R/calculate.R

In SchlossLab/schtools: Schloss Lab Tools for Reproducible Microbiome Research

#' Calculate OTU relative abundances from a shared file
#'
#' @param abs_abun_dat a data frame from reading in a [shared file](https://mothur.org/wiki/shared_file/).
#'   Should contain a `Group` column for sample names,
#'   `Otu` columns for absolute counts of each OTU,
#'   and rows as each sample.
#'
#' @return a new data frame with OTU relative abundances in long format.
#' @export
#' @author Kelly Sovacool \email{sovacool@@umich.edu}
#'
#' @examples
#' shared_dat <- readr::read_tsv(system.file("extdata", "test.shared",
#'   package = "schtools"
#' ))
#' shared_dat %>% calc_relabun()
calc_relabun <- function(abs_abun_dat) {
  count <- Group <- mutate <- otu <- rel_abun <- total_counts <- NULL
  abs_abun_dat$total_counts <- rowSums(abs_abun_dat %>%
    dplyr::select(dplyr::starts_with("Otu")))
  rel_abun_dat <- abs_abun_dat %>%
    dplyr::rename(sample = Group) %>%
    tidyr::pivot_longer(dplyr::starts_with("Otu"),
      names_to = "otu", values_to = "count"
    ) %>%
    dplyr::mutate(rel_abun = count / total_counts) %>%
    dplyr::select(sample, otu, rel_abun)
  return(rel_abun_dat)
}