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Last data update: 2014.03.03

R: Plot strand-specific read coverage for a GRanges object

plotStrandedCoverage

R Documentation

Plot strand-specific read coverage for a GRanges object

Description

Plot read counts within fixed bin across the entire chromosome.

Usage

plotStrandedCoverage(gr, binSize = 1000, plotLegend = FALSE, ylim, ...)

Arguments

`gr`	`GRanges` object containing the alignments.
`binSize`	Integer indicate the size of the bin used to compute and plot the read counts.
`plotLegend`	Binary indcator. If TRUE, legend will be plotted on the top left the plot. Legend is expected to be the chromsome name and length, which must be available in the GRange object argument.
`ylim`	A two element scale on the y-axis, indicating the maximum read counts on the + and - strand to be plotted (e.g., ylim=c(-200, 200)).
`...`	Extra arguments passed to `plotCoverage`.

Details

Read count on + and - strand are displayed as red and blue bars on the positive and negative y-axis, respectively. The x-axis indicates the positions across the chromosmoe. The plot can be used to examine for each chromosome the overall alignment properties such as strand specificity (expected in non-strand-specific sequencing) and aggregation of reads.

Author(s)

Yue Li

References

P. Aboyoun, H. Pages and M. Lawrence (). GenomicRanges: Representation and manipulation of genomic intervals. R package version 1.8.9.

Examples

# Retrieve system files
extdata.dir <- system.file("extdata", package="RIPSeeker") 

bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)

bamFiles <- grep("PRC2", bamFiles, value=TRUE)

alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9")

alignGR <- as(alignGal, "GRanges")

alignGRList <- GRangesList(as.list(split(alignGR, seqnames(alignGR))))

binSize <- 1000

plotStrandedCoverage(gr=alignGRList$chrX, binSize=binSize,

		xlab="", ylab="", plotLegend=TRUE, box.lty=0, legend.cex=2 )

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(RIPSeeker)
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
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")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicAlignments
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RIPSeeker/plotStrandedCoverage.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotStrandedCoverage
> ### Title: Plot strand-specific read coverage for a GRanges object
> ### Aliases: plotStrandedCoverage
> 
> ### ** Examples
> 
> # Retrieve system files
> extdata.dir <- system.file("extdata", package="RIPSeeker") 
> 
> bamFiles <- list.files(extdata.dir, ".bam$", recursive=TRUE, full.names=TRUE)
> 
> bamFiles <- grep("PRC2", bamFiles, value=TRUE)
> 
> alignGal <- getAlignGal(bamFiles[1], reverseComplement=TRUE, genomeBuild="mm9")
Processing /home/ddbj/local/lib64/R/library/RIPSeeker/extdata/PRC2/SRR039210_processed_tophat/accepted_hits_noDup_sel_chrX.bam ... All hits are returned with flags.
> 
> alignGR <- as(alignGal, "GRanges")
> 
> alignGRList <- GRangesList(as.list(split(alignGR, seqnames(alignGR))))
> 
> binSize <- 1000
> 
> plotStrandedCoverage(gr=alignGRList$chrX, binSize=binSize,
+ 
+ 		xlab="", ylab="", plotLegend=TRUE, box.lty=0, legend.cex=2 )
Warning messages:
1: In plot.window(...) : "box.lty" is not a graphical parameter
2: In plot.xy(xy, type, ...) : "box.lty" is not a graphical parameter
3: In axis(side = side, at = at, labels = labels, ...) :
  "box.lty" is not a graphical parameter
4: In axis(side = side, at = at, labels = labels, ...) :
  "box.lty" is not a graphical parameter
5: In box(...) : "box.lty" is not a graphical parameter
6: In title(...) : "box.lty" is not a graphical parameter
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>