R/plot_browser_tracks.R

In ALPS: AnaLysis routines for ePigenomicS data

getChrStartEnd <- function(x) {

    x_chr <- gsub(":.*", "", x) %>% as.character()
    x_start <- gsub(".*:", "", x) %>% gsub("-.*",
        "", .) %>% as.numeric()
    x_end <- gsub(".*:", "", x) %>% gsub(".*-",
        "", .) %>% as.numeric()

    x_res <- list(chr = x_chr, from = x_start,
        to = x_end)

    return(x_res)
}

#' UCSC Genome browser like plots
#' @description Function to plot genome browser like plots
#' given a very minimal information such as a set of bigwig files
#' and a genomics region. Tracks are arranged as they are in given
#' input data.frame. Function uses highly customizable Gviz
#' R/bioconductor package to plot browser like plots.
#'
#' @param data_table a dataframe that contains \code{bw_path}, \code{sample_id} and \code{color_code}. Tracks are colored according to \code{color_code}. Default \code{NULL}
#' @param gene_range genomic region for which browser-like plots needed in format \code{chr:start-end}. Default \code{NULL}
#' @param ref_gen reference genome, to get gene annotations, currently supports  \code{hg19} and \code{hg38}. Default, \code{hg38}
#' @param cex.axis axis label size, default \code{0.5}
#' @param cex.title axis title size, default \code{0.8}
#' @param ... additional arguments to change the appearence of a plot. All arguments that can be passed to base R graphics are supported
#'
#' @importFrom TxDb.Hsapiens.UCSC.hg38.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene
#' @importFrom TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg19.knownGene
#' @importFrom dplyr filter pull
#' @importFrom Gviz GeneRegionTrack DataTrack plotTracks
#'
#' @return plot of genome browser tracks
#'
#' @export
#'
#' @examples
#'
#' ## load example data
#'
#' chr21_data_table <- system.file('extdata/bw', 'ALPS_example_datatable.txt', package = 'ALPS', mustWork = TRUE)
#'
#' ## attach path to bw_path and bed_path
#' d_path <- dirname(chr21_data_table)
#'
#' chr21_data_table <- read.delim(chr21_data_table, header = TRUE)
#' chr21_data_table$bw_path <- paste0(d_path, '/', chr21_data_table$bw_path)
#' chr21_data_table$bed_path <- paste0(d_path, '/', chr21_data_table$bed_path)
#'
#' gene_range = 'chr21:45643725-45942454'
#'
#' plot_browser_tracks(data_table = chr21_data_table,
#' gene_range = gene_range, ref_gen = 'hg38')

plot_browser_tracks <- function(data_table,
                                gene_range = NULL,
                                ref_gen = "hg38",
                                cex.axis = 0.5,
                                cex.title = 0.8, ...) {

    assertthat::assert_that(is.data.frame(data_table), msg = "Please provide `data_table`")
    assertthat::assert_that(assertthat::has_name(data_table, "bw_path"))
    assertthat::assert_that(assertthat::has_name(data_table, "sample_id"))
    assertthat::assert_that(assertthat::has_name(data_table, "color_code"))

    assertthat::assert_that(!is.null(gene_range), msg = "Please provide `gene_range` in format; chr:start-end")

    gene_range_split <- getChrStartEnd(x = gene_range)

    ## build genetrack
    if (ref_gen == "hg38") {

        txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene

    } else {

        txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
    }

    ##
    grtrack <- Gviz::GeneRegionTrack(txdb,
                                     genome = ref_gen,
                                     chromosome = gene_range_split$chr,
                                     window = -1, name = NULL, background.title = "white",
                                     col.frame = "white", col.axis = "black",
                                     col = "black", col.title = "black",
                                     geneSymbol = TRUE, showId = TRUE,
                                     from = gene_range_split$from, to = gene_range_split$to)

    ## build enrichment tracks
    dt_list <- list()
    all_sample_ids <- data_table$sample_id %>%
      as.character()

    for (i in seq_along(all_sample_ids)) {

        x_id <- all_sample_ids[i]
        x_dat <- data_table %>% dplyr::filter(sample_id == get("x_id"))

        x_bw <- x_dat %>% dplyr::pull(bw_path) %>% as.character()
        x_col <- x_dat %>% dplyr::pull(color_code) %>% as.character()

        x_dt <- Gviz::DataTrack(range = x_bw,
                                genome = ref_gen,
                                chromosome = gene_range_split$chr,
                                name = x_id, type = "hist", window = -1,
                                fill.histogram = x_col, col.histogram = "NA",
                                background.title = "white", col.frame = "white",
                                col.axis = "black", col = "black",
                                col.title = "black")

        dt_list[[i]] <- x_dt

    }

    gtrack_pos <- length(dt_list) + 1
    dt_list[[gtrack_pos]] <- grtrack

    Gviz::plotTracks(dt_list, from = gene_range_split$from,
                     to = gene_range_split$to, cex.axis = cex.axis,
                     cex.title = cex.title, ...)

}