R/plotBED.R

In RepViz: Replicate oriented Visualization of a genomic region

###############################################################################
## plotRegiont.R -- plot a snapshot of a genomic region
## 30 november 2018 Thomas Faux
## Medical Bioinformatics Centre
###############################################################################

# plot the regions that are contained in BED
# @param BED list of dataframes containing the peaks
# @param region GRanges object containing the region to plot
# @param colorPalette Contain vector of colors to be used for each line
# @param verbose Prompt the progress

plotBED <- function(BED, region, colorPalette, verbose) {

    overlaps <- takePeaksOverlap(BED, region, verbose)
    mysegment <- function(GRanges, y, colorPalette) {
        graphics::segments(x0 = GenomicRanges::start(GRanges[[1]]), y0 = y - 0.5,
                        x1 = GenomicRanges::end(GRanges[[1]]),
                        y1 = y - 0.5, col = colorPalette[y], lwd = 6)
    }

    graphics::plot(x = 1, ylim = c(0, length(overlaps)), xlim = c(GenomicRanges::start(region),
        GenomicRanges::end(region)), ylab = "", yaxt = "n")
    if (dim(GenomicRanges::as.data.frame(overlaps))[1] > 0) {
        index <- 0
        for (i in names(overlaps)) {

            index <- index + 1
            if (dim(GenomicRanges::as.data.frame(overlaps[i]))[1] == 1) {
                mysegment(overlaps[i], index, colorPalette)
            }
            if (dim(GenomicRanges::as.data.frame(overlaps[i]))[1] > 1) {
                mysegment(overlaps[i][1], index, colorPalette)

            }

        }
    } else {
        warning(paste0("There is no overlaps with the given region :", region))
    }
}

# take the peaks that are overlaping with the region to plot
# @param BED list of dataframes containing the peaks
# @param region GRanges object containing the region to plot
# @param verbose Prompt the progress
# @return returns a list of dataframes containing the peaks

takePeaksOverlap <- function(BED, region, verbose) {
    if (verbose == TRUE) {
        message("overlapping peaks with region \n")
    }
    peaks <- loadPeaks(BED = BED, verbose)

    return_object <- GenomicRanges::GRangesList()
    for (software in names(peaks)) {
        temp <- peaks[[software]][c(1, 2, 3)]
        colnames(temp) <- c("seqname", "start", "end")
        temp <- GenomicRanges::GRanges(temp)
        return_object[[software]] <- temp[S4Vectors::queryHits(GenomicRanges::findOverlaps(temp,
            region))]
    }

    return(return_object)
}

# load the peaks from the bed files listed in the info
# @param BED list of dataframes containing the peaks
# @param verbose Prompt the progress
# @return returns a list of dataframes

loadPeaks <- function(BED, verbose) {
    if (verbose == TRUE) {
        message("load the peak files \n")
    }
    temp <- lapply(X = BED$files, FUN = function(x) utils::read.table(file = x, sep = "\t"))
    names(temp) <- BED$software
    return(temp)
}