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

## ----setup--------------------------------------------------------------------
library(ape)
library(phylobar)
library(phyloseq)
library(miaViz)
library(scater)

## ----phyloseq-phylo-----------------------------------------------------------
data(GlobalPatterns, package = "phyloseq")
chlamydiae <- subset_taxa(GlobalPatterns, Phylum == "Chlamydiae")
x_phylo <- t(otu_table(chlamydiae))

## ----handle-zeros-------------------------------------------------------------
tree_phylo <- phy_tree(chlamydiae)
x_phylo <- x_phylo[rowSums(x_phylo) > 0, ]
x_phylo <- x_phylo / rowSums(x_phylo)

## ----phylobar-phyloseq--------------------------------------------------------
phylobar(x_phylo, tree_phylo, width = 900)

## ----phyloseq-taxonomy--------------------------------------------------------
taxa <- tax_table(chlamydiae) |>
    as.data.frame()
taxa$ASV <- rownames(taxa)
taxa <- phylobar::add_prefix(taxa)

## ----construct_taxonomy-------------------------------------------------------
tax_tree <- taxonomy_to_tree(taxa)
plot(tax_tree)

## ----phylobar-taxon-----------------------------------------------------------
phylobar(x_phylo, tax_tree, width = 900)

## ----tse-data-prep------------------------------------------------------------
data(GlobalPatterns, package = "mia")
prev_species <- getPrevalent(GlobalPatterns, rank = "Species", detection = 0.01)
GlobalPatterns_tse <- GlobalPatterns[
    rowData(GlobalPatterns)$Species %in% prev_species,
]
GlobalPatterns_tse <- transformAssay(
    GlobalPatterns_tse,
    method = "relabundance"
)

## ----tse-phylobar-x-----------------------------------------------------------
x_tse <- t(assay(GlobalPatterns_tse, "relabundance"))
x_tse <- x_tse[, colSums(x_tse) > 0]
tree_tse <- rowTree(GlobalPatterns_tse) |>
    keep.tip(colnames(x_tse))

## ----phylobar-tse-------------------------------------------------------------
phylobar(x_tse, tree_tse, width = 900)

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