plotting: Lattice-style plots for granges and SnpArrayExperiment...
In VanillaICE: A Hidden Markov Model for high throughput genotyping arrays

Description Usage Arguments See Also Examples

Data for the graphic is generated by a call to grangesData.

xyplotList(granges, se, param = HmmTrellisParam())

## S4 method for signature 'HmmGRanges,SnpArrayExperiment'
xyplotList(granges, se, param = HmmTrellisParam())

## S4 method for signature 'GRangesList,SnpArrayExperiment'
xyplotList(granges, se, param = HmmTrellisParam())

xygrid(trellis_plot, viewports, granges)

`granges`	a `HmmGRanges` object
`se`	a `SnpArrayExperiment`
`param`	trellis parameters for plotting HMM
`trellis_plot`	an object of class `trellis`
`viewports`	a list of viewports as provided by the `viewports` function

viewports

if(require("BSgenome.Hsapiens.UCSC.hg18")){
  bsgenome <- BSgenome.Hsapiens.UCSC.hg18
  snp_exp <- getExampleSnpExperiment(bsgenome)
  seqlevels(snp_exp, pruning.mode="coarse") <- "chr22"
  fit <- hmm2(snp_exp)
  g <- reduce(hemizygous(fit), min.gapwidth=500e3)
  trellis_param <- HmmTrellisParam()
  fig <- xyplotList(g, snp_exp, trellis_param)
  vps <- viewports()
  xygrid(fig[[1]], vps, g)
}