plotChromosome: Display the chromosome distribution of structural variations

In venyao/intansv: Integrative analysis of structural variations

Display the chromosome distribution of structural variations

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

    plotChromosome(genome, structuralVariation, windowSize=1000000)

Arguments

genome	A data frame with ID and length of all Chromosomes.
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

    delly <- readDelly(system.file("extdata/ZS97.DELLY.vcf",package="intansv"))
    str(delly)

    genome.file.path <- system.file("extdata/chr05_chr10.genome.txt", package="intansv")
    genome <- read.table(genome.file.path, head=TRUE, as.is=TRUE)
    str(genome)

    plotChromosome(genome,delly,1000000)
	

venyao/intansv documentation built on Jan. 3, 2024, 6:15 p.m.