R/convert_biom_to_taxon_table.R

In gauravsk/ranacapa: Utility Functions and 'shiny' App for Simple Environmental DNA Visualizations and Analyses

if(getRversion() >= "2.15.1")  utils::globalVariables(c("sum.taxonomy", ".", "id"))

#' Takes a biom table imported in using phyloseq::import_biom() and converts it
#' into an Anacapa-formmated taxonomy table
#' @param physeq_object phyloseq object with a OTU table and a Taxon Table embedded
#' @export
convert_biom_to_taxon_table <- function(physeq_object) {

  # Make data frames out of these objects
  community_table <- physeq_object@otu_table %>%
    as.data.frame() %>%
    tibble::rownames_to_column("id")
  taxon_table <- data.frame(methods::as(physeq_object@tax_table, "matrix"))

  # Summarize the taxonomy and clean it up by removing some info that never gets used
    taxon_table$sum.taxonomy <- paste(taxon_table$Rank2,
                                      taxon_table$Rank3,
                                      taxon_table$Rank4,
                                      taxon_table$Rank5,
                                      taxon_table$Rank6,
                                      taxon_table$Rank7,
                                      sep = ";")

  taxon_table <- taxon_table %>%
    tibble::rownames_to_column("id") %>%
    dplyr::select(id, sum.taxonomy)

  taxon_table$sum.taxonomy <- stringr::str_replace_all(taxon_table$sum.taxonomy,
                                                       pattern = "(p|c|o|f|g|s)__", "")

  # Merge the taxonomy and the community matrix back together
  dplyr::left_join(community_table, taxon_table) %>%
    dplyr::select(-id) %>%
    dplyr::select(sum.taxonomy, dplyr::everything())
}