plot_tree_with_post_pred: Plot a tree and the PGLMM posterior predictive
In biobakery/anpan: Quantifying Microbial Strain-Host Associations

plot_tree_with_post_pred

R Documentation

Plot a tree and the PGLMM posterior predictive

Description

Plot a tree and the PGLMM posterior predictive

Usage

plot_tree_with_post_pred(
  tree_file,
  meta_file,
  covariates = c("age", "gender"),
  offset = NULL,
  outcome = "crc",
  omit_na = FALSE,
  ladderize = TRUE,
  color_bars = FALSE,
  verbose = TRUE,
  fit,
  labels,
  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.
`fit`	a pglmm fit from `anpan_pglmm()`
`labels`	the ordered tip labels from the tree
`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.

Details

The whiskers of each box plot are the 90 box is the 50 case of binary outcomes, the dot for each leaf represents the mean of the posterior predictions (which is a proportion).