VanillaICE (version 1.34.0)

xyplotList: Lattice-style plots for granges and SnpArrayExperiment objects

Description

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

Usage

xyplotList(granges, se, param = HmmTrellisParam())
"xyplotList"(granges, se, param = HmmTrellisParam())
"xyplotList"(granges, se, param = HmmTrellisParam())
xygrid(trellis_plot, viewports, granges)

Arguments

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

See Also

viewports

Examples

if(require("BSgenome.Hsapiens.UCSC.hg18")){
  bsgenome <- BSgenome.Hsapiens.UCSC.hg18
  snp_exp <- getExampleSnpExperiment(bsgenome)
  seqlevels(snp_exp, force=TRUE) <- "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)
}