R/plot_patient_trees.R

In caravagn/revolver: REVOLVER - Repeated Evolution in Cancer

#' Plot REVOLVER trees for a patient.
#'
#' @description
#'
#' This function is like \code{plot_data}, as it uses base plotting
#' functions to assemble a summary plot for a patient. This function
#' assembled the plot via \code{ggpubr}. The first line of plots
#' represents the top tree for a patient, and its information transfer.
#' The strip below represents up to the top-10 trees for this patient,
#' as they are obtained from the standard tree-scoring (which means
#' that the score is not accounting for the actual transfer, but just
#' for the tree structure).
#'
#' @param x A REVOLVER cohort object
#' @param patient The patient for which the trees should be plot
#'
#' @param ... Extra parameters, not used.
#'
#' @return A figure assembled with \code{ggpubr}.
#'
#' @export
#'
#' @import ggpubr
#' @import ctree
#' @import mtree
#'
#' @examples
#' # Data released in the 'evoverse.datasets'
#' data('TRACERx_NEJM_2017_REVOLVER', package = 'evoverse.datasets')
#'
#' # This returns a figure assembled with ggpubr
#' plot_patient_trees(TRACERx_NEJM_2017_REVOLVER, patient = 'CRUK0002')
plot_patient_trees = function(x, patient, ...)
{
  if(!has_patient_trees(x, patient))
    stop(patient, " does not have the patient trees, aborting.")

  cex = 1
  
  # =-=-=-=-=-=-=-=-
  # Top panel: top-ranking tree and its information transfer
  # =-=-=-=-=-=-=-=-
  top_tree = Phylo(x, patient, rank = 1)

  first = ggarrange(
    top_tree %>% plot,
    top_tree %>% plot_information_transfer,
    ncol = 2,
    nrow = 1
  )

  # =-=-=-=-=-=-=-=-
  # Second panel: top-10 ranking trees in icon format
  # =-=-=-=-=-=-=-=-

  # Other 10 trees in 1x10 icon format
  ntrees =  min(
    Stats_trees(x, patient)$numTrees,
    10)

  # Strip plot
  strip = lapply(1:ntrees, Phylo, x = x, p = patient)
  strip = lapply(strip, plot_icon)

  scores = plot_patient_trees_scores(x, patient)

  strip = ggarrange(
    plotlist = append(strip, list(scores)),
    nrow = 1, ncol = 11)

  second = annotate_figure(
    strip,
    fig.lab = paste0("Top-",  ntrees, ' trees'))

  # Assembly
  ggarrange(
    first,
    second,
    heights = c(1, .3),
    ncol = 1,
    nrow = 2
  )
}