R/filterSummary.R

In chutter/FilterZone: R Package For Detecting the Anomaly Zone and Alignment Filtering in Large Phylogenomic Datasets

#' @title filterSummary
#'
#' @description Summarizes filtered datasets when provided with filter parameters
#'
#' @param alignment.data Alignment summary stats calculcated from summarizeAlignments
#'
#' @param alignment.folder The alignment folder from which the stats were calculated from in alignment.data
#'
#' @param dataset.name The name of your dataset, where all filtered datasets will be placed in this folder
#'
#' @param file.out if you wish to save to file, provide a file name for the summary
#'
#' @param overwrite if TRUE overwrites file if it exists; FALSE the dataset is skipped
#'
#' @param length.filters Your selected length filters as a vector of values for the alignment length
#'
#' @param sample.filters Your selected sampling fraction filters as a vector of values between 0-1
#'
#' @param prop.pis.filters Your selected parsimony informatives sites filter as a vector of values between 0-1
#'
#' @param count.pis.filters Your selected parsimony informatives sites filter as a vector of base pair counts
#'
#' @return Returns a summary of your selected filters applied to the dataset
#'
#' @examples
#'
#' your.tree = ape::read.tree(file = "file-path-to-tree.tre")
#' astral.data = astralPlane(astral.tree = your.tree,
#'                           outgroups = c("species_one", "species_two"),
#'                           tip.length = 1)
#'
#'
#' @export

filterSummary = function(alignment.data = NULL,
                         alignment.folder = NULL,
                         dataset.name = NULL,
                         file.out = NULL,
                         overwrite = FALSE,
                         length.filters = NULL,
                         sample.filters = NULL,
                         prop.pis.filters = NULL,
                         count.pis.filters = NULL) {

  # alignment.data = align.summary
  # alignment.folder = alignment.directory
  # dataset.name  = dataset.name
  # file.out = "filter_summary"
  # length.filters = filter.length
  # sample.filters = filter.sample
  # prop.pis.filters = filter.prop.pis
  # count.pis.filters = filter.count.pis
  # overwrite = overwrite

  #parameter checks
  if (is.null(alignment.data) == TRUE){ stop("Error: No alignment summary data provided.") }
  if (is.null(alignment.folder) == TRUE){ stop("Error: No directory of alignments provided.") }
  if (is.null(dataset.name) == TRUE){ stop("Error: No dataset name provided.") }

  #Check if files exist or not
  if (dir.exists(alignment.folder) == F){
    return(paste0("Directory of alignments could not be found. Exiting."))
  }#end file check

  #Overwrite checker
  if (overwrite == TRUE){
    if (file.exists(paste0(file.out, ".csv")) == T){
      #Checks for output directory and creates it if not found
      system(paste0("rm ", file.out, ".csv"))
    }#end file exists
  } else {
    if (file.exists(paste0(file.out, ".csv")) == T){
      return(paste0("File exists for ", file.out, " and overwrite = FALSE. Exiting."))
    }#end file check
  }#end else

  #Read in alignment data and set up
  if (length(alignment.data) == 1) {
    alignment.stats = data.table::fread(alignment.data, header = T)
  } else {
    alignment.stats = alignment.data
  }

  filter.summary = c()
  if (is.null(length.filters) != TRUE){
    filter.summary = rbind(filter.summary,
                           filterStats(data = alignment.stats,
                                       filter.name = "alignment_length",
                                       filter.values = length.filters,
                                       align.dataset = dataset.name) )
  }#end length

  #Sampling
  if (is.null(sample.filters) != TRUE){
    filter.summary = rbind(filter.summary,
                           filterStats(data = alignment.stats,
                                       filter.name = "proportion_samples",
                                       filter.values = sample.filters,
                                       align.dataset = dataset.name) )
  }#end sample

  #Count
  if (is.null(count.pis.filters) != TRUE){
    filter.summary = rbind(filter.summary,
                           filterStats(data = alignment.stats,
                                       filter.name = "count_pis",
                                       filter.values = count.pis.filters,
                                       align.dataset = dataset.name) )
  }#end sample

  #filter.prop.pis
  if (is.null(prop.pis.filters) != TRUE){
    filter.summary = rbind(filter.summary,
                           filterStats(data = alignment.stats,
                                       filter.name = "proportion_pis",
                                       filter.values = prop.pis.filters,
                                       align.dataset = dataset.name) )
  }#end sample

  if (is.null(file.out) != T) {
    #Saves the alignment stats
    write.csv(filter.summary, file = paste0(file.out, ".csv"), row.names = F)
  }#end if

  return(filter.summary)

}#end function