Plot positional variance diagram

Usage

plot_positional_var(
  results,
  samples_sequence = results$samples_sequence,
  samples_f = results$samples_f,
  n_samples = nrow(results$ml_subtype),
  score_vals = build_score_vals(biomarker_levels),
  biomarker_labels = labelled:::var_label.data.frame(biomarker_levels, null_action =
    "fill", unlist = TRUE),
  biomarker_groups = attr(results, "biomarker_groups"),
  biomarker_levels = attr(results, "biomarker_levels"),
  biomarker_events_table = get_biomarker_events_table(biomarker_levels),
  biomarker_event_names = get_biomarker_event_names(biomarker_events_table),
  biomarker_plot_order = NULL,
  ml_f_EM = NULL,
  cval = FALSE,
  subtype_order = seq_len(dim(samples_sequence)[1]),
  biomarker_order = NULL,
  title_font_size = 12,
  stage_font_size = 10,
  stage_label = "Sequential order",
  stage_rot = 0,
  stage_interval = 1,
  label_font_size = 10,
  label_rot = 0,
  cmap = "original",
  biomarker_colours = NULL,
  subtype_titles = NULL,
  separate_subtypes = FALSE,
  save_path = NULL,
  save_kwargs = NULL,
  synchronize_y_axes = FALSE,
  use_labels = TRUE,
  ...
)

Arguments

results

todo

samples_sequence

todo

samples_f

todo

n_samples

todo

score_vals

todo

biomarker_labels

todo

biomarker_groups

biomarker groupings

biomarker_levels

doesn't do much right now

biomarker_events_table

todo

biomarker_event_names

todo

biomarker_plot_order

todo

ml_f_EM

todo

cval

todo

subtype_order

todo

biomarker_order

todo

title_font_size

todo

stage_font_size

todo

stage_label

todo

stage_rot

todo

stage_interval

todo

label_font_size

todo

label_rot

todo

cmap

a character

biomarker_colours

a character vector of colors

subtype_titles

todo

separate_subtypes

todo

save_path

todo

save_kwargs

todo

synchronize_y_axes

todo

use_labels

whether to use biomarker labels or variable names

...

Arguments passed on to autoplot.PF

object: a "PF" object (created by compute_position_frequencies())
size.y: size of biomarker event labels
color_label: label for legend color scale

Value

a "PVD_list (a list of PVD objects from autoplot.PF())

Examples

if (FALSE) { # \dontrun{
  output_folder <-
    "output/output.fixed_CV-scid-no-subthres/"

  results <-
    output_folder |>
    extract_results_from_pickle(
      output_folder = _,
      n_s = 1,
      use_rds = TRUE
    )

  plot1 <-
    plot_positional_var(
      results = results,
      use_labels = TRUE)

  plot1 |>
    vdiffr::expect_doppelganger(title = "plot1")
} # }