R/plotDotp.R

In daewoooo/SVbyEye: Visualization of genomic structural variants

#' Plot simple dotplot of two sequences.
#'
#' This function takes alignment coordinates from 'nucmer' or 'minimap2' aligner and
#' construct a simple dot plot.
#'
#' @param coords.file A path to a PAF or NUCMER specific file containing alignments to be loaded.
#' @param format Is either 'mm2' or 'nucmer' for minimap2 or NUCmer specific input 'coords.file', respectively.
#' @param shape A shape used to plot aligned sequences: Either 'segment' or 'point'.
#' @param keep.longest.aln Set to \code{TRUE} if a target sequence with a single longest alignment should be kept.
#' @param genome.coord Set to \code{TRUE} if the target sequence should be reported in genomic coordinates.
#' @inheritParams filterPaf
#' @inheritParams plotSelf
#' @return A \code{ggplot} object.
#' @import ggplot2
#' @importFrom scales comma
#' @author David Porubsky
#' @export
#' @examples
#' ## Get NUCmer alignment coordinates to plot
#' nucmer.coords <- system.file("extdata", "HG00438_1_nucmer.coords", package = "SVbyEye")
#' ## Make a dotplot
#' simpledotplot(coords.file = nucmer.coords, format = "nucmer")
#' ## Get minimap2 alignments to plot
#' mm2.coords <- system.file("extdata", "HG01071_2_mm2.paf", package = "SVbyEye")
#' ## Make a dotplot
#' simpledotplot(coords.file = mm2.coords, format = "mm2")
#' ## Highlight desired genomic positions
#' highlight.pos <- c(330000, 560000)
#' simpledotplot(coords.file = mm2.coords, format = "mm2", highlight.pos = highlight.pos)
#'
simpledotplot <- function(coords.file = NULL, format = "nucmer", shape = "segment", min.align.len = 1000, keep.longest.aln = FALSE, highlight.pos = NULL, highlight.region = NULL, genome.coord = FALSE) {
    ## Helper function
    remapCoord <- function(x = NULL, new.range = NULL) {
        offset <- (min(new.range) + x[1]) - 1
        dist <- cumsum(diff(x))
        new.x <- c(offset, (offset + dist))
        return(new.x)
    }

    ## Check if the submitted file exists
    if (!nchar(coords.file) > 0 | !file.exists(coords.file)) {
        stop("Submitted file in 'coords.file' does not exists !!!")
    }

    ## Data input ##
    ################
    if (format == "nucmer") {
        ## Read in coordinates from nucmer output
        coords <- utils::read.table(file = coords.file, skip = 5, stringsAsFactors = FALSE, comment.char = "&")
        coords.df <- data.frame(
            s1.start = coords$V1,
            s1.end = coords$V2,
            s2.start = coords$V4,
            s2.end = coords$V5,
            s1.width = abs(coords$V1 - coords$V2),
            s2.width = abs(coords$V4 - coords$V5),
            s1.id = coords$V12,
            s2.id = coords$V13,
            stringsAsFactors = FALSE
        )
    } else if (format == "mm2") {
        paf.data <- readPaf(paf.file = coords.file, include.paf.tags = FALSE)
        coords.df <- data.frame(
            s1.start = paf.data$q.start,
            s1.end = paf.data$q.end,
            s2.start = paf.data$t.start,
            s2.end = paf.data$t.end,
            s1.width = paf.data$aln.len,
            s2.width = paf.data$aln.len,
            s1.id = paf.data$q.name,
            s2.id = paf.data$t.name,
            stringsAsFactors = FALSE
        )

        ## Flip start and end for reverse oriented alignments
        coords.df[paf.data$strand == "-", ] <- transform(coords.df[paf.data$strand == "-", ],
            "s2.start" = coords.df[paf.data$strand == "-", ]$s2.end,
            "s2.end" = coords.df[paf.data$strand == "-", ]$s2.start
        )
    }

    ## Get max position (for x-axis plotting)
    max.pos <- max(c(coords.df$s1.start, coords.df$s1.end, coords.df$s2.start, coords.df$s2.end))

    ## Translate sequence coordinates to genome-wide coordinates [only works for nucmer]
    if (format == "mm2") {
        genome.coord <- FALSE
    }
    if (genome.coord) {
        s2.region <- unique(coords.df$s2.id)
        s2.region <- strsplit(s2.region, ":")[[1]][2]
        s2.range <- as.numeric(strsplit(s2.region, "-")[[1]])
        coords.df$s2.start <- remapCoord(x = coords.df$s2.start, new.range = s2.range)
        coords.df$s2.end <- remapCoord(x = coords.df$s2.end, new.range = s2.range)
    }

    ## Data filtering ##
    ####################
    ## Filter by alignment length
    if (min.align.len > 0) {
        coords.df <- coords.df[coords.df$s1.width >= min.align.len & coords.df$s2.width >= min.align.len, ]
    }
    ## Remove duplicated ranges
    xmin <- apply(coords.df[, c("s1.start", "s1.end", "s2.start", "s2.end")], 1, min)
    xmax <- apply(coords.df[, c("s1.start", "s1.end", "s2.start", "s2.end")], 1, max)
    coords.df <- coords.df[!duplicated(paste(xmin, xmax, sep = "_")), ]

    ## Keep only the target sequence with the longest alignment
    if (keep.longest.aln) {
        # s2.aln.len <- sapply(split(coords.df$s2.width, coords.df$s2.id), sum)
        s2.aln.len <- vapply(split(coords.df$s2.width, coords.df$s2.id), sum, FUN.VALUE = numeric(1))
        to.keep <- names(s2.aln.len)[which.max(s2.aln.len)]
        coords.df <- coords.df[coords.df$s2.id == to.keep, ]
    }
    ## If there are more than one query sequence concatenate into a single string
    if (length(unique(coords.df$s1.id)) > 1) {
      coords.df$s1.id <- paste(unique(coords.df$s1.id), collapse = ';')
    }

    ## Data transformations ##
    ##########################
    ## Add alignment directionality
    coords.df$dir <- "rev"
    forw.mask <- (coords.df$s1.start < coords.df$s1.end) & (coords.df$s2.start < coords.df$s2.end)
    coords.df$dir[forw.mask] <- "forw"

    ## Prepare data for plotting ##
    ###############################
    ## Order alignments by size
    coords.df$aln.size <- coords.df$s1.width + coords.df$s2.width
    coords.df <- coords.df[order(coords.df$aln.size, decreasing = TRUE), ]

    ## Coerce shape segment in minimap alignments are loaded
    if (format == "mm2" & shape == "point") {
        shape <- "segment"
        message("     Coercing shape == 'segm' for alignments in 'mm2' format!")
    }

    if (shape == "segment") {
        ## Plot alignments
        plt <- ggplot2::ggplot(data = coords.df, ggplot2::aes(x = .data$s1.start, xend = .data$s1.end, y = .data$s2.start, yend = .data$s2.end, color = .data$dir)) +
            ggplot2::geom_segment()
    } else if (shape == "point") {
        coords.df$s1.midpoint <- coords.df$s1.start + ((coords.df$s1.end - coords.df$s1.start) / 2)
        coords.df$s2.midpoint <- coords.df$s2.start + ((coords.df$s2.end - coords.df$s2.start) / 2)
        plt <- ggplot2::ggplot(data = coords.df, ggplot2::aes(x = .data$s1.midpoint, y = .data$s2.midpoint, color = .data$dir)) +
            ggplot2::geom_point()
    } else {
        warning("Paremeter shape can only take values 'segment' or 'point' !!!")
        plt <- ggplot2::ggplot()
    }
    ## If there are multiple alignment to the target sequence use facets to divide the dotplot
    n.seq <- length(unique(coords.df$s2.id))
    if (n.seq > 1) {
        plt <- plt +
            ggplot2::facet_grid(s2.id ~ ., space = "free", scales = "free") +
            ggplot2::xlab(unique(coords.df$s1.id)) +
            ggplot2::ylab(paste(unique(coords.df$s2.id), collapse = ";")) +
            ggplot2::theme_bw() +
            ggplot2::scale_color_manual(values = c("chartreuse4", "darkgoldenrod2")) +
            ggplot2::scale_x_continuous(labels = scales::comma) +
            ggplot2::scale_y_continuous(labels = scales::comma)
    } else {
        plt <- plt +
            ggplot2::xlab(unique(coords.df$s1.id)) +
            ggplot2::ylab(unique(coords.df$s2.id)) +
            ggplot2::theme_bw() +
            # theme(aspect.ratio=1) + #force x and y axis to have the same proportion
            ggplot2::scale_color_manual(values = c("chartreuse4", "darkgoldenrod2")) +
            ggplot2::scale_x_continuous(labels = scales::comma) +
            ggplot2::scale_y_continuous(labels = scales::comma)
    }

    ## Highlight user defined positions
    if (!is.null(highlight.pos) & is.numeric(highlight.pos)) {
        highlight.pos <- highlight.pos[highlight.pos > 0 & highlight.pos <= max.pos]

        if (length(highlight.pos) > 0) {
            plt <- plt + ggplot2::geom_vline(xintercept = highlight.pos)
        }
    }

    ## Highlight user defined region
    if (!is.null(highlight.region)) {
        highlight.region <- highlight.region[highlight.region$xmin > 0 & highlight.region$xmax <= max.pos, ]

        if (nrow(highlight.region) > 0) {
            plt <- plt +
                ggplot2::geom_rect(data = highlight.region, ggplot2::aes(xmin = xmin, xmax = xmax, ymin = 0, ymax = Inf), color = "red", alpha = 0.25)
        }
    }

    ## Return final plot
    return(plt)
}