plotRegion {intansv} | R Documentation

## Display structural variations in a specific genomic region

### Description

Display the structural variations in a specific genomic region in circular view.

### Usage

        plotRegion(structuralVariation, genomeAnnotation,
                   regionChromosome, regionStart, regionEnd)

### Arguments

`structuralVariation` | A list of structural variations.
`genomeAnnotation` | A data frame of genome annotations.
`regionChromosome` | The chromosome identifier of a specific region to view.
`regionStart` | The start coordinate of a specific region to view.
`regionEnd` | The end coordinate of a specific region to view.

### Details

Different SVs were shown as rectangles in different layers. See the package vignette and the example dataset for more details.

### Value

A circular plot of all the structural variations and genes in a specific region with four layers:

- The composition of genes of a specific genomic region.

- The composition of deletions of a specific genomic region.

- The composition of duplications of a specific genomic region.

- The composition of inversions of a specific genomic region.

### Author(s)

Wen Yao

### Examples

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

        anno.file.path <- system.file("extdata/chr05_chr10.anno.txt", package="intansv")
        msu_gff_v7 <- read.table(anno.file.path, head=TRUE, as.is=TRUE)
        str(msu_gff_v7)

        plotRegion(delly,msu_gff_v7,"chr05",1,200000)

[Package intansv version 1.22.0 Index]