Basic4Cseq (version 1.8.0)

plotTransInteractions: 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

interactionFile

Interaction interval data; either a file name or a data frame

chromosomeViewpoint

Viewpoint chromosome of the 4C-seq experiment

coordViewpoint

Viewpoint coordinates of the 4C-seq experiment

ideogramData

Ideogram data to be visualized in the RCirco-plot; either a file name or a data frame

PlotColor

Plot colours for the visualized interactions

expandBands

If TRUE, add a specified value to the size of the interaction intervals to increase the visibility of very small interactions

expansionValue

Value that is added to each interaction interval end

plotFileName

Optional name for an output file

picDim

Dimensions of the plot

Value

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.

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 = "")
  }