Run ANCOMBC2 on phyloseq object — ancombc

A wrapper for the ancombc2() function

Usage

ancombc_pq(physeq, fact, levels_fact = NULL, tax_level = "Class", ...)

Arguments

physeq: (required) a phyloseq-class object obtained using the phyloseq package.
fact: (required) Name of the factor in physeq@sam_data used to plot different lines
levels_fact: (default NULL) The order of the level in the factor. Used for reorder levels and select levels (filter out levels not present en levels_fact)
tax_level: (default NULL) The taxonomic level passed on to ancombc2(). If NULL do not perform agglomeration, and the ANCOM-BC2 analysis will be performed at the lowest taxonomic level of the input data.
...: Additional arguments passed on to ancombc2() function.

Value

The result of ancombc2() function

Details

This function is mainly a wrapper of the work of others. Please make a reference to ancombc2() if you use this function.

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
if (requireNamespace("mia")) {
  data_fungi_mini@tax_table <- phyloseq::tax_table(cbind(
    data_fungi_mini@tax_table,
    "taxon" = taxa_names(data_fungi_mini)
  ))
  res_height <- ancombc_pq(
    data_fungi_mini,
    fact = "Height",
    levels_fact = c("Low", "High"),
    verbose = TRUE
  )

  ggplot(
    res_height$res,
    aes(
      y = reorder(taxon, lfc_HeightHigh),
      x = lfc_HeightHigh,
      color = diff_HeightHigh
    )
  ) +
    geom_vline(xintercept = 0) +
    geom_segment(aes(
      xend = 0, y = reorder(taxon, lfc_HeightHigh),
      yend = reorder(taxon, lfc_HeightHigh)
    ), color = "darkgrey") +
    geom_point()

  res_time <- ancombc_pq(
    data_fungi_mini,
    fact = "Time",
    levels_fact = c("0", "15"),
    tax_level = "Family",
    verbose = TRUE
  )
}
} # }