draw_cophy: Internal tree plot function

In treeducken: Nested Phylogenetic Tree Simulator

Description

internal plot function from ape::plotCophylo2 under GPL v. 2

Usage

draw_cophy(
  x,
  y,
  assoc = assoc,
  use_edge_length = use_edge_length,
  length_line = length_line,
  type = type,
  return = return,
  col = col,
  lwd = lwd,
  lty = lty,
  show_tip_label = show_tip_label,
  font = font,
  fsize = fsize,
  gap = gap,
  show_scalebar = show_scalebar,
  scalebar_fsize = scalebar_fsize,
  ...
)

Arguments

x	Host tree as phylo object
y	Symb tree as phylo object
assoc	Association matrix
use_edge_length	Boolean to draw trees with edge length or not
length_line	Length of interactions lines
type	string "phylogram" or "cladogram"
return	Return an object or no (default = FALSE)
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
font	What font to use (bold, italic (default), etc.)
fsize	What size font as a character expansion factor (same as cex)
gap	Gap between tips and tip names
show_scalebar	Boolean for turning on and off the scalebar
scalebar_fsize	Font size of scalebar
...	Other plotting parameters

References

Paradis E. & Schliep K. 2019. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35: 526-528.

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