show.genome.annotation.plot: Draw genome annotation features

In ChrispinChaguza/RCandy: RCandy: an R package for rapid visualisation of homologous recombination events in bacterial genomes

Draw genome annotation features

Description

This function reads a reference genome in GFF format and then plots the genetic features (coding sequences) on both forward and reverse strands.

Usage

show.genome.annotation.plot(
  genome.name,
  genome.start = NULL,
  genome.end = NULL,
  genome.start.upstream = 0,
  genome.end.downstream = 0,
  show.gene.label = FALSE,
  gene.feature.width = 1.5
)

Arguments

genome.name	Path to the input file name.
genome.start	Start position of the genome to show in the plot.
genome.end	End position of the genome to show in the plot.
genome.start.upstream	Start drawing the genome plot from the specified bases upstream of the genome.
genome.end.downstream	End drawing the genome plot from the specified bases upstream of the genome.
show.gene.label	Show genetic feature label.
gene.feature.width	Width of the genetic features.

Value

None

Author(s)

Chrispin Chaguza, [e-mail]

References

https://github.com/ChrispinChaguza/RCandy

Examples

## Not run: 
Read genome in GFF formatted file (generated usign readseq) and plot the genomic features

ref.genome.gff<-system.file("extdata", "Hungary19A-6.gff", package = "RCandy",mustWork = TRUE)

show.genome.annotation.plot(ref.genome.gff)

## End(Not run)

ChrispinChaguza/RCandy documentation built on June 23, 2022, 1:03 p.m.