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Jump to navigationJump to searchCode Sample: Generating QQ Plots in R (view source)
Revision as of 14:14, 12 November 2013
, 14:14, 12 November 2013→A Fancier QQ Plot by Matthew Flickinger
[[File:Pval-qq-sample.png|center]]
[[File:Pval-qq-sample.png|center]]
= Credit =
This page is based on a tutorial originally written by [mailto:mflick@umich.edu Matthew Flickinger]
== Credits ==
== Credits ==
ylab=expression(paste("Observed (",-log[10], " p-value)")),
ylab=expression(paste("Observed (",-log[10], " p-value)")),
draw.conf=TRUE, conf.points=1000, conf.col="lightgray", conf.alpha=.05,
draw.conf=TRUE, conf.points=1000, conf.col="lightgray", conf.alpha=.05,
already.transformed=FALSE, pch=20, aspect="iso",
already.transformed=FALSE, pch=20, aspect="iso", prepanel=prepanel.qqunif,
par.settings=list(superpose.symbol=list(pch=pch)), ...) {
par.settings=list(superpose.symbol=list(pch=pch)), ...) {
stop("pvalue vector is not numeric, can't draw plot")
stop("pvalue vector is not numeric, can't draw plot")
if (any(is.na(unlist(pvalues)))) stop("pvalue vector contains NA values, can't draw plot")
if (any(is.na(unlist(pvalues)))) stop("pvalue vector contains NA values, can't draw plot")
if (any(unlist(pvalues)==0)) stop("pvalue vector contains zeros, can't draw plot")
if (already.transformed==FALSE) {
if (any(unlist(pvalues)==0)) stop("pvalue vector contains zeros, can't draw plot")
} else {
if (any(unlist(pvalues)<0)) stop("-log10 pvalue vector contains negative values, can't draw plot")
}
gc()
gc()
prepanel.origin = function(x,y,...) {
prepanel.qqunif= function(x,y,...) {
A = list()
A = list()
A$xlim = range(x, y)*1.02
A$xlim = range(x, y)*1.02
#draw the plot
#draw the plot
xyplot(pvalues~exp.x, groups=grp, xlab=xlab, ylab=ylab, aspect=aspect,
xyplot(pvalues~exp.x, groups=grp, xlab=xlab, ylab=ylab, aspect=aspect,
prepanel=prepanel.origin, scales=list(axs="i"), pch=pch,
prepanel=prepanel, scales=list(axs="i"), pch=pch,
panel = function(x, y, ...) {
panel = function(x, y, ...) {
if (draw.conf) {
if (draw.conf) {
