#' plot a panel of gsea histograms
#' From a GSEA object, plot a histogram of the nominal p values,
#' FDR q values, or FWER p values.
#'
#' @param x a gsea object
#' @param main the plot titles
#' @param which one or more of \dQuote{p}, \dQuote{q}, or \dQuote{FWER},
#' corresponding to these columns in a GSEA report: \dQuote{NOM.p.val},
#' \dQuote{FDR.q.val}, \dQuote{FWER.p.val}, respectively.
#' @return none. creates a panel of histograms.
#' @author Mark Cowley, 2011-10-20
#' @export
plot_gsea.statistic.histograms <- function(x, main="", which=c("p", "q", "FWER")) {
!missing(x) && is.gsea(x) || stop("x must be a gsea object")
which <- match.arg(which, c("p", "q", "FWER"), several.ok=TRUE)
if( length(which) > 1 ) par(mfrow=c(1,length(which)))
col <- colours.mjc("reds", 20)
for(i in 1:length(which)) {
cn <- switch(which[i],
p="NOM.p.val",
q="FDR.q.val",
FWER="FWER.p.val"
)
vals <- x$tt[,cn]
hist(vals, breaks=seq(0,1,0.05), main=main, xlab=cn, col=col)
}
}
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