There should be an exported function that plots the true model

[rdiaz02]

This works for DAGs

plot_model <- function(x, main = "") {
    method_info <- igraph::graph_from_data_frame(x[, c("From", "To")])
    parent_set <- evamtools:::parent_set_from_edges(x)
    evamtools:::plot_method(method_info = method_info,
                            parent_set = parent_set,
                            edges = x, 
                            method = main)
  }

where is the usual data frame with From, To, etc.

Improve and do something similar for MHN.

The above is simplified from plot_evam in file evam_plotting.R

[rdiaz02]

And it should also include the paths (transitions) between genoytpes:

plot_hypercube_transitions <- function(x, main = "") {
    obj <- list(edges = x,
                parent_set = evamtools:::parent_set_from_edges(x))
    tmat <- as.matrix(evamtools:::cpm2tm(obj)$trans_mat_genots)
    evamtools:::plot_genot_fg(tmat, plot_type = "trans_mat")
  }
  
So we can do
  pdf(file = "true_models.pdf", width = 11, height = 11)
  par(mfrow = c(2, 2))
  par(oma = c(2, 2, 2, 2))
  plot_model(dag1)
  plot_model(dag2)
  plot_hypercube_transitions(dag1)
  title("dag1: \nTrue transitions between genotypes")
  plot_hypercube_transitions(dag2)
  title("dag2: \nTrue transitions between genotypes")
  dev.off()