In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  message = FALSE,
  results = "hide"
)

library(MiscMetabar)
data(data_fungi)

summary_plot_pq(data_fungi)

Explore samples metadata

sam_tab <- tibble::as_tibble(unclass(data_fungi@sam_data))

summarytools::dfSummary(sam_tab)

datawizard::data_codebook(sam_tab)

pillar::glimpse(sam_tab)

pointblank::scan_data(sam_tab, sections = "OVSCMI")

pointblank::create_informant(
  tbl = sam_tab,
  tbl_name = "Sample data",
  label = "data_fungi"
)

gtExtras::gt_plt_summary(sam_tab)

Explore taxonomic data

tax_tab <- tibble::as_tibble(unclass(data_fungi@tax_table))

summarytools::dfSummary(tax_tab)

datawizard::data_codebook(tax_tab)

pillar::glimpse(tax_tab)

pointblank::scan_data(tax_tab, sections = "OVSCM")

pointblank::create_informant(
  tbl = tax_tab,
  tbl_name = "Taxonomic table",
  label = "data_fungi"
)

gtExtras::gt_plt_summary(tax_tab)

fungi_order <- tax_glom(data_fungi, taxrank = "Order")
taxa_names(fungi_order) <- fungi_order@tax_table[, "Order"]
heatmap(fungi_order@otu_table)

Session information

sessionInfo()

adrientaudiere/MiscMetabar documentation built on Feb. 7, 2025, 5:47 p.m.