Visualize Host-Symbiont Codiversification

Draws a tanglegram: the host tree on the left, the symbiont tree mirrored on the right, and a line for each host-symbiont association. Optionally rotates the symbiont tree to align it with the host tree and colours the association lines.

Usage

plot_codiv_trees(
  Host_tree,
  Symbiont_tree,
  Host_to_Symbiont_df,
  codiv_results = NULL,
  color_by = c("host", "none", "significance"),
  significance_threshold = 0.05,
  line_width = 0.5,
  line_alpha = 0.6,
  title = NULL,
  use_procrustes = TRUE,
  show_host_labels = TRUE,
  show_symbiont_labels = FALSE,
  label_size = 3.2,
  use_branch_lengths = FALSE
)

Arguments

Host_tree

A phylo object; host phylogenetic tree

Symbiont_tree

A phylo object; symbiont phylogenetic tree

Host_to_Symbiont_df

A data frame with columns "Host" and "Symbiont" linking symbionts to hosts

codiv_results

Optional codiv() result; required for color_by = "significance"

color_by

How to colour the association lines: "host" (default, by host), "none", or "significance" (symbionts in significant nodes)

significance_threshold

p-value threshold for color_by = "significance"; default 0.05

line_width

Width of the association lines; default 0.5

line_alpha

Transparency of the association lines (0-1); default 0.6

title

Plot title; default NULL

use_procrustes

If TRUE (default), rotate the symbiont tree to align it with the host tree and reduce line crossings

show_host_labels

If TRUE (default), label host tips

show_symbiont_labels

If TRUE, label symbiont tips; default FALSE (symbiont trees are often large)

label_size

Tip label text size; default 3.2

use_branch_lengths

If FALSE (default), use a cladogram layout (tips aligned, nodes spread by topology) for an uncluttered view; if TRUE, scale horizontal position by branch length

Value

A ggplot object, customizable with further ggplot2 layers and saveable with ggplot2::ggsave().

Details

Requires the ggplot2 package. The tree layout is computed with ape and the alignment uses ape::rotateConstr(). By default a cladogram layout is used (tips aligned, nodes spread by topology); set use_branch_lengths = TRUE to position nodes by branch length instead.

Examples

# \donttest{
if (requireNamespace("ggplot2", quietly = TRUE)) {
  sim <- simulate_codiv_data(n_hosts = 8, n_clades = 2, seed = 1)
  plot_codiv_trees(sim$host_tree, sim$symbiont_tree, sim$links,
                   color_by = "host")
}

# }