gRxPlotClumps {geneRxCluster} | R Documentation |
Plot gRxCluster object clumps
gRxPlotClumps(object, data, seqlens, panelExpr = quote(grid()))
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 |
Plot Relative Frequencies of the two classes according to region. Regions typically alternate between clusters and non-clusters on each chromosome.
Charles Berry
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)