rview: Visualize aligned reads

In compbiomed/scuff: Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

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

compbiomed/scuff documentation built on March 28, 2024, 10:54 a.m.