plot.lcm_tree: plots the groups discovered by lcm_tree on the tree for...

In zhenkewu/lotR: Latent class analysis with Observed Trees in R (lotR)

plots the groups discovered by lcm_tree on the tree for observations.

Description

plots the groups discovered by lcm_tree on the tree for observations.

Usage

## S3 method for class 'lcm_tree'
plot(
  x,
  layout = "circular",
  colnames_offset_y = 0,
  font_size = 4,
  heatmap_width = 1,
  add_scale = FALSE,
  ...
)

Arguments

x	An lcm_tree class object; Output from lcm_tree()
layout	layout for the tree, by default it is "circular"; other layouts such as "rectangular" can run, but currently has issues.
colnames_offset_y	default is 0; see gheatmap from ggtree.
font_size	default is 4; see gheatmap from ggtree
heatmap_width	default is 1; see gheatmap from ggtree.
add_scale	logical; add a scale for the branch lengths; default to FALSE
...	Not used.

Value

A plot showing the groups discovered by MOReTreeS on the original leaf_ids tree.

References

https://guangchuangyu.github.io/ggtree-book/chapter-ggtree.html#tree-annotation-using-data-from-evolutionary-analysis-software

Examples

# See vignette

zhenkewu/lotR documentation built on April 24, 2022, 2:36 a.m.