plot_synteny_gff_files: Take a list of "x" gff3 files and create a synteny plot
In djw533/micro.gen.extra: Microbial genomics extensions and functions

plot_synteny_gff_files

R Documentation

Take a list of "x" gff3 files and create a synteny plot

Description

Take gff files, read annotation and extract fasta sequence. Then create genoplotR data structures, then plot genoplotR synteny plot. This uses the dnaseqs from micro_gen_extra::create_dnaseqs() and the blast comparisons from micro_gen_extra::create_blast_comparisons()

Usage

plot_synteny_gff_files(
  gff_list,
  output_prefix = "synteny_plot",
  temp_dir = "temp_fasta",
  clean_up = TRUE
)

Arguments

`gff_list`	Input list of gff files (with extensions to paths)
`output_prefix`	Prefix for the output files (svg and png)
`temp_dir`	Directory to put fasta files into [Default = "temp_fasta"]
`clean_up`	TRUE/FALSE - clean up the temp fasta directory [Default = TRUE]