plot_vcf: Plot variants from a VCF

In robertopreste/mitovizR: Plot Human Mitochondrial Variants

Description

Adds a geom_point layer to the output of mito_plot showing mitochondrial variants contained in the given VCF file.

Usage

plot_vcf(vcf_file, show_loci_names = TRUE, show_loci_legend = TRUE,
  show_var_labels = FALSE, title = "", save_plot = FALSE,
  save_to = "mitoviz_plot.png", verbose = FALSE)

Arguments

vcf_file	Path of the input VCF file
show_loci_names	Show labels of loci names on the genome (default = TRUE)
show_loci_legend	Show legend for locus type colours (default = TRUE)
show_var_labels	Show labels with the position for each variant (default = FALSE)
title	Set plot title (default = "")
save_plot	Save the current plot to a file (default = FALSE)
save_to	Path or filename to which the current plot will be saved (default = "mitoviz_plot.png")
verbose	Show messages returned by the vcfR package functions (default = FALSE)

Value

p ggplot2 polar plot variants on the human mitochondrial genome

robertopreste/mitovizR documentation built on May 22, 2019, 2:46 p.m.