Plot copy number and physical position for a set of genomic intervals.

Description

Plot copy number and physical position given by a CNSet object for a set of genomic intervals stored in a RangedDataCVN object.

Usage

xyplot2(x, data, range, frame=50e3L, ...)

Arguments

Details

These functions plot copy number estimates versus physical position. The function is particularly useful for multi-panel displays in which the copy number estimates for a single range of a GRanges object appears in one panel. The size of the multi-panel display depends on the number of ranges (rows) in the GRanges object.

Value

An object of class trellis.

Author(s)

R. Scharpf

See Also

xyplot, xypanel

To modify the plot appearance from the default, additional arguments can be passed to panel.xyplot, lpoints, and lrect.

Examples

  ## simulated data
  library(oligoClasses)
  library(IRanges)
  library(VanillaICE)
  data(oligoSetExample, package="oligoClasses")
  ## The oligoSnpSet class will likely be deprecated and made defunct
  ## in a future release.  Instead, we favor
  ## RangedSummarizedExperiment-derived classes defined in VanillaICE
  oligoSet <- oligoSet[chromosome(oligoSet) == 1, ]
  grl <- hmm(oligoSet, p.hom=0, TAUP=1e10, is.log=FALSE)
  g <- grl[[1]]

  ## To visualize each range in it's own panel surrounded by a
  ## frame of 2,000,000 bases:
  ## (here the frames are overlapping, but the method could be
  ## applied more generally to a collection of ranges from
  ## different chromsomes and samples)
  xyplot2(cn~x | range, data=oligoSet,
	       range=g,
	       frame=2e6, panel=xypanel,
	       cex=2,
	       pch=".",
	       col.het="salmon",
	       fill.het="salmon",
	       col.hom="royalblue",
	       fill.hom="royalblue",
	       state.cex=0.5,
	       border="orange", scales=list(x="free"),
	       par.strip.text=list(cex=0.5),
	       xlab="Mb", ylab=expression(log[2]("copy number")))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(SNPchip)
Welcome to SNPchip version 2.18.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SNPchip/xyplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: xyplot
> ### Title: Plot copy number and physical position for a set of genomic
> ###   intervals.
> ### Aliases: xyplot2 xyplot2,formula,gSet-method
> ###   xyplot2,formula,SnpSet-method
> ### Keywords: dplot methods
> 
> ### ** Examples
> 
>   ## simulated data
>   library(oligoClasses)
Welcome to oligoClasses version 1.34.0
>   library(IRanges)
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

>   library(VanillaICE)
Loading required package: GenomicRanges
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
>   data(oligoSetExample, package="oligoClasses")
>   ## The oligoSnpSet class will likely be deprecated and made defunct
>   ## in a future release.  Instead, we favor
>   ## RangedSummarizedExperiment-derived classes defined in VanillaICE
>   oligoSet <- oligoSet[chromosome(oligoSet) == 1, ]
>   grl <- hmm(oligoSet, p.hom=0, TAUP=1e10, is.log=FALSE)
Warning message:
executing %dopar% sequentially: no parallel backend registered 
>   g <- grl[[1]]
> 
>   ## To visualize each range in it's own panel surrounded by a
>   ## frame of 2,000,000 bases:
>   ## (here the frames are overlapping, but the method could be
>   ## applied more generally to a collection of ranges from
>   ## different chromsomes and samples)
>   xyplot2(cn~x | range, data=oligoSet,
+ 	       range=g,
+ 	       frame=2e6, panel=xypanel,
+ 	       cex=2,
+ 	       pch=".",
+ 	       col.het="salmon",
+ 	       fill.het="salmon",
+ 	       col.hom="royalblue",
+ 	       fill.hom="royalblue",
+ 	       state.cex=0.5,
+ 	       border="orange", scales=list(x="free"),
+ 	       par.strip.text=list(cex=0.5),
+ 	       xlab="Mb", ylab=expression(log[2]("copy number")))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>