ts_draw: Plot a graphical representation of a single tree

In bodkan/slendr: A Simulation Framework for Spatiotemporal Population Genetics

Plot a graphical representation of a single tree

Description

This function first obtains an SVG representation of the tree by calling the draw_svg method of tskit and renders it as a bitmap image in R. All of the many optional keyword arguments of the draw_svg method can be provided and will be automatically passed to the method behind the scenes.

Usage

ts_draw(
  x,
  width = 1000,
  height = 1000,
  labels = FALSE,
  sampled_only = TRUE,
  title = NULL,
  ...
)

Arguments

x	A single tree extracted by ts_tree
width, height	Pixel dimensions of the rendered bitmap
labels	Label each node with the individual name?
sampled_only	Should only individuals explicitly sampled through simplification be labeled? This is relevant in situations in which sampled individuals can themselves be among the ancestral nodes.
title	Optional title for the figure
...	Keyword arguments to the tskit draw_svg function.

Value

No return value, called for side effects

Examples

init_env()

# load an example model with an already simulated tree sequence
slendr_ts <- system.file("extdata/models/introgression_slim.trees", package = "slendr")
model <- read_model(path = system.file("extdata/models/introgression", package = "slendr"))

# load the tree-sequence object from disk
ts <- ts_read(slendr_ts, model)

# extract the first tree in the tree sequence and draw it
tree <- ts_tree(ts, i = 1)

# ts_draw accepts various optional arguments of tskit.Tree.draw_svg
ts_draw(tree, time_scale = "rank")

bodkan/slendr documentation built on Dec. 19, 2024, 11:41 p.m.