rview {scruff} | R Documentation

## Visualize aligned reads

### Description

Visualize read alignments for UMI tagged single cell RNA-sequencing data. Read names must contain UMI sequences at the end delimited by ":". Arrow represents orientation of alignment. Reads are colored by their UMI and sorted by their start positions and UMI.

### Usage

    rview(
      bamGA,
      chr = "1",
      start = 1,
      end = max(BiocGenerics::end(bamGA)),
      legend = FALSE
    )

### Arguments

`bamGA` | A GenomicAlignment object
`chr` | Chromosome. Integer or "X", "Y", "MT".
`start` | Genomic coordinate of the start position.
`end` | Genomic coordinate of the end position.
`legend` | Show legend. Default is FALSE.

### Value

A ggplot object of aligned reads

### Examples

    data(bamExample, package = "scruff")
    g <- rview(bamExample, chr = "MT", legend = TRUE)
    g

[Package scruff version 1.12.1 Index]