plot_genoplot_data: Plot a genoplotR synteny plot

In djw533/micro.gen.extra: Microbial genomics extensions and functions

Plot a genoplotR synteny plot

Description

Plot a genoplotR synteny plot, using the dnaseqs from micro_gen_extra::create_dnaseqs() and the blast comparisons from micro_gen_extra::create_blast_comparisons()

Usage

plot_genoplot_data(input_genoplotR_set, output_prefix)

Arguments

input_genoplotR_set	Input list of the dna_seqs and the blast comparisons
output_prefix	Prefix for the output files (svg and png)

Value

A png and svg file of synteny plots produced using genoplotR

Examples

plot_genoplot_data(input_genoplotR_data, "output_prefix_name")

More specifically:

#First create an empty list
genoplotr_data <- list()

#Add the dnaseqs:
genoplotr_data$dnaseqs <- micro.gen.extra::create_dnaseqs(input_gggenes_df)

#Then add the blast comparisons:
genoplotr_data$comparisons <- micro.gen.extra::create_blast_comparisons(blast_order_list, "dir_with_fasta_files")

#Then plot:
plot_genoplot_data(genoplotr_data, "output_prefix_name")

#To add colours, and change blast parameters (to be added), see the documentation for micro_gen_extra::create_dnaseqs
#and micro_gen_extra::create_blast_comparisons

djw533/micro.gen.extra documentation built on Nov. 8, 2024, 5:11 a.m.