xyplotList {VanillaICE} | R Documentation

## 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())

    ## 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)

### 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, 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)
    }

[Package VanillaICE version 1.46.0 Index]