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Last data update: 2014.03.03

R: Nucleosome calling plot function

plotPeaks

R Documentation

Nucleosome calling plot function

Description

Helper function for a quick and convenient overview of nucleosome calling data.

This function is intended to plot data previously processed with nucleR pipeline. It shows a coverage/intensity profile toghether with the identified peaks. If available, score of each peak is also shown.

Usage

plotPeaks(peaks, data, ...)
## S4 method for signature 'IRanges'
plotPeaks(peaks, data, threshold=0, scores=NULL, start=1,
		end=length(data),dyn.pos=TRUE, xlab="position", type="l", col.points="red",
		thr.lty=1,	thr.lwd="1", thr.col="darkred", rect.thick=2, rect.lwd=1,
		rect.border="black", scor.col=col.points, scor.font=2, scor.adj=c(0.5,0),
		scor.cex=0.75, scor.digits=2, indiv.scores=TRUE, ...)
## S4 method for signature 'numeric'
plotPeaks(peaks, data, threshold=0, scores=NULL, start=1,
    end=length(data), xlab="position", type="l", col.points="red",
    thr.lty=1,  thr.lwd="1", thr.col="darkred", scor.col=col.points, scor.font=2,
		scor.adj=c(0.5,0), scor.cex=0.75, scor.digits=2,...)

Arguments

`peaks`	`numeric`, `data.frame`, `IRanges` or `RangedData` object containing the detected peaks information. See help of `peakDetection` or `peakScoring` for more details.
`data`	Coverage or Tiling Array intensities
`threshold`	Threshold applied in `peakDetection`
`scores`	If `peaks` is a `data.frame` or a `RangedData` it's obtained from 'score' column, otherwise, `scores` can be given here as a `numeric` vector
`start, end`	Start and end points defining a subset in the range of `data`. This is a convenient way to plot only a small region of data, without dealing with subsetting of range or score objects.
`dyn.pos`	If peaks are ranges, should they be positioned dynamicaly on top of the peaks or staticaly at `threshold` baseline. Spacing of overlapping ranges is automatically applied if `FALSE`.
`xlab, type, col.points`	Default values to be passed to `plot` and `points`
`thr.lty, thr.lwd, thr.col`	Default values to be passed to `abline` for threshold representation
`rect.thick, rect.lwd, rect.border`	Default values for `rect` representation or ranges. `rect.thick` indicates the thickness (in percentage relative to y-axis range) of the rectangles.
`scor.col, scor.font, scor.adj, scor.cex, scor.digits`	Default values for `text` representation for score numbers, if available.
`indiv.scores`	Show or hide individual scores for width and height in brakets besides the mixed score
`...`	Other parameters passed to `plot` function

Value

(none)

Author(s)

Oscar Flores oflores@mmb.pcb.ub.es

Examples


  #Generate a random peaks profile
  reads = syntheticNucMap(nuc.len=40, lin.len=130)$syn.reads
  cover = coverage(reads)

  #Filter them
  cover_fft = filterFFT(cover)

  #Detect peaks
  peaks = peakDetection(cover_fft, threshold="40%", score=TRUE, width=140)

	#Plot peaks and coverage profile (show only a window)
  plotPeaks(peaks, cover_fft, threshold="40%", start=1000, end=6000)

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(nucleR)
Loading required package: ShortRead
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: BiocParallel
Loading required package: Biostrings
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: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/nucleR/plotPeaks.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotPeaks
> ### Title: Nucleosome calling plot function
> ### Aliases: plotPeaks plotPeaks,numeric-method plotPeaks,data.frame-method
> ###   plotPeaks,RangedData-method plotPeaks,IRanges-method
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
>   #Generate a random peaks profile
>   reads = syntheticNucMap(nuc.len=40, lin.len=130)$syn.reads
>   cover = coverage(reads)
> 
>   #Filter them
>   cover_fft = filterFFT(cover)
> 
>   #Detect peaks
>   peaks = peakDetection(cover_fft, threshold="40%", score=TRUE, width=140)
> 
> 	#Plot peaks and coverage profile (show only a window)
>   plotPeaks(peaks, cover_fft, threshold="40%", start=1000, end=6000)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>