NULL, ylab = NULL,
  ...
) {
  if (is.null(col)) {
    col <- .choose_palette()
    col <- colorRampPalette(col)
    col <- col(255)
  }
  if (is.null(zlim)) {
    zlim <- x$z
    diag(zlim) <- 0
    zlim <- range(zlim)
    diag(x$z) <- zlim[2]
  }
  if (is.null(xlab)) {
    xlab <- paste0(attr(x, "chrom"), " (Mb)")
    x$x <- x$x / 1e6
  }
  if (is.null(ylab)) {
    ylab <- paste0(attr(x, "chrom"), " (Mb)")
    x$y <- x$y / 1e6
  }
  
  image.default(x = x$x, y = x$y, z = x$z, 
                zlim = zlim, xlab = xlab, ylab = ylab,
                col = col, ...)
}