MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Documented in lulu

#' Post Clustering Curation of Amplicon Data.
#'
#' @description
#'
#' <a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle">
#' <img src="https://img.shields.io/badge/lifecycle-stable-green" alt="lifecycle-stable"></a>
#'
#'  The original function and documentation was written by Tobias Guldberg Frøslev
#' in the [lulu](https://github.com/tobiasgf/lulu) package.
#'
#'  This algorithm \code{lulu} consumes an OTU table and a matchlist, and
#'   evaluates cooccurence of 'daughters' (potential analytical artefacts) and
#'   their 'parents' (~= real biological species/OTUs). The algorithm requires an
#'   OTU table (species/site matrix), and a match list. The OTU table can be
#'   made with various r-packages (e.g. \code{DADA2}) or
#'   external pipelines (\code{VSEARCH, USEARCH, QIIME}, etc.), and the
#'   match-list can be made with external bioinformatic tools like
#'   \code{VSEARCH, USEARCH, BLASTN} or another algorithm
#'   for pair-wise sequence matching.
#' @param otu_table a data.frame with with an OTU table that has sites/samples as
#'   columns and OTUs (unique OTU id's) as rows, and observations as read
#'   counts.
#' @param matchlist a data.frame containing three columns: (1) OTU id of
#'   potential child, (2) OTU id of potential parent, (3) match - % identiti
#'   between the sequences of the potential parent and potential child OTUs.
#'   \strong{NB: The matchlist is the product of a mapping of OTU sequences against each other. This is
#'   currently carried out by an external script in e.g. Blastn or VSEARCH, prior to running lulu!}
#' @param minimum_ratio_type sets whether a potential error must have lower
#'   abundance than the parent in all samples \code{min} (default), or if an error
#'   just needs to have lower abundance on average \code{avg}. Choosing lower
#'   abundance on average over globally lower abundance will greatly increase
#'   the number of designated errors. This option was introduced to make it
#'   possible to account for non-sufficiently clustered intraspecific variation,
#'   but is not generally recommended, as it will also increase the potential of
#'   cluster well-separated, but co-occuring, sequence similar species.
#' @param minimum_ratio sets the minimim abundance ratio between a potential error
#'   and a potential parent to be identified as an error. If the \code{minimum_ratio_type} is
#'   set to \code{min} (default), the \code{minimum_ratio} applies to the lowest observed
#'   ration across the samples.  If the \code{minimum_ratio_type} is
#'   set to \code{avg} (default), the \code{minimum_ratio} applies to the mean of observed
#'   ration across the samples.\code{avg}. (default is 1).
#' @param minimum_match minimum threshold of sequence similarity
#'   for considering any OTU as an error of another can be set (default 84%).
#' @param minimum_relative_cooccurence minimum co-occurrence rate, i.e. the
#'   lower rate of occurrence of the potential error explained by co-occurrence
#'   with the potential parent for considering error state.
#' @param progress_bar (Logical, default TRUE) print progress during the calculation or not.
#' @param log_conserved (Logical, default FALSE) conserved log files writed in the disk
#' @return Function \code{lulu} returns a list of results based on the input OTU
#'   table and match list.
#'
#'   - \code{curated_table} - a curated
#'   OTU table with daughters merged with their matching parents.
#'   - \code{curated_count} - number of curated (parent) OTUs.
#'   - \code{curated_otus} - ids of the OTUs that were accepted as valid OTUs.
#'   - \code{discarded_count} - number of discarded (merged with parent) OTUs.
#'   - \code{discarded_otus} - ids of the OTUs that were identified as
#'   errors (daughters) and merged with respective parents.
#'   - \code{runtime} - time used by the script.
#'   - \code{minimum_match} - the id threshold
#'   (minimum match \% between parent and daughter) for evaluating co-occurence (set
#'   by user).
#'   - \code{minimum_relative_cooccurence} - minimum ratio of
#'   daughter-occurences explained by co-occurence with parent (set by user).
#'   - \code{otu_map} - information of which daughters were mapped to which
#'   parents.
#'   - \code{original_table} - original OTU table.
#'
#' The matchlist is the product of a mapping of OTU sequences against each other. This is
#'   currently carried out by an external script in e.g. BLASTN or VSEARCH, prior to running \code{lulu}!
#'   Producing the match list requires a file with all the OTU sequences (centroids) - e.g. \code{OTUcentroids.fasta}. The matchlist can be produced by mapping all OTUs against each other with an external algorithm like VSEARCH or BLASTN. In \code{VSEARCH} a matchlist can be produced e.g. with the following command: \code{vsearch --usearch_global OTUcentroids.fasta --db OTUcentroids.fasta --strand plus --self --id .80 --iddef 1 --userout matchlist.txt --userfields query+target+id --maxaccepts 0 --query_cov .9 --maxhits 10}. In \code{BLASTN} a matchlist can be produces e.g. with the following commands. First we produce a blast-database from the fasta file: \code{makeblastdb -in OTUcentroids.fasta -parse_seqids -dbtype nucl}, then we match the centroids against that database: \code{blastn -db OTUcentoids.fasta -num_threads 10 -outfmt'6 qseqid sseqid pident' -out matchlist.txt -qcov_hsp_perc .90 -perc_identity .84 -query OTUcentroids.fasta}
#'
#' @importFrom  utils setTxtProgressBar txtProgressBar
#' @importFrom stats ave kruskal.test
#' @details
#'   Please cite the lulu original paper: https://www.nature.com/articles/s41467-017-01312-x
#' @author Tobias Guldberg Frøslev (orcid: [0000-0002-3530-013X](https://orcid.org/0000-0002-3530-013X)),
#' modified by Adrien Taudière
#' @export
lulu <- function(otu_table, matchlist, minimum_ratio_type = "min", minimum_ratio = 1, minimum_match = 84, minimum_relative_cooccurence = 0.95, progress_bar = TRUE, log_conserved = FALSE) {
  start.time <- Sys.time()
  otutable <- otu_table
  colnames(matchlist) <- c("OTUid", "hit", "match")
  # remove no hits (vsearch)
  matchlist <- matchlist[which(matchlist$hit != "*"), ]
  # remove self-hits
  matchlist <- matchlist[which(matchlist$hit != matchlist$OTUid), ]

  # Making a separate table with stats (total readcount and spread).
  statistics_table <- otutable[, 0]
  statistics_table$total <- rowSums(otutable)

  # calculating spread (number of presences (samples with 1+ read) pr OTU)
  statistics_table$spread <- rowSums(otutable > 0)
  statistics_table <- statistics_table[with(
    statistics_table,
    order(spread,
      total,
      decreasing = TRUE
    )
  ), ]
  otutable <- otutable[match(
    row.names(statistics_table),
    row.names(otutable)
  ), ]

  statistics_table$parent_id <- "NA"
  log_con <- file(paste0("lulu.log_", format(start.time, "%Y%m%d_%H%M%S")),
    open = "a"
  )
  # make a progressline
  pb <- txtProgressBar(
    min = 0, # Minimum value of the progress bar
    max = nrow(statistics_table), # Maximum value of the progress bar
    style = 3, # Progress bar style (also available style = 1 and style = 2)
    width = 50, # Progress bar width. Defaults to getOption("width")
    char = "="
  ) # Character used to create the bar
  for (line in seq(1, nrow(statistics_table))) {
    if (progress_bar) {
      setTxtProgressBar(pb, line)
    }
    potential_parent_id <- row.names(otutable)[line]
    message(paste0("\n", "####processing: ", potential_parent_id, " #####"),
      file = log_con
    )
    daughter_samples <- otutable[line, ]
    hits <- matchlist[which(matchlist$OTUid == potential_parent_id &
      matchlist$match > minimum_match), "hit"]
    message(paste0("\n", "---hits: ", hits), file = log_con)
    last_relevant_entry <- sum(statistics_table$spread >=
      statistics_table$spread[line])
    potential_parents <- which(row.names(otutable)[1:last_relevant_entry]
    %in% hits)
    message(paste0(
      "\n", "---potential parent: ",
      row.names(statistics_table)[potential_parents]
    ), file = log_con)
    success <- FALSE
    if (length(potential_parents) > 0) {
      for (line2 in potential_parents) {
        message(paste0("\n", "------checking: ", row.names(statistics_table)[line2]),
          file = log_con
        )
        if (!success) {
          relative_cooccurence <-
            sum((daughter_samples[otutable[line2, ] > 0]) > 0) /
              sum(daughter_samples > 0)
          message(paste0(
            "\n", "------relative cooccurence: ",
            relative_cooccurence
          ), file = log_con)
          if (relative_cooccurence >= minimum_relative_cooccurence) {
            message(paste0(" which is sufficient!"), file = log_con)
            if (minimum_ratio_type == "avg") {
              relative_abundance <-
                mean(otutable[line2, ][daughter_samples > 0] /
                  daughter_samples[daughter_samples > 0])
              message(paste0(
                "\n", "------mean avg abundance: ",
                relative_abundance
              ), file = log_con)
            } else {
              relative_abundance <-
                min(otutable[line2, ][daughter_samples > 0] /
                  daughter_samples[daughter_samples > 0])
              message(paste0(
                "\n", "------min avg abundance: ",
                relative_abundance
              ), file = log_con)
            }
            if (relative_abundance > minimum_ratio) {
              message(paste0(" which is OK!"), file = log_con)
              if (line2 < line) {
                statistics_table$parent_id[line] <-
                  statistics_table[row.names(otutable)[line2], "parent_id"]
                message(
                  paste0(
                    "\n", "SETTING ",
                    potential_parent_id, " to be an ERROR of ",
                    (statistics_table[
                      row.names(otutable)[line2],
                      "parent_id"
                    ]), "\n"
                  ),
                  file = log_con
                )
              } else {
                statistics_table$parent_id[line] <- row.names(otutable)[line2]
                message(paste0(
                  "\n", "SETTING ", potential_parent_id,
                  " to be an ERROR of ", (row.names(otutable)[line2]),
                  "\n"
                ), file = log_con)
              }
              success <- TRUE
            }
          }
        }
      }
    }
    if (!success) {
      statistics_table$parent_id[line] <- row.names(statistics_table)[line]
      message(paste0("\n", "No parent found!", "\n"), file = log_con)
    }
  }

  close(log_con)

  curation_table <- cbind(nOTUid = statistics_table$parent_id, otutable)
  statistics_table$curated <- "merged"
  curate_index <- row.names(statistics_table) == statistics_table$parent_id
  statistics_table$curated[curate_index] <- "parent"
  statistics_table <- transform(statistics_table,
    rank = ave(total, FUN = function(x) {
      rank(-x, ties.method = "first")
    })
  )
  curation_table <- as.data.frame(curation_table %>%
    group_by(nOTUid) %>%
    summarise_all(list(sum)))
  row.names(curation_table) <- as.character(curation_table$nOTUid)
  curation_table <- curation_table[, -1]
  curated_otus <- names(table(statistics_table$parent_id))
  curated_count <- length(curated_otus)
  discarded_otus <- setdiff(row.names(statistics_table), curated_otus)
  discarded_count <- length(discarded_otus)
  end.time <- Sys.time()
  time.taken <- end.time - start.time
  result <- list(
    curated_table = curation_table,
    curated_count = curated_count,
    curated_otus = curated_otus,
    discarded_count = discarded_count,
    discarded_otus = discarded_otus,
    runtime = time.taken,
    minimum_match = minimum_match,
    minimum_relative_cooccurence = minimum_relative_cooccurence,
    otu_map = statistics_table,
    original_table = otutable
  )

  if (!log_conserved) {
    file.remove(list.files(pattern = "lulu.log_"))
  }
  return(result)
}