## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    message = FALSE,
    warning = FALSE
)

## ----load-libs----------------------------------------------------------------
library(phylobar)
library(phyloseq)
library(DESeq2)

## ----download-data------------------------------------------------------------
data("dietswap", package = "microbiome")
diet_temp <- subset_samples(dietswap, timepoint == 1)
diet <- subset_taxa(diet_temp, taxa_sums(diet_temp) > 0)

## ----preprocess---------------------------------------------------------------
otu <- as(otu_table(diet), "matrix")
x <- t(deseq_normalize(otu))

## ----build-tree---------------------------------------------------------------
taxa <- tax_table(diet) |>
    phylobar::add_prefix()
taxa <- cbind(Kingdom = "k_Bacteria", taxa)
tree <- taxonomy_to_tree(taxa)

## ----render-phylobar----------------------------------------------------------
phylobar(x, tree, width = 800)

## ----session-info-------------------------------------------------------------
sessionInfo()