plot_outcome_tree: Plot a tree file showing the outcome variable
In biobakery/anpan: Quantifying Microbial Strain-Host Associations

plot_outcome_tree

R Documentation

Plot a tree file showing the outcome variable

Description

Plot a tree file, and show the outcome variable as a colored dot on the end of each tip.

Usage

plot_outcome_tree(
  tree_file,
  meta_file,
  covariates = c("age", "gender"),
  offset = NULL,
  outcome = "crc",
  omit_na = FALSE,
  ladderize = TRUE,
  color_bars = FALSE,
  verbose = TRUE,
  trim_pattern = NULL,
  return_tree_df = FALSE
)

Arguments

`tree_file`	either a path to a tree file readable by ape::read.tree() or an object of class "phylo" that is already read into R.
`meta_file`	either a data frame of metadata or a path to file containing the metadata
`covariates`	covariates to account for (as a vector of strings)
`offset`	a variable to include as an offset
`outcome`	the name of the outcome variable
`omit_na`	logical indicating whether to omit incomplete cases of the metadata
`ladderize`	logical indicating whether to run `ape::ladderize()` on the tree before running the model
`color_bars`	if true, show color bars below the plot showing the covariates and outcome variables.
`trim_pattern`	optional pattern to trim from tip labels of the tree
`return_tree_df`	if true, return a list containing 1) the plot, 2) the segment data frame, and 3) the labelled terminal segment data frame. Otherwise, just return the plot.