R/inspect_read_quality.R

In peterolah001/BiMiCo: Biomap Microbiome Core methods

## TODO: combine mmultipl plots par(mfrow)

#' inspect read trimming results
#'
#' Convenience wrapper for DADA2 read processing functions. Generates QC plots from a given fastq file before and after quality control by DADA2.
#' @param readfiles (Required) Path to single-end 454 demultiplexed fastq files
#' @param filtfiles (Required) Path to quality-filtered fastq files generated by std_(454/illum_SE/illum_PE)_preprocess
#' @param filenum (Optional) Number of fastq read file to plot (numeric).
#' @keywords read processing dada2
#' @export
#' @examples
#' insp_reads()

# Inspect read quality

insp_reads <- function(readfiles, filtfiles, filenum=1){

  # store raw fastq file names
  fqs <- sort(
    list.files(
      readfiles,
      pattern = "*.f*q",
      full.names = TRUE
    )
  )


  # store filtered fastq file names

  ffqs <- sort(
    list.files(
      filtfiles,
      full.names = TRUE
    )
  )

# create a composite before-after plot

  qgraph <- dada2::plotQualityProfile(
    fqs[filenum]
    #main="Before filtering"
  )

  qgraph2 <- dada2::plotQualityProfile(
    ffqs[filenum]
    #main="After filtering"
  )

  pl <- list("p1" = qgraph, "p2" = qgraph2)

  return(pl)

}