R/plot.cnv.probabilities.R

In isglobal-brge/CNVassoc: Association analysis of CNVs and imputed SNPs incorporating uncertainty

plot.cnv.probabilities <- function(x, my.colors = c("black", 
        "red", "blue"), case.control, ylab = "CNV probability", 
        xlab, ...) {
        probs <- attr(x, "probabilities")
        if (missing(case.control)) {
            names(probs) <- attr(x, "num.copies")
            if (missing(xlab)) 
                xlab <- "copy number"
            mp <- barplot(colMeans(probs), ylab = ylab, 
                xlab = xlab, col = my.colors, 
                ...)
            axis(1, mp, attr(x, "num.copies"), 
                tick = FALSE)
        } else {
            tt <- unique(case.control)
            if (length(tt) != 2) 
                stop("case.control should be a dicotomous variable")
            cc <- length(cl <- unique(case.control))
            tt <- unlist(by(probs, case.control, 
                colMeans))
            tt <- matrix(tt, ncol = cc)
            if (missing(xlab)) 
                xlab <- "case/control status"
            mp <- barplot(tt, ylab = ylab, xlab = xlab, 
                col = my.colors, ...)
            old.xpd <- par()$pxd
            par(xpd = NA)
            legend(mean(mp), 1.1, legend = attr(x, 
                "num.copies"), fill = my.colors, 
                xjust = 0.5, yjust = 0.5, horiz = TRUE, 
                title = "copy number")
            axis(1, mp, cl, tick = FALSE)
            par(xpd = old.xpd)
        }
        invisible()
}