R/plot_other.R

In caravagnalab/basilica: bascule

plot_mixture_weights = function(x, empirical=FALSE) {

  if (empirical) {
    pis = get_cluster_assignments(x) %>%
      dplyr::group_by(clusters) %>%
      dplyr::summarise(value=dplyr::n()) %>%
      dplyr::ungroup() %>%
      dplyr::mutate(value=value)
  } else {
    pis = get_mixing_proportions(x)
  }

  if (!have_groups(x) || is.null(pis)) return(NULL)
  cls = gen_palette(n=nrow(pis)) %>% setNames(pis$clusters)

  return(
    pis %>%
      ggplot() +
      geom_bar(aes(x=clusters, y=value, fill=clusters), stat="identity") +
      scale_fill_manual(values=cls) +
      guides(fill="none") +
      xlab("Clusters") + theme_bw() +
      theme(axis.title.y.right=element_text(angle=90))
  )
}


plot_beta_star = function(x, types=get_types(x)) {
  lapply(types, function(tid) {
    get_params(x, what="nmf", type=tid)[[1]]$beta_star %>%
      as.data.frame() %>%
      wide_to_long(what="beta") %>%
      reformat_contexts(what=tid) %>%
      dplyr::mutate(type=tid)
  }) %>% do.call(rbind, .) %>%
    plot_signatures_aux()
}


plot_alpha_star = function(x, types=get_types(x)) {
  lapply(types, function(tid) {
    get_params(x, what="nmf", type=tid)[[1]]$alpha_star %>%
      as.data.frame() %>%
      wide_to_long(what="exposures") %>%
      dplyr::mutate(type=tid)
  }) %>% do.call(rbind, .) %>%
    plot_exposures_aux()
}


plot_beta_weights = function(x, types=get_types(x)) {
  beta_w = get_beta_weights(x, types=types)
  if (is.null(beta_w)) return(NULL)

  beta_w %>%
    ggplot() +
    geom_point(aes(x=sigs, y=sigid, size=value)) +
    facet_grid(~type, scales="free") +
    theme_bw()
}