plot_ancestral_states: Plot ancestral states on the phylogeny.

In maribraga/evolnets: Reconstruct Ancestral Networks Inferred In RevBayes

Plot ancestral states on the phylogeny.

Description

Plot ancestral states on the phylogeny.

Usage

plot_ancestral_states(
  tree,
  at_nodes,
  modules,
  module_order = NULL,
  type = "states",
  state = 2,
  repertoire = "fundamental",
  layout = "rectangular",
  threshold = 0.9,
  point_size = 3,
  point_shape = NULL,
  dodge_width = 0.025,
  legend = TRUE,
  colors = NULL,
  state_alpha = c(0.5, 1),
  ladderize = FALSE
)

Arguments

tree	The phylogeny, a phylo object.
at_nodes	A list of length 2, output from posterior_at_nodes().
modules	A moduleWeb or a data.frame object defining the modules in the network. If a data.frame is passed, it must contain three columns: $name with taxon names, $module with the module the taxon was assigned to, and $type which defines if the taxon is a "host" or a "symbiont".
module_order	A character vector giving the order that modules should be plotted. Should contain each module only once.
type	One of 'states' or 'repertoires'. If 'states', will plot the presence of a state when its posterior probability is higher than threshold. If 'repertoires', will plot the same but for the given repertoire.
state	Which state? Default is 2. For analyses using the 3-state model, choose 1 or 2 (where 1 is a potential host and 2 an actual host). Only used if type is 'states'.
repertoire	Either the 'realized' repertoire which is defined as state 2, or the 'fundamental' repertoire (default) which is defined as having any state (usually 1 or 2), and in the 3-state model includes both actual and potential hosts.
layout	One of 'rectangular', 'slanted', 'fan', 'circular', 'radial', 'equal_angle', 'daylight' or 'ape'.
threshold	The posterior probability above which the ancestral states should be shown. Defaults to 90% (0.9). Numeric vector of length 1.
point_size	How large the ancestral state points should be, default at 3. Play with this and dodge_width to get a pleasing result. Numeric vector of length 1.
point_shape	What point shape should be used for the ancestral states? When left NULL, a reasonable default will be chosen. Otherwise, a numeric vector of length 1.
dodge_width	How far the points should be pushed apart, when there is multiple states at a single node, default at 0.025. Play with this and point_size to get a pleasing result. Numeric vector of length 1.
legend	Whether to display a legend for the colors. Logical vector of length 1.
colors	Override the default colors. Should be a character vector with as many color values as there are modules.
state_alpha	A numeric vector of length 2. Gives the alpha (transparency) values for the interaction type in the three-state model
ladderize	Logical. Whether to ladderize the tree. Default to FALSE. The ancestral states are automatically colored by module. To change what colors are used, you can add color scales to the resulting ggplot, e.g. ggplot2::scale_color_manual().

Value

A ggplot object.

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 <- read.tree(paste0(data_path,"/host_tree_pieridae.phy"))
  history <- read_history(paste0(data_path,"/history_thin_pieridae.txt"), burnin = 0)
  extant_net <- read.csv(paste0(data_path,"/interaction_matrix_pieridae.csv"), row.names = 1)

  # calculate posterior probability of interactions at internal nodes
  at_nodes <- posterior_at_nodes(history, tree, host_tree, 66 + 1:65)

  # find modules in the extant network
  mods <- mycomputeModules(extant_net)

  # plot ancestral states
  plot_ancestral_states(tree, at_nodes, mods)
  # Manual colors
  plot_ancestral_states(tree, at_nodes, mods, colors = rainbow(20))

## End(Not run)

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