R/fvalVolcanoPlot.R

In fcros: A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

fvalVolcanoPlot <- function(af, thr = 0.05) {
    ratio <- af$FC2;
    pval <- af$f.value;
    idx <- (pval > 0.5);
    pval[idx] <- (1.0 - pval[idx]);
    de.idx <- (pval <= thr);
    x <- log2(ratio);
    y <- -log10(pval);
    plot(x, y, ylab = "-log10(p-Value)", xlab = "log2(FC)", col = "blue", main = "Volcano plot");
    lines(x[de.idx], y[de.idx], type = "p", col = "red");
}