R/IgvFunctions.R

In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

#' create IGV viewer batch script (single range, as many tracks as you like)
#'
#' @description this will create a batch script that may be run with the igv
#'   browser. An example command is given in the examples below. See the extern
#'   data for an example of what one of these scripts looks like.
#'
#' @importFrom stringr str_replace
#' @importFrom purrr map
#'
#' @param bam_list list of bamfiles -- multiple files means multiple tracks
#' @param granges granges describing the range you wish to visualize -- range
#'   must be on one chromosome/contig
#' @param igv_genome .genome file created by IGV tools
#' @param output_dir where to deposit both the script and the browser shots
#' @param output_file_basename this will serve as both the name of the browser
#'   shot after running IGV, and the name o the batchscript itself
#' @param exit_browser Default is TRUE, which means that the batchscript will be
#'   written in a way that the browser will take an image, save it, and exit. Set
#'   to false and this script may be used to launch an interactive session.
#' @param maxPanelHeight default 500. height of the IGV window
#'
#'
#' @return None. This prints a batch script to the output dir
#'
#' @note run on the command line like so xvfb-run --auto-servernum igv.sh -b script.bat
#'
#' @export
createIgvBatchscript = function(bam_list,
                                granges,
                                igv_genome,
                                output_dir,
                                output_file_basename,
                                exit_browser = TRUE,
                                maxPanelHeight=500){

  output_file_basename = tools::file_path_sans_ext(output_file_basename)
  output_img_filename = paste0(output_file_basename, ".png")

  load_samples = paste0(map(bam_list, ~sprintf("\tload %s\n", .)), collapse=" ")

  parsed_range = paste(as.character(granges@seqnames),
                       as.character(granges@ranges), sep=":")

  if(parsed_range == ""){
    stop("range object cannot be empty")
  }

  batch_script = paste0("new\nsnapshotDirectory %s\nmaxPanelHeight %s\ngenome %s\n",
                        load_samples, "goto %s")

  batch_script = sprintf(batch_script,
                         path.expand(output_dir),
                         maxPanelHeight,
                         path.expand(igv_genome),
                         parsed_range)

  if(exit_browser){
    batch_script = paste0(batch_script, "\nsnapshot %s\nexit")
    batch_script = sprintf(batch_script, output_img_filename)
  }

  script_output_dir = path.expand(file.path(output_dir, "scripts"))
  dir.create(script_output_dir, recursive = TRUE)

  output_filename = file.path(script_output_dir,
                              str_replace(output_file_basename, ".png", ".txt"))

  cat(batch_script, file = output_filename)
}