R/plot_circos.R

In pdiakumis/rock: Rocking R at UMCCR

#' Generate Perl Circos Plot Files
#'
#' Generates required files for a Perl circos plot containing
#' Manta structural variants and/or CNVkit/FACETS/PURPLE/TitanCNA
#' copy number variants.
#'
#' @param outdir Directory to write the files to.
#' @param manta Path to Manta VCF file.
#' @param cnv Path to copy number call file.
#' @param genome Genome assembly. "hg19" (default) or "hg38".
#'   hg19 gets converted to GRCh37 automatically.
#' @param ... Additional arguments for `prep_manta_vcf`.
#' @return Generates the required files for a Perl circos plot with structural
#'   variant links and/or copy number variant segments.
#'   Returns the paths to these files invisibly.
#'
#' @examples
#' \dontrun{
#' manta <- system.file("extdata", "HCC2218_manta.vcf", package = "pebbles")
#' cnv <- system.file("extdata", "HCC2218_cnvkit-call.cns", package = "pebbles")
#' outdir <- "~/Desktop/tmp/circos"
#'
#' circos_prep(outdir = outdir, manta = manta, cnv = cnv)
#' circos_prep(outdir = outdir, manta = manta) # no CNVs provided
#' circos_prep(outdir = outdir, manta = manta, genome = "hg19") # no CNVs provided
#' circos_prep(outdir = outdir, cnv = cnv) # no SVs provided
#' }
#' @export
circos_prep <- function(outdir = "circos", manta = NULL, cnv = NULL, genome = "hg19", ...) {

  template <- NULL
  stopifnot((!is.null(manta) && file.exists(manta)) || (!is.null(cnv) && file.exists(cnv)))
  stopifnot(genome %in% c("hg19", "hg38"), length(genome) == 1)
  if (!dir.exists(outdir)) {
    dir.create(outdir, recursive = TRUE)
  }
  message(glue::glue("Exporting Manta and/or CNV circos files to '{outdir}'."))
  # prepare Manta/CNVkit circos files
  # template can be 'cnvsv', 'sv', or 'cnv'
  if (!is.null(manta)) {
    template <- "sv"
    manta <- prep_manta_vcf2(manta, ...)
    readr::write_tsv(manta, file.path(outdir, "SAMPLE.link.circos"), col_names = FALSE)
  }
  if (!is.null(cnv)) {
    template <- paste0("cnv", template)
    cnv <- prep_cnv_circos(cnv)
    readr::write_tsv(cnv, file.path(outdir, "SAMPLE.cnv.circos"), col_names = FALSE)
  }

  message(glue::glue("Copying circos templates to '{outdir}'."))
  message(glue::glue("'template' is {template}. 'genome' is {genome}."))

  circos_template_dir <- glue::glue("templates/circos{ifelse(genome == 'hg38', '/hg38', '')}")
  file.copy(from = system.file(circos_template_dir, glue::glue("circos_{template}.conf"), package = "pebbles"),
            to = file.path(outdir, "circos.conf"), overwrite = TRUE)
  file.copy(from = system.file(circos_template_dir, "gaps.txt", package = "pebbles"),
            to = file.path(outdir), overwrite = TRUE)
  file.copy(from = system.file(circos_template_dir, "ideogram.conf", package = "pebbles"),
            to = file.path(outdir), overwrite = TRUE)

  invisible(list(sv = manta, cnv = cnv))
}

#' Generate Perl Circos Plot
#'
#' Generates a Perl circos plot containing
#' Manta structural variants and/or CNV calls.
#'
#' @param outdir Directory where the files are located, and where the plot will
#'   be written to.
#' @param name Prefix of plot file (suffix: `_circos.png`) (default: `x`).
#' @return Generates a Perl circos plot in the outdir.
#'
#' @examples
#' \dontrun{
#' manta <- system.file("extdata", "HCC2218_manta.vcf", package = "pebbles")
#' cnv <- system.file("extdata", "HCC2218_cnvkit-call.cns", package = "pebbles")
#' outdir <- "circos"
#'
#' circos_prep(outdir, manta, cnvkit)
#' plot_circos(outdir, name = "foo")
#' }
#' @export
plot_circos <- function(outdir = "circos", name = "x") {

  if (Sys.which("circos") != "") {
    cmd <- glue::glue("circos -nosvg -conf {outdir}/circos.conf -outputdir {outdir} -outputfile {name}_circos.png")
    system(cmd)
  } else {
    stop("Can't find 'circos' in your PATH. Exiting.")
  }
}


#' Generate Perl Circos PURPLE BAF Plot
#'
#' Generates a Perl circos plot containing
#' structural variant links, CNV calls, and BAF values from PURPLE.
#'
#' @param purple_dir Directory where the circos files are located ('purple/circos').
#' @param tumor_name Tumor sample name.
#' @param out_dir Directory where the new circos plot will be written,
#'   along with the input/config files.
#' @return Generates a Perl circos plot in the outdir.
#'
#' @examples
#' \dontrun{
#' purple_dir <- '/path/to/purple/circos'
#' out_dir <- '~/Desktop/tmp/circos_new'
#' tumor_name <- 'sampleA_tumor'
#'
#' plot_circos_baf(purple_dir, out_dir, tumor_name)
#' }
#' @export
plot_circos_baf <- function(purple_dir = NULL, out_dir = "circos_baf", tumor_name = NULL) {

  stopifnot(!is.null(purple_dir), !is.null(tumor_name))
  stopifnot(dir.exists(purple_dir))

  req_files <- file.path(purple_dir, paste0(tumor_name, c(".baf.circos", ".cnv.circos", ".map.circos", ".link.circos")))
  stopifnot(all(file.exists(req_files)))
  target_files <- file.path(out_dir, sub(tumor_name, "SAMPLE", basename(req_files)))

  dir.create(out_dir, recursive = TRUE)
  message(glue::glue("Copying circos templates to '{out_dir}'."))
  file.copy(system.file("templates/circos", "circos_baf.conf", package = "pebbles"), out_dir, overwrite = TRUE)
  file.copy(system.file("templates/circos", "gaps.txt", package = "pebbles"), out_dir, overwrite = TRUE)
  file.copy(system.file("templates/circos", "ideogram.conf", package = "pebbles"), out_dir, overwrite = TRUE)

  message(glue::glue("Copying circos input files to '{out_dir}'."))
  file.copy(from = req_files, to = target_files)
  if (Sys.which("circos") != "") {
    cmd <- glue::glue("circos -nosvg -conf {out_dir}/circos_baf.conf -outputdir {out_dir} -outputfile {tumor_name}_circos_baf.png")
    system(cmd)
  } else {
    stop("Can't find 'circos' in your PATH. Exiting.")
  }
}