Plot a network with modules as an adjacency matrix, with aligned phylogenies.

Usage

plot_matrix_phylo(
  net,
  at_nodes,
  tree,
  host_tree,
  type = "states",
  state = 2,
  repertoire = "fundamental",
  modules = NULL,
  module_order = NULL,
  find_modules = TRUE,
  threshold = 0.9,
  point_size = 3,
  dodge_width = 0.025,
  colors = NULL,
  ladderize = FALSE
)

Arguments

net

An adjacency matrix for a bipartite network. This should be the extant network. Parasites should be the rows, hosts should be columns. If all values are 0 or 1 an binary network is represented, otherwise a weighted network is assumed.

at_nodes

A list of length 2, output from posterior_at_nodes().

tree

The phylogeny of the symbiont clade (e.g. parasites, herbivores). Object of class phylo.

host_tree

The phylogeny belonging to the hosts. Object of class phylo.

See the examples on how to change the color scale.

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.

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.

find_modules

Logical. Search for modules if nothing is provided in modules?

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.

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.

colors

Override the default colors. Should be a character vector with as many color values as there are modules.

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

An assembly of plots, of class patchwork.

Examples

if (FALSE) {
  # 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)
  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)

  # plot
  plot_matrix_phylo(extant_net, at_nodes, tree, host_tree)
  # manual_colors
  plot_matrix_phylo(extant_net, at_nodes, tree, host_tree, colors = rainbow(20))
}