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

## ----libraries----------------------------------------------------------------
library(ape)
library(phylobar)
library(microbiome)

## ----download-data------------------------------------------------------------
data(atlas1006)
pseq3 <- atlas1006 |>
    subset_samples(DNA_extraction_method == "r") |>
    transform(transform = "compositional")

## ----naive-tree---------------------------------------------------------------
tree <- taxonomy_to_tree(tax_table(pseq3))
checkValidPhylo(tree)

## ----valid-tree---------------------------------------------------------------
taxa <- tax_table(pseq3)
taxa <- cbind(Kingdom = "Bacteria", taxa)
taxa <- phylobar::add_prefix(taxa)

tree <- taxonomy_to_tree(taxa)
checkValidPhylo(tree)

## ----phylobar-full------------------------------------------------------------
x <- t(otu_table(pseq3))
phylobar(x, tree, sample_show_all = FALSE, rel_width = 0.2)

## ----phylobar-subset----------------------------------------------------------
x_sub <- subset_cluster(x)
x_sub <- x_sub[, colSums(x_sub) > 0]

leaves_to_keep <- intersect(tree$tip.label, colnames(x_sub))
filtered_tree <- drop.tip(tree, setdiff(tree$tip.label, leaves_to_keep))
phylobar(x_sub, filtered_tree)

## ----bray-curtis-result-------------------------------------------------------
x_sub_bc <- subset_cluster(x, method = "medoid")
x_sub_bc <- x_sub[, colSums(x_sub) > 0]

leaves_to_keep <- intersect(tree$tip.label, colnames(x_sub_bc))
filtered_tree <- drop.tip(tree, setdiff(tree$tip.label, leaves_to_keep))
phylobar(x_sub_bc, filtered_tree)

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