plot_ancombc_pq: Plot ANCOMBC2 result for phyloseq object

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Plot ANCOMBC2 result for phyloseq object

Description

Graphical representation of ANCOMBC2 result.

Usage

plot_ancombc_pq(
  physeq,
  ancombc_res,
  filter_passed = TRUE,
  filter_diff = TRUE,
  min_abs_lfc = 0,
  tax_col = "Genus",
  tax_label = "Species",
  add_marginal_vioplot = TRUE,
  add_label = TRUE,
  add_hline_cut_lfc = NULL
)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
ancombc_res	(required) the result of the ancombc_pq function For the moment only bimodal factors are possible.
filter_passed	(logical, default TRUE) Do we filter using the column passed_ss? The passed_ss value is TRUE if the taxon passed the sensitivity analysis, i.e., adding different pseudo-counts to 0s would not change the results.
filter_diff	(logical, default TRUE) Do we filter using the column diff? The diff value is TRUE if the taxon is significant (has q less than alpha)
min_abs_lfc	(integer, default 0) Minimum absolute value to filter results based on Log Fold Change. For ex. a value of 1 filter out taxa for which the abundance in a given level of the modalty is not at least the double of the abundance in the other level.
tax_col	The taxonomic level (must be present in tax_table slot) to color the points
tax_label	The taxonomic level (must be present in tax_table slot) to add label
add_marginal_vioplot	(logical, default TRUE) Do we add a marginal vioplot representing all the taxa lfc from ancombc_res.
add_label	(logical, default TRUE) Do we add a label?
add_hline_cut_lfc	(logical, default NULL) Do we add two horizontal lines when min_abs_lfc is set (different from zero)?

Details

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

Value

A ggplot2 object. If add_marginal_vioplot is TRUE, this is a patchworks of plot made using patchwork::plot_layout().

Author(s)

Adrien Taudière

Examples

if (requireNamespace("mia")) {
  data_fungi_mini@tax_table <- phyloseq::tax_table(cbind(
    data_fungi_mini@tax_table,
    "taxon" = taxa_names(data_fungi_mini)
  ))

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

  plot_ancombc_pq(data_fungi_mini, res_time,
    filter_passed = FALSE,
    tax_label = "Genus", tax_col = "Order"
  )
  plot_ancombc_pq(data_fungi_mini, res_time, tax_col = "Genus")
  plot_ancombc_pq(data_fungi_mini, res_time,
    filter_passed = FALSE,
    filter_diff = FALSE, tax_col = "Family", add_label = FALSE
  )
}

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.