Plot a network with modules as an adjacency matrix

Usage

plot_extant_matrix(
  net,
  modules = NULL,
  module_order = NULL,
  find_modules = TRUE,
  parasite_order = NULL,
  host_order = NULL,
  state_alpha = c(0.5, 1)
)

Arguments

net: An adjacency matrix for a bipartite network. Parasites should be the rows, hosts should be columns. If all values are 0/1 (or 0/2), a binary network is represented; if all values are 0/1/2, a network with potential and actual interactions is represented; otherwise a weighted network is assumed.
modules: A moduleWeb or a data.frame object defining the models in the network. If left NULL the modules are automatically calculated. 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?
parasite_order: A character vector giving the order the parasite should be listed in. Should contain each parasite only once, and include the row names of net.
host_order: A character vector giving the order the hosts should be listed in. Should contain each host only once, and include the column names of net.
state_alpha: A numeric vector of length 2. Gives the alpha (transparency) values for the interaction type in the three-state model

Value

A ggplot object.

Examples

if (FALSE) {
  # The slow portion of this function is the calculation of the modules.
  plot_extant_matrix(extant_net)

  # Change our network to a weighted one:
  extant_net_weighted <- extant_net
  extant_net_weighted[extant_net == 1] <- runif(sum(extant_net))
  plot_extant_matrix(extant_net_weighted)
}