Display the chromosome distribution of structural variations

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Description

Display the chromosome distribution of structural variations by splitting the chromosomes into windows of specific size and counting the number of structural variations in each window.

Usage

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    plotChromosome(genomeAnnotation, structuralVariation, windowSize=1000000)

Arguments

genomeAnnotation

GenomicRanges of the chromosome length.

structuralVariation

A list of structural variations.

windowSize

A specific size (in base pair) to split chromosomes into windows.

Details

To visualize the distribution of structural variations in the whole genome, chromosomes were splitted into windows of specific size (default 1 Mb) and the number of structural variations in each window were counted. The number of structural variations were shown using circular barplot.

Value

A circular plot with five layers:

  • the circular view of genome ideogram.

  • the chromosome coordinates labels.

  • the circular barplot of number of deletions in each chromosome window.

  • the circular barplot of number of duplications in each chromosome window.

  • the circular barplot of number of inversions in each chromosome window.

Author(s)

Wen Yao

Examples

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    delly <- readDelly(system.file("extdata/delly",package="intansv"))
    str(delly)

    load(system.file("extdata/genome.anno.RData",package="intansv"))
    str(genome)

    plotChromosome(genome,delly,1000000)