plot_tree: Plots an ape phylo tree

In NickWilliamsSanger/rsimpop: Simulates Cellular Evolution using a Continous Time Birth Death Model

Plots an ape phylo tree

Description

This is similar to APE plot.phylo but returns useful information on each branch to facilitate annotation of tree. Be careful not to unintentionally supply population scale simpop

Usage

plot_tree(
  tree,
  direction = "down",
  cex.label = 1,
  offset = 0,
  b_do_not_plot = FALSE,
  lwd = 1,
  bars = NULL,
  default_edge_color = "darkgrey",
  ymax = NULL,
  cex.terminal.dots = 0,
  mar = NULL,
  b.add.scale = TRUE,
  left.margin.prop = 0.1
)

Arguments

tree	phylo/simpop
direction	character. Only "down" is currently supported.
cex.label	numeric. Size of tip labels (0 results in no tip labels)
offset	numeric (0-1). Fractional offset of tip labels from branch terminus
b_do_not_plot	Boolean.
lwd	numeric. Line width
bars	numeric. vector with named elements that should all match tip labels - adds barplot under tree.
default_edge_color	colour.
ymax	numeric max y
cex.terminal.dots	numeric - size of terminal dots
mar	numeric vector Override default resetting of mar as in par("mar")
b.add.scale	Boolean - whether to add scale axis
left.margin.prop	numeric - leaves this fraction empty on left

Value

simpop object

Examples

test=rtree(20)
tree=plot_tree(test,cex.terminal=0.5,bars=sapply(sprintf("s%d",seq(2,20,2)),function(x) runif(1)))
node_labels(tree)

NickWilliamsSanger/rsimpop documentation built on Sept. 6, 2024, 12:42 a.m.