draw.incompletely.sampled: For a sample with or without unsampled hosts, draw the...

In STraTUS: Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny

Description

For a sample with or without unsampled hosts, draw the annotated phylogeny using ggtree

Usage

draw.incompletely.sampled(generator, sample)

Arguments

generator	A list of class tt.generator produced by tt.generator.
sample	A list of class tt produced by sample.tt or sample.partial.tt

Value

A ggtree object

Examples

generator <- tt.generator(stratus.example.tree, max.unsampled = 2)
samples <- sample.tt(generator, 1, unsampled=2)
# Tree is annotated with the number of unsampled hosts along each branch
draw.incompletely.sampled(generator, samples[[1]])
# This still works if there are no unsampled hosts
samples <- sample.tt(generator, 1)
draw.incompletely.sampled(generator, samples[[1]])

STraTUS documentation built on April 4, 2020, 5:07 p.m.