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

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)
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(VanillaICE)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to VanillaICE version 1.34.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/VanillaICE/plotting.Rd_%03d_medium.png", width=480, height=480)
> ### Name: xyplotList
> ### Title: Lattice-style plots for granges and SnpArrayExperiment objects
> ### Aliases: xygrid xyplotList
> ###   xyplotList,GRangesList,SnpArrayExperiment-method
> ###   xyplotList,HmmGRanges,SnpArrayExperiment-method
> 
> ### ** 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)
+ }
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:VanillaICE':

    deletion

Loading required package: rtracklayer
Writing parsed files to /home/ddbj/DataUpdator-rgm3/target
Warning message:
executing %dopar% sequentially: no parallel backend registered 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>