R/plot_CCF.R

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

#' Plot the CCF estimates in the data.
#'
#' @description
#'
#' This function extracts the plots of the Cancer Cell Fractions (CCFs) estimates
#' from a `CNAqc` object, after they have been computed using
#' function `compute_CCF`. The plots - one per computed karyotype - are assembled
#' into a `ggpubr` figure.
#'
#' @param x An object of class \code{cnaqc}, where CCF have been computed using
#' function `compute_CCF`.
#' @param strip If \code{TRUE}, shows little detail and a strip horizontal plot.
#' Otherwise it shows a detailed report (multiple rows). This parameter is now
#' deprecated.
#' @param empty_plot If data for one karyotype is missing, an empty plot is returned.
#' Otherwise the plot is not returned (NULL is forwarded).
#' @param assembly_plot If \code{TRUE}, a unique figure is returned with all the
#' plots assembled. Otherwise a list of plot is returned.
#'
#' @return A `ggpubr` figure of the CCF estimates.
#'
#' @export
#'
#' @examples
#' data('example_dataset_CNAqc')
#' x = init(mutations = example_dataset_CNAqc$mutations, cna =example_dataset_CNAqc$cna, purity = example_dataset_CNAqc$purity)
#'
#' x = compute_CCF(x)
#' plot_CCF(x)
plot_CCF = function(x,
                    strip = FALSE,
                    empty_plot = TRUE,
                    assembly_plot = TRUE)
{
  stopifnot(inherits(x, 'cnaqc'))

  with_CCF = all(!is.null(x$CCF_estimates))
  if(!with_CCF){
    warning("Input does not have CCF estimates, see ?compute_CCF to determine CCF values.")
    return(CNAqc:::eplot())
  }

  if(strip) {
    message("Parameter `strip` is deprecated - will not be used.")
    # return(CNAqc:::plot_CCF_strip(x))
  }

  method = x$CCF_estimates[[1]]$QC_table$method[1]

  USE_KARYOTYPES = c("1:0", '1:1', '2:0', '2:1', '2:2')
  ccf_plot = lapply(
    USE_KARYOTYPES,
    function(k)
    {
      if(!(k %in% names(x$CCF_estimates)))
      {
        if(empty_plot) return(CNAqc:::eplot())
        else return(NULL)
      }

      if(method == 'ENTROPY') return(suppressWarnings(plot_mutation_multiplicity_entropy(x, k)))
      if(method == 'ROUGH') return(suppressWarnings(plot_mutation_multiplicity_rough(x, k)))
      return(CNAqc:::eplot())
    }
  )

  ccf_plot = ccf_plot[!sapply(ccf_plot, is.null)]
  if(length(ccf_plot) == 0) {
    cli::cli_alert_warning("Nothing to plot")
    return(CNAqc:::eplot())
  }

  # Plots assembly
  if (assembly_plot)
    ccf_plot = ggpubr::ggarrange(
      plotlist = ccf_plot,
      ncol = length(ccf_plot),
      nrow = 1
    )

  return(ccf_plot)
}

plot_CCF_strip = function(x)
{
  stopifnot(inherits(x, 'cnaqc'))

  method = x$CCF_estimates[[1]]$QC_table$method[1]

  USE_KARYOTYPES = c("1:0", '1:1', '2:0', '2:1', '2:2')
  ccf_plot = lapply(
    USE_KARYOTYPES,
    function(k)
    {
      if(!(k %in% names(x$CCF_estimates))) return(CNAqc:::eplot())

      if(method == 'ENTROPY') return(suppressWarnings(plot_mutation_multiplicity_entropy_strip(x, k)))
      if(method == 'ROUGH') return(suppressWarnings(plot_mutation_multiplicity_rough_strip(x, k)))
      return(CNAqc:::eplot())
    }
  )

  ggpubr::ggarrange(
    plotlist = ccf_plot,
    nrow = 1,
    ncol = length(ccf_plot)
  )
}