IdiogramParams-class: Paramater class for plotting idiograms
In VanillaICE: A Hidden Markov Model for high throughput genotyping arrays

Description Usage Arguments Slots Examples

Paramater class for plotting idiograms

1 2	## S4 method for signature 'IdiogramParams' show(object)

object

an IdiogramParam object

seqnames: length-one character vector providing chromosome name
seqlengths: length-one numeric vector indicating size of chromosome
unit: character string indicating unit for genomic position (default is 'kb')
genome: character string indicating genome build
box: a list of parameters for plotting the box around the part of the idiogram that is plotted.

if(require(BSgenome.Hsapiens.UCSC.hg18) && require(grid)){
   si <- seqinfo(BSgenome.Hsapiens.UCSC.hg18)
   iparam <- IdiogramParams(seqnames="chr1",
                            genome="hg18",
                            seqlengths=seqlengths(si)["chr1"],
                            box=list(xlim=c(20e6L, 25e6L), color="blue", lwd=2))
   iparam
   idiogram <- plot(iparam)
   vp <- viewport(x=0.05, y=0.8, width=unit(0.9, "npc"), height=unit(0.2, "npc"),
                  name="vp1", just=c("left", "bottom"))
   grid.newpage()
   pushViewport(vp)
   print(idiogram, vp=vp, newpage=FALSE)
}