gview {scruff} | R Documentation

## Visualize gene isoforms

### Description

Visualize reference genome. Rectangles represent exons. Arrow represents orientation of transcripts.

### Usage

    gview(
      gtfFile,
      chr = 1,
      start = 1,
      end = max(data.table::as.data.table(rtracklayer::import(gtfFile))[seqnames == chr,
        end]),
      rect_width = 0.3,
      line_width = 0.5,
      arrow_segments = 10,
      arrow_width = 30,
      arrow_length = 0.08,
      arrow_type = "open",
      text_size = 4
    )

### Arguments

`gtfFile` | A genome annotation file in GTF format.
`chr` | Chromosome name. Integer or "X", "Y", "MT".
`start` | Genomic coordinate of the start position.
`end` | Genomic coordinate of the end position.
`rect_width` | Exon widths. Default 0.3.
`line_width` | Line weight. Default 0.5.
`arrow_segments` | The number of segments lines be divided to. The greater the number, more arrows there are. Default 10.
`arrow_width` | The angle of the arrow head in degrees (smaller numbers produce narrower, pointier arrows). Essentially describes the width of the arrow head. Passed to the angle parameter of arrow function. Default 30.
`arrow_length` | The length of the arrow head. Passed to the length argument of arrow function. Default 0.08.
`arrow_type` | One of "open" or "closed" indicating whether the arrow head should be a closed triangle. Passed to the type argument of arrow function. Default "open".
`text_size` | Size of text. Passed to the size argument of the geom_text function. Default 4.

### Value

A ggplot object of genomic view

### Examples

    gtf <- system.file("extdata", "GRCm38_MT.gtf", package = "scruff")
    g <- gview(gtf, chr = "MT")
    g

[Package scruff version 1.5.12 Index]