Visualize trans interaction intervals

Description

This function visualizes trans interaction intervals of a 4C-seq experiment with the help of the RCircos package. Significant interactions can be obtained by use of Splinter et al's significant_interactions code or similar algorithms.

Usage

plotTransInteractions(interactionFile, chromosomeViewpoint, coordViewpoint, ideogramData, PlotColor = "default", expandBands = FALSE, expansionValue = 0, plotFileName = "", picDim = c(8, 8))

Arguments

Details

The code of Splinter et al to determine significant interactions provides chromosome, start and end of interaction intervals and a forth column with information on far-cis or trans data. This column is ignored by plotTransInteractions; it is assumed that all interactions for trans visualization are indeed trans interactions. Otherwise, far-cis interactions are visualized as well. While not a mistake per se, the (usually more numerous) far-cis interactions are easier to interpret if visualized with Splinter et al's spider-plot functions.

Value

An RCircos-plot of trans interaction intervals

Note

PDF export and output as TIFF format are supported. The export format is chosen depending on the plot file name's ending. If no plot file name is provided, the result is plotted on screen.

Author(s)

Carolin Walter

References

Zhang, H., Meltzer, P. and Davis, S. (2013) RCircos: an R package for Circos 2D track plots, BMC Bioinformatics, 14, 244

Splinter, E., de Wit, E., van de Werken, H., et al. (2012) Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation, Methods, 58, 221-230.

Examples

  if(interactive()) {
    library(RCircos)
    interactions <- system.file("extdata", "transInteractionData.txt", package="Basic4Cseq")
    ideograms <- system.file("extdata", "RCircos_GRCm38_ideogram.csv", package="Basic4Cseq")
    plotTransInteractions(interactions, "10", c(20000042, 20001000), ideograms, PlotColor = "blue", expandBands = TRUE, expansionValue = 1000000, plotFileName = "")
  }

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(Basic4Cseq)
Loading required package: Biostrings
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: XVector
Loading required package: GenomicAlignments
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
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: caTools

Attaching package: 'caTools'

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

    runmean

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

    runmean

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Basic4Cseq/plotTransInteractions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotTransInteractions
> ### Title: Visualize trans interaction intervals
> ### Aliases: plotTransInteractions
> ###   plotTransInteractions,character,character,numeric,character-method
> ###   plotTransInteractions,data.frame,character,numeric,data.frame-method
> ### Keywords: plotTransInteractions
> 
> ### ** Examples
> 
> #  if(interactive()) {
>     library(RCircos)
>     interactions <- system.file("extdata", "transInteractionData.txt", package="Basic4Cseq")
>     ideograms <- system.file("extdata", "RCircos_GRCm38_ideogram.csv", package="Basic4Cseq")
>     plotTransInteractions(interactions, "10", c(20000042, 20001000), ideograms, PlotColor = "blue", expandBands = TRUE, expansionValue = 1000000, plotFileName = "")
> #  }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>