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

qqhex

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    colMeans, colSums, expand, rowMeans, rowSums

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

The following object is masked from 'package:stats':

    getCall

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGtools/qqhex.Rd_%03d_medium.png", width=480, height=480)
> ### Name: qqhex
> ### Title: 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
> ### Aliases: qqhex binqq binnedQQ
> ### Keywords: models
> 
> ### ** 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")
Warning message:
In mtext(4, "FDR") : NAs introduced by coercion
> par(opar)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>