R/signalPlot.R In CNVassoc: Association Analysis of CNV Data and Imputed SNPs

Documented in plotSignal

```plotSignal <-
function (x, my.colors = c("black", "red", "blue"), ylab = "Peak Intensity",
xlab = c("individuals", "Phenotype"), case.control = NULL,
cex.leg = 0.6, dens.bw = "nrd0", dens.adjust = 1, n = 0,
...)
{
foo <- function(...) {
old.mfrow <- par("mfrow")
old.mar <- par("mar")
on.exit(par(mfrow = old.mfrow, mar = old.mar))
mm <- matrix(c(2:1), nrow = 1, ncol = 2, byrow = TRUE)
layout(mm, widths = c(1, 0.4))
par(mar = c(5.1, 0, 4.1, 2.1))
plot(den\$y, den\$x, type = "l", axes = FALSE, xlab = "density",
ylab = "", col = "red")
polygon(den\$y, den\$x, col = "red1")
ll <- par("usr")[3:4]
par(mar = c(5.1, 4.1, 4.1, 2.1))
if (!is.null(cutoffs)) {
if (all(x <= max(cutoffs)))
cat("WARNING! No data above maximum cutoff point\n")
if (all(x >= min(cutoffs)))
cat("WARNING! No data below minimum cutoff point\n")
x.ord <- as.integer(cut(x, c(-Inf, cutoffs, Inf)))
}
else x.ord <- rep(1, length(x))
if (is.null(case.control)) {
plot(x, ylim = ll, yaxs = "i", xlab = xlab[1], type = "n", ylab = ylab, ...)
points(x, col = my.colors[x.ord])
}
else {
tt <- unique(case.control)
if (length(tt) == 1) {
stop("case.control must have 2 differents values at least")
}
if (length(tt) > 2) {
plot(case.control, x, col = my.colors[x.ord],
ylim = ll, yaxs = "i", xlab = xlab[2], ylab = ylab,
...)
}
if (length(tt) == 2) {
plot(x, ylim = ll, yaxs = "i", xlab = xlab[1],
type = "n", ylab = ylab, ...)
o <- case.control == tt[1]
n <- sum(o)
points(1:n, x[o], col = my.colors[x.ord[o]],
pch = 16)
o <- case.control == tt[2]
points((n + 1):(n + sum(o)), x[o], col = my.colors[x.ord[o]],
pch = 4)
legend("bottomright", as.character(tt), pch = c(16,
4), title = "Case-control status", bty = "n",
horiz = TRUE, cex = cex.leg)
}
}
if (!is.null(cutoffs)) {
cutoffs <- sort(cutoffs)
legend("bottomleft", legend = round(rev(cutoffs),
4), bty = "n", lty = rev(1:length(cutoffs)),
title = "Cut off points:", cex = cex.leg)
abline(h = cutoffs, lty = 1:length(cutoffs))
}
}
cutoffs = NULL
foo()
if (n > 0) {
cat("Place cut off point(s) using locator...\n")
cutoffs <- locator(n)\$y
foo()
}
invisible(cutoffs)
}
```

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CNVassoc documentation built on May 30, 2017, 12:50 a.m.