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#' Plots the summary matrix
#'
#' Plots the summary matrix with counts on y-axis and classification on x-axis.
#'
#' @param x Summary matrix returned from dbcompare
#' @param log Specifies whether log(Counts) should be plotted (default)
#' @param las Direction of the labels on x-axis. Default is 3 which gives
#' perpendicular labels
#' @param xlab Axis label
#' @param ylab Axis label
#' @param ... Other plot options
#' @return A plot of the summary matrix. The counts are on log10 scale and the
#' x-axis is labeled by appropriate matching/partially-matching levels.
#' @author James Curran and Torben Tvedebrink
#' @seealso dbCompare,print.dbcompare
#' @examples
#'
#' \dontrun{
#' data(dbExample)
#' M = dbCompare(dbExample,hit=5)
#' plot(M)
#' }
#'
#' @rawNamespace S3method(plot, dbcompare)
#' @importFrom graphics plot axis box
#' @export plot.dbcompare
plot.dbcompare <- function(x, log = "y", las = 3, xlab = "Match/Partial", ylab = "Counts", ...) {
nl <- attributes(x)$call$loci
levs <- dbCats(nl, vector = TRUE)
if (is.matrix(x$m))
mvec <- t(x$m)[up.tri(x$m)] else mvec <- x$m
mvec[mvec == 0] <- NA
if (attributes(x)$call$collapse) {
mcol <- ifelse(x$m == 0, NA, x$m)
if (xlab == "Match/Partial")
xlab <- "Total number of matching alleles"
graphics::plot(0:(length(mcol) - 1), mcol, log = log, xlab = xlab, ylab = ylab, ...)
} else {
graphics::plot(1:length(levs), mvec, axes = FALSE, xlab = xlab, ylab = ylab, log = log, ...)
graphics::axis(1, at = 1:length(levs), labels = levs, las = las)
graphics::axis(2)
graphics::box()
}
}
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