rnaseq2g.plot.pvalue <- function(res, nm1, nm2, typ, mth) {
if (!is.null(res)) {
if (nm1=='' | nm2=='') plot(0, type='n', axes=FALSE, xlab='', ylab='') else {
p1 <- res[[2]][[nm1]][, 5];
p2 <- res[[2]][[nm2]][, 5];
p1[is.na(p1)] <- 1;
p2[is.na(p2)] <- 1;
par(mar=c(5,5,2,2));
if (typ == '1') {
x <- sort(-log10(p1));
y <- sort(-log10(p2));
lb <- paste('-Log10(p value)', c(mth[nm1, 1], mth[nm2, 1]), sep=', ');
plot(x, y, pch=18, cex=1, col='#88888888', cex.lab=2, xlab=lb[1], ylab=lb[2]);
abline(0, 1, col=4, lty=2, lwd=2);
} else {
rk1 <- rank(p1);
rk2 <- rank(p2);
lb <- paste('P value ranking', c(mth[nm1, 1], mth[nm2, 1]), sep=', ');
len <- length(rk1);
plot(rk1, rk2, log='xy', pch=18, cex=1, col='#88888888', cex.lab=2, xlab=lb[1], ylab=lb[2], xlim=c(1, len), ylim=c(1, len));
abline(0, 1, col=4, lty=2, lwd=2);
}
box();
}
} else plot(0, type='n', axes=FALSE, xlab='', ylab='');
}
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