plot_tree_with_post: Plot a tree and the PGLMM posterior on phylogenetic effects

In biobakery/anpan: Quantifying Microbial Strain-Host Associations

Plot a tree and the PGLMM posterior on phylogenetic effects

Description

Plot a tree and the PGLMM posterior on phylogenetic effects

Usage

plot_tree_with_post(
  tree_file,
  meta_file,
  fit,
  labels,
  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
fit	a pglmm fit from anpan_pglmm()
labels	the ordered tip labels from the tree
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.

Details

The whiskers of each box plot are the 90% posterior intervals, the box is the 50% interval, and the middle line is the posterior mean.

The labels needs to contain the leaf labels in the order produced by the Cholesky factorization of the correlation matrix (which is how the data are passed to the sampler). This is not necessarily the order of the leaves on the x-axis of the tree, nor the order of the samples in the metadata. The simplest way to get the sample_ids in the proper order is to take the sample_id column from the model_input result from anpan_pglmm().

Value

either the plot or (if return_tree_df = TRUE) a list containing the plot, the segment df, the terminal segment df, and the yrep df.

Examples

## Not run: 
# Using the result simulated in the vignette:
plot_tree_with_post(tr, metadata,
                    fit        = result$pglmm_fit,
                    labels     = result$model_input$sample_id,
                    outcome    = 'outcome',
                    covariate  = 'covariate',
                    color_bars = TRUE)

## End(Not run)

biobakery/anpan documentation built on Aug. 14, 2024, 8:19 a.m.