Plot coverage around a virtual 4C viewpoint

Description

Plots coverage of interactions around a given viewpoint. This function requires the output of 'viewPoint()' as input. You should additionally specify the total region you wish to plot.

Usage

plotViewpoint(x, region, ylab = "Signal", xlab = NULL, ...)

Arguments

Value

Coverage that is plotted (invisibly)

Examples

data(hic_example_data)
library(GenomicRanges)
pos <- GRanges(seqnames="chr15", ranges=IRanges(start=59477709, end=59482708))
region <- GRanges(seqnames="chr15", ranges=IRanges(start=58980209, end=59980208))
vp <- viewPoint(hic_example_data, pos, region)
plotViewpoint(vp, region)

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)

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(GenomicInteractions)
Loading required package: InteractionSet
Loading required package: GenomicRanges
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: 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")'.

Warning message:
replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomicInteractions/plotViewpoint.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotViewpoint
> ### Title: Plot coverage around a virtual 4C viewpoint
> ### Aliases: plotViewpoint
> 
> ### ** Examples
> 
> data(hic_example_data)
> library(GenomicRanges)
> pos <- GRanges(seqnames="chr15", ranges=IRanges(start=59477709, end=59482708))
> region <- GRanges(seqnames="chr15", ranges=IRanges(start=58980209, end=59980208))
> vp <- viewPoint(hic_example_data, pos, region)
> plotViewpoint(vp, region)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>