qqhex {GGtools} | R Documentation

## 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)

[Package GGtools version 5.25.3 Index]