plotChromosome {intansv} | R Documentation

## 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/delly",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)

[Package intansv version 1.22.0 Index]