GGtools (version 5.8.0)

qqhex: 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

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)