plot.cophy: Plot host and symbiont pair with current associations

In treeducken: Nested Phylogenetic Tree Simulator

Description

This function plots a host and symbiont tree given the object returned by 'sim_cophyBD'.

Usage

## S3 method for class 'cophy'
plot(
  x,
  use_edge_length = TRUE,
  type = "phylogram",
  col = par("fg"),
  lwd = par("lwd"),
  lty = par("lty"),
  show_tip_label = TRUE,
  gap = 1,
  font = 3,
  fsize = 1,
  show_div_bar = FALSE,
  ...
)

## S3 method for class 'multiCophy'
plot(x, ...)

Arguments

x	object of class multiCophy
use_edge_length	Boolean to draw trees with edge length or not
type	string "phylogram" or "cladogram"
col	What color to draw links between trees
lwd	Width of links between trees
lty	Type of line to draw between trees
show_tip_label	Boolean for showing labels
gap	Size of the gap between the tips and tip names
font	What font to use (bold, italic (default), etc.)
fsize	What size font as a character expansion factor (same as cex)
show_div_bar	Shows a bar under both trees with ticks where the divergences are (default: F)
...	other plotting parameters

Details

This function is mostly an altered version of the cophyloplot function written by Damien de Vienne Copyright 2008 - 2010 under GPL.

Value

a plot of the host and symbiont tree with extant interactions

Functions

• plot.multiCophy: Plots multiple cophy plots

Author(s)

Wade Dismukes and Damien de Vienne

Examples

host_mu <- 1.0 # death rate
host_lambda <- 2.0 # birth rate
numb_replicates <- 10
time <- 1.0
symb_mu <- 0.2
symb_lambda <- 0.4
host_shift_rate <- 0.0
cosp_rate <- 2.0

cophylo_pair <- sim_cophyBD(hbr = host_lambda,
                           hdr = host_mu,
                           cosp_rate = cosp_rate,
                           host_exp_rate = host_shift_rate,
                           sdr = symb_mu,
                           sbr = symb_lambda,
                           numbsim = numb_replicates,

                           time_to_sim = time)
plot.cophy(cophylo_pair[[1]])

treeducken documentation built on March 3, 2021, 1:11 a.m.