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Last data update: 2014.03.03

R: Plotting ranges from GRanges

plotReads

R Documentation

Plotting ranges from GRanges

Description

Function plots cDNA inserts from GRanges created by readsamples() function. Similar to Figure 4A in HRF-Seq paper (see References).

Usage

plotReads(euc_GR, RNAid, cutoff = 1, order_by = 1, ylab, xlab, main, ylim,
  xlim, ...)

Arguments

`euc_GR`	GRanges generated by readsamples() function
`RNAid`	Transcript identifier, for which transcript plot should be generated.
`cutoff`	specifies cutoff length, only inserts of this length or longer will be used for processing (default: 1)
`order_by`	how displayed reads in plotReads function should be sorted. 1 - for sorting by termination location, 2 for sorting by reverse transcription start site
`ylab`	a title for the y axis: see `title`.
`xlab`	a title for the x axis: see `title`.
`main`	an overall title for the plot: see `title`.
`xlim,ylim`	numeric vectors of length 2, giving the x and y coordinates ranges.
`...`	Arguments to be passed to methods, such as `graphical parameters` (see `par`).

Value

Plotting function.

Author(s)

Lukasz Jan Kielpinski

References

Kielpinski, L.J., and Vinther, J. (2014). Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res.

Examples

dummy_euc_GR <- GRanges(seqnames="DummyRNA",
                        IRanges(start=round(runif(100)*100),
                        width=round(runif(100)*100+1)), strand="+",
                        EUC=round(runif(100)*100))
plotReads(dummy_euc_GR, RNAid="DummyRNA")

Results


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

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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: plyr

Attaching package: 'plyr'

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

    desc

The following object is masked from 'package:S4Vectors':

    rename

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RNAprobR/plotReads.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotReads
> ### Title: Plotting ranges from GRanges
> ### Aliases: plotReads
> 
> ### ** Examples
> 
> dummy_euc_GR <- GRanges(seqnames="DummyRNA",
+                         IRanges(start=round(runif(100)*100),
+                         width=round(runif(100)*100+1)), strand="+",
+                         EUC=round(runif(100)*100))
> plotReads(dummy_euc_GR, RNAid="DummyRNA")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>