R/epiRomics_chromatin_tracks.R

In Huising-Lab/epiRomics: Epigenomic Analysis Package Built for R (epiRomics)

#' Visualizes chromatin availability
#'
#' @param epiRomics_gene_name character of name of gene to visualize
#' @param epiRomics_dB epiRomics class database containing all data initially loaded
#' @param epiRomics_track_connection data frame containing bigwig track locations and their names
#' @return GViz plot
#' @export
epiRomics_chromatin_tracks <-
  function(epiRomics_gene_name,
           epiRomics_dB,
           epiRomics_track_connection) {
    epiRomics_entrez_id <-
      base::as.vector(AnnotationDbi::mapIds(
        base::eval(base::parse(text = epiRomics_dB@organism)),
        epiRomics_gene_name,
        "ENTREZID",
        "SYMBOL"
      ))
    epiRomics_gene_map <-
      GenomicFeatures::genes((base::eval(base::parse(text = epiRomics_dB@txdb))))
    epiRomics_gene_map_track <-
      epiRomics_gene_map[epiRomics_gene_map$gene_id == epiRomics_entrez_id, ]
    #Gviz::GeneRegionTrack(eval(parse(text = epiRomics_dB@txdb)), start = epiRomics_gene_map_track@ranges@start, end = data.frame(epiRomics_gene_map_track@ranges)$end, chromosome = epiRomics_gene_map_track@seqnames@values)
    # Uncommented the below line to fix max width issue for certain genes, such as MafA
    epiRomics_gene_map_track <-
      GenomicRanges::resize(
        epiRomics_gene_map_track,
        width = BiocGenerics::width(epiRomics_gene_map_track) + (4000 * 2),
        fix = "center"
      )
    chr <-
      base::as.character(BiocGenerics::unique(GenomeInfoDb::seqnames(epiRomics_gene_map_track)))
    gtrack <- Gviz::GenomeAxisTrack()
    txTr <-
      Gviz::GeneRegionTrack(
        base::eval(base::parse(text = epiRomics_dB@txdb)),
        start = as.data.frame(epiRomics_gene_map_track)[, "start"],
        end = as.data.frame(epiRomics_gene_map_track)[, "end"],
        chromosome = chr,
        symbol = epiRomics_gene_name,
        name = epiRomics_gene_name,
        transcriptAnnotation = "symbol",
        geneSymbol = TRUE,
        showId = TRUE
      )
    itrack <- Gviz::IdeogramTrack(genome = "mm10", chromosome = chr)
    epiRomics_track_connection_chromatin <-
      epiRomics_track_connection[epiRomics_track_connection$type == "atac", ]
    
    range_max <-
      maxCovFiles(
        epiRomics_track_connection_chromatin[, 1],
        epiRomics_gene_map_track
      )
    max_cov <-
      plyr::round_any((range_max$X + (range_max$X * 0.1)), accuracy = 10, f = ceiling)
    chromatin_tracks <- list()
    for (i in 1:base::dim(epiRomics_track_connection_chromatin)[1]) {
      chromatin_tracks <- c(
        chromatin_tracks,
        Gviz::DataTrack(
          size = 10,
          epiRomics_track_connection_chromatin[i, 1],
          col = epiRomics_track_connection_chromatin[i, 3],
          fill = epiRomics_track_connection_chromatin[i, 3],
          col.histogram = epiRomics_track_connection_chromatin[i, 3],
          ylim = c(0, max_cov),
          range = epiRomics_track_connection_chromatin[i, 1],
          genome = epiRomics_dB@genome,
          type = "hist",
          chromosome = chr,
          strand = epiRomics_gene_map_track@strand,
          name = epiRomics_track_connection_chromatin[i, 2]
        )
      )
    }
    if (table(epiRomics_track_connection$type == "rna")[[TRUE]] > 0) {
      rna_tracks <- list()
      epiRomics_track_connection_rna <-
        epiRomics_track_connection[epiRomics_track_connection$type == "rna", ]
      range_max <-
        maxCovFiles(
          epiRomics_track_connection_rna[, 1],
          epiRomics_gene_map_track
        )
      max_cov <-
        plyr::round_any((range_max$X + (range_max$X * 0.1)), accuracy = 10, f = ceiling)
      for (i in 1:base::dim(epiRomics_track_connection_rna)[1]) {
        rna_tracks <- c(
          rna_tracks,
          Gviz::DataTrack(
            size = 10,
            epiRomics_track_connection_rna[i, 1],
            col = epiRomics_track_connection_rna[i, 3],
            fill = epiRomics_track_connection_rna[i, 3],
            col.histogram = epiRomics_track_connection_rna[i, 3],
            ylim = c(0, max_cov),
            range = epiRomics_track_connection_rna[i, 1],
            genome = epiRomics_dB@genome,
            type = "hist",
            chromosome = chr,
            strand = epiRomics_gene_map_track@strand,
            name = epiRomics_track_connection_rna[i, 2]
          )
        )
      }
    }
    Gviz::plotTracks(
      base::c(itrack, gtrack, txTr, chromatin_tracks, rna_tracks),
      extend.right = 1000,
      extend.left = 1000
    )
  }