plot_ancestral_networks: Plot ancestral networks with module information

In maribraga/evolnets: Reconstruct Ancestral Networks Inferred In RevBayes

Plot ancestral networks with module information

Description

Plot ancestral networks with module information

Usage

plot_ancestral_networks(
  summary_networks,
  matched_modules,
  tree,
  module_levels = NULL,
  colors = NULL,
  node_size = NULL,
  level_names = c("Host", "Symbiont")
)

Arguments

summary_networks	A list of incidence matrices (summary network) for each time slice in ages. Output of get_summary_network()
matched_modules	A list of lists containing the module information for each node at each network. Output of modules_across_ages().
tree	The phylogeny of the symbiont clade (e.g. parasites, herbivores). Object of class phylo.
module_levels	Order in which the modules should be organized. Affects which color each module will be assigned. If NULL, takes the order of appearance in matched_modules$module.
colors	Color vector used to plot module information.
node_size	Size of the nodes in every network. If NULL, the default size is plotted.
level_names	Optional string vector with two elements used by legend: name of the clade modeled as "host" and the name of the clade modeled as "symbiont".

Value

A list of plots of class patchwork. Each element contains the tree and network at a given time slice.

Examples

## Not run: 
  # read data that comes with the package
  data_path <- system.file("extdata", package = "evolnets")
  tree <- read_tree_from_revbayes(paste0(data_path,"/tree_pieridae.tre"))
  host_tree <- ape::read.tree(paste0(data_path,"/host_tree_pieridae.phy"))
  history <- read_history(paste0(data_path,"/history_thin_pieridae.txt"), burnin = 0)

  # find and match modules of summary networks at ages
  ages <- c(60, 50, 40, 0)
  at_ages <- posterior_at_ages(history, ages, tree, host_tree)
  summary_networks <- get_summary_networks(at_ages, threshold = 0.5, weighted = TRUE)
  all_mod <- modules_across_ages(summary_networks, tree)

  # plot
  plot <- plot_ancestral_networks(summary_networks, all_mod, tree)
  patchwork::wrap_plots(plot, guides = "collect")

## End(Not run)

maribraga/evolnets documentation built on Feb. 3, 2025, 6:46 p.m.