Plot data along the genome

Description

Plot location data and chromosome boundaries from a GenoSet or GRanges object against data from a numeric or Rle. Specifying a chromosome name and optionally a 'xlim' will zoom into one chromosome region. If more than one chromosome is present, the chromosome boundaries will be marked. Alternatively, for a numeric x and a numeric or Rle y, data in y can be plotted at genome positions x. In this case, chromosome boundaries can be taken from the argument locs. If data for y-axis comes from a Rle lines are plotted representing segments. X-axis tickmarks will be labeled with genome positions in the most appropriate units.

Usage

genoPlot(x, y, ...)

## S4 method for signature 'numeric,numeric'
genoPlot(x, y, add = FALSE, xlab = "",
  ylab = "", col = "black", locs = NULL, ...)

## S4 method for signature 'numeric,Rle'
genoPlot(x, y, add = FALSE, xlab = "", ylab = "",
  col = "red", locs = NULL, lwd = 2, xlim = NULL, ...)

## S4 method for signature 'GenoSetOrGenomicRanges,ANY'
genoPlot(x, y, chr = NULL,
  add = FALSE, pch = ".", xlab = "", ylab = "", ...)

Arguments

Value

TRUE

Methods

signature(x = "GenoSetOrGenomicRanges", y = "ANY")

Plot feature locations and data from one sample.

signature(x = "numeric", y = "numeric")

Plot numeric location and a vector of numeric data.

signature(x = "numeric", y = "Rle")

Plot numeric location and a vector of Rle data. Uses lines for Rle runs.

See Also

Other "genome plots": genomeAxis

Examples

data(genoset,package="genoset")
genoPlot( x=genoset.ds,y=genoset.ds[,1,"lrr"] )
genoPlot( genoPos(genoset.ds), genoset.ds[,1,"lrr"], locs=rowRanges(genoset.ds) ) # The same
genoPlot( 1:10, Rle(c(rep(0,5),rep(3,4),rep(1,1))) )

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(genoset)
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")'.


*** Genoset API Changes ***
The genoset class has transitioned to the
RangedSummarizedExperiment API from the eSet API (e.g. use colnames instead of sampleNames). ***

Attaching package: 'genoset'

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

    pos

The following objects are masked from 'package:S4Vectors':

    colMeans, colSums, rowMeans, rowSums

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

    colMeans, colSums, rowMeans, rowSums

Warning messages:
1: multiple methods tables found for 'colMeans' 
2: multiple methods tables found for 'colSums' 
3: multiple methods tables found for 'rowMeans' 
4: multiple methods tables found for 'rowSums' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genoset/genoPlot-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: genoPlot
> ### Title: Plot data along the genome
> ### Aliases: genoPlot genoPlot,GenoSetOrGenomicRanges,ANY-method
> ###   genoPlot,numeric,Rle-method genoPlot,numeric,numeric-method
> 
> ### ** Examples
> 
> data(genoset,package="genoset")
> genoPlot( x=genoset.ds,y=genoset.ds[,1,"lrr"] )
> genoPlot( genoPos(genoset.ds), genoset.ds[,1,"lrr"], locs=rowRanges(genoset.ds) ) # The same
> genoPlot( 1:10, Rle(c(rep(0,5),rep(3,4),rep(1,1))) )
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>