gview: Visualize gene isoforms

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

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

scruff documentation built on Feb. 13, 2021, 2 a.m.