geneRxCluster (version 1.8.0)

gRxPlotClumps: gRxPlotClumps

Description

Plot gRxCluster object clumps

Usage

gRxPlotClumps(object, data, seqlens, panelExpr = quote(grid()))

Arguments

object

result of gRxCluster

data

(optional) GRanges like that from which args to gRxCluster were derived

seqlens

(optional) seqlengths(data) or similar. Can be given if data is missing

panelExpr

- an expression to evaluate after drawing each panel

Details

Plot Relative Frequencies of the two classes according to region. Regions typically alternate between clusters and non-clusters on each chromosome.

Examples

x.seqnames <- rep(letters[1:3],each=50)
x.starts <- c(seq(1,length=50),seq(1,by=2,length=50),seq(1,by=3,length=50))
x.lens <- rep(c(5,10,15,20,25),each=2)
x.group <- rep(rep(c(TRUE,FALSE),length=length(x.lens)),x.lens)
## add a bit of fuzz:
x.group <- 1==rbinom(length(x.group),1,pr=ifelse(x.group,.8,.2))
x.kvals <- as.integer(sort(unique(x.lens)))
x.res <- gRxCluster(x.seqnames,x.starts,x.group,x.kvals)
gRxPlotClumps(x.res)
rm( x.seqnames, x.starts, x.lens, x.group, x.kvals, x.res)