R/data_generator.r

In gtsitsiridis/metatranscriptome: Visualization tool for the metatranscriptome project

#' @include methods.r
#' @include metaSRA_data.r

#' @title Transform Data
#'
#' Convert tables into input compatible with the webtool.
#'
#' @param tables A directory containing the tables or or list that contains the following files: study_info, sample_info, feature_info, counts
#' @param output_dir The directory where the transformed data will be saved. The default is inside the package.
#' @param log A logical value indicating whether a log file should be generated with info about the process. The default is \code{FALSE}
#'
#' @export
transformData <-
  function(tables,
           output_dir = pkg_file("data"),
           log = FALSE) {
    metaSRA.file <- ""
    doid.file <- ""
    if (inherits(tables, "character")) {
      metaSRA.file <- file.path(tables, "metasra.json")
      doid.file <- file.path(tables, "doid.json")
      tmp <- c("study_info", "sample_info", "counts", "feature_info")
      tables <- as.list(file.path(tables, paste0(tmp, ".RData")))
      names(tables) <- tmp
    } else if (!inherits(tables, "list")) {
      message("Invalid argument tables!")
      return()
    }

    # read the data
    load(tables$study_info)
    load(tables$sample_info)
    load(tables$counts)
    load(tables$feature_info)

    dir.create(output_dir, showWarnings = FALSE)

    # Use metaSRA annotation
    if (file.exists(metaSRA.file)){
      metaSRA.tables <- getMetaSRA(sample_info, metaSRA.file)
      metaSRA.dt <- metaSRA.tables[[1]]
      ontologyInfo.dt <- metaSRA.tables[[2]]
      save(metaSRA.dt, ontologyInfo.dt, file = file.path(output_dir, "metaSRA_annot.RData"))

      if(file.exists(doid.file)){
        disease.tables <- annotateDisease(metaSRA.dt, doid.file)
        diseaseRun.dt <- disease.tables[[1]]
        diseaseTerms.dt <- disease.tables[[2]]
        save(diseaseRun.dt, diseaseTerms.dt, file = file.path(output_dir, "disease_annot.RData"))
        setkey(diseaseRun.dt, run)
        sample_info$metaSRA.disease.status <- diseaseRun.dt[sample_info$run, disease.status]
        sample_info$infection.status <- diseaseRun.dt[sample_info$run, infected]
        sample_info$metaSRA.sample.type <- diseaseRun.dt[sample_info$run, sample_type]
      }
    }

    dir.create(file.path(output_dir, "studies"), showWarnings = FALSE)

    lineage <- generateLineage(feature_info)

    r <- runDG(study_info,
             sample_info,
             counts,
             lineage,
             output_dir,
             log)

    if (log) {
      write.table(r, file.path(output_dir, "errors.txt"), row.names = FALSE)
    }
    #add column sample_size to study_info
    study_info$sample_size <-
      sapply(study_info$study, function(x)
        sum(x == sample_info$study))

    study_info$study_abstract <-
      as_native_character(study_info$study_abstract) %>%
      {
        Encoding(.) <- "UTF-8"
        .
      } %>%
      as_native_character %>%
      {
        Encoding(.) <- "UTF-8"
        .
      }

    save(study_info, file = file.path(output_dir, "study_info.RData"))


    studies <- list.files(file.path(output_dir, 'studies')) %>%
      str_split_fixed("\\.", n = 2) %>% .[, 1]
    mf_tbl <- mfMeans(study_info, studies, output_dir)

    save(mf_tbl, file =  file.path(output_dir, "metafeatures_table.RData"))
  }


# generate phyloseq objects
runDG <-
  function(study_info,
           sample_info,
           counts,
           lineage,
           output_dir,
           log) {
    env <- environment()
    error <- data.frame()
    lapply(study_info$study, function(study) {
      path <- file.path(output_dir, "studies", paste0(study, ".RData"))
      print(path)
      if (file.exists(path))
        return()
      phylo <-
        try(generatePhylo(study, counts, sample_info, lineage))
      if (inherits(phylo, "try-error")) {
        error <-
          rbind(error, c(study, geterrmessage()), stringsAsFactors = FALSE)
        if (log)
          assign("error", error, env)
      } else{
        save(phylo, file = path)
      }
      # print(phylo)
    })
    try(colnames(error) <- c("Study", "Message"), silent = TRUE)
    error
  }