qqhex: obtain qqplot coordinates for the specific case of comparing...

In GGtools: software and data for analyses in genetics of gene expression

Description

obtain qqplot coordinates for the specific case of comparing a given distribution to that of multiple realizations from a permutation distribution, and bin these coordinates using hexbin, useful for very large samples

Usage

binnedQQ(dt, nxbins=20,
  ylim=c(0,76), xlim=c(0,30), end45=5, thrs=c(0,.001,.005,.01,.05), 
  tempmar = c(6,4,4,5), ...)
qqhex(sco, p1, p2, p3, fdr, nxbins = 20, thrs = c(0, 0.001, 0.005, 0.01, 0.05))
binqq(qqob, ylim = c(0, 76), xlim = c(0, 30), end45=5, ...)

Arguments

dt	a data.table instance with association scores and scores obtained under permutation along with FDR, as returned by cgff2dt or ciseqByCluster
sco	numeric vector of observed statistics
p1	realization of null distribution for sco, independent of p2 and p3
p2	realization of null distribution for sco, independent of p1 and p3
p3	realization of null distribution for sco, independent of p1 and p2
fdr	vector of FDR associated with elements of sco
nxbins	number of bins to be used for samples from the null distribution
thrs	vector of thresholds in FDR to be used for ruling the plot
qqob	for binhex(), output of qqhex
ylim	vertical limits of rendering
xlim	horizontal limits of rendering
end45	a segment is drawn from (0,0) to (end45,end45) to depict the line of identity
tempmar	numerical vector with 4 elements serving as a temporary setting of the mar parameter of par
...	not currently used

Value

for qqhex, a list with elements

hb	output of hexbin
thrs	vector of input thrs
scothrs	vector of observed statistics corresponding to FDRs in thrs

Examples

opar = par(no.readonly=TRUE)
set.seed(123)
x = c(rchisq(9000,1), rchisq(1000,12))
nn = lapply(1:3, function(x) rchisq(10000,1))
fd = pifdr(x, unlist(nn))
qqh = qqhex(x, nn[[1]], nn[[2]], nn[[3]], fd)
par(mar=c(4,4,4,7))
binqq(qqh,xlim=c(0,10), ylim=c(0,20))
mtext(4, "FDR")
par(opar)

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.