R/plot_signatures.R

In caravagnalab/basilica: bascule

#' Function to visualize the estimated and reference signatures.
#'
#' @param x bascule object.
#' @param types List of variant types to visualize.
#' @param context Logical. If `TRUE`, context names will be reported on the x axis.
#' @param cls Custom color palette for signatures.
#' @param signames List of signatures to visualize.
#'
#' @return ggplot object.
#' @export plot_signatures
plot_signatures = function(x, types=get_types(x), context=T, cls=NULL,
                           signames=get_signames(x)) {

  signatures = lapply(types, function(tid)
    get_signatures(x, types=tid)[[tid]] %>%
      reformat_contexts(what=tid) %>%
      dplyr::mutate(type=tid)) %>%
    do.call(rbind, .) %>% dplyr::filter(sigs %in% unlist(signames))

  if (is.null(cls)) {
    cls = gen_palette(x, types=types)
  } else if (!is.character(cls)) {
    stop("cls must be character")
  } else if ( !(length(cls)==length(unlist(signames))) ) {
    stop("cls must be same length as the number of signatures.")
  }

  lapply(types, function(t) plot_signatures_aux(signatures %>% dplyr::filter(type==t),
                                                what=t, context=context, cls=cls)) %>%
    purrr::discard(is.null) %>%
    patchwork::wrap_plots(ncol=length(.))
}



plot_signatures_aux = function(signatures, what="SBS",
                               context=T, cls=NULL, signames=NULL) {

  if (nrow(signatures) == 0) return(NULL)

  if (is.null(signames)) signames = signatures$sigs %>% unique()
  if (is.null(cls)) cls = gen_palette(n=length(unlist(signames)))

  p = signatures %>%
    ggplot() +
    geom_bar(aes(value, x=context, fill=sigs), stat="identity") +
    ggh4x::facet_nested(sigs ~ type + factor(variant, levels=signatures$variant %>% unique()), scales="free") +
    theme_bw() +
    scale_fill_manual(values=cls) +
    theme(axis.text.x=element_text(angle=90), legend.position="bottom") +
    guides(fill="none") +
    labs(y="", x="")

  if(!context)
    p = p + theme(axis.ticks.x=element_blank(), axis.text.x=element_blank()) + labs(x="")

  return(p)
}