#' Specialized plots for objects from the \code{cytoqc} package
#'
#' This is a generic function for plotting functionality specific
#' to objects from the \code{\link[=cytoqc-package]{cytoqc}} package.
#'
#' It is currently only implemented for results of \code{\link{cqc_cluster}}.
#'
#' @param y object to be plotted
#' @param ... additional arguments (currently unused)
#' @export
cqc_plot <- function(y, ...) UseMethod("cqc_plot")
#' @param y an object of class cqc_cluster resulting from a cqc_cluster call
#' @rdname cqc_cluster
#' @export
cqc_plot.cqc_cluster <- function(y, ...){
# Maybe look in to how to override stats:::plot.hclust
# or just work with the args there
plot(y$cluster_results,
xlab="Group Number",
sub="")
if(!is.null(y$height))
abline(a=y$height, b=0, col="blue", lty=2)
if(y$ngroup > 1 && y$ngroup < length(unique(y$group_membership$old_group)))
rect.hclust(y$cluster_results, k = y$ngroup, cluster=y$plot_groups, border = "red")
}
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