R/plot_vcf.R

In robertopreste/mitovizR: Plot Human Mitochondrial Variants

#' Plot variants from a VCF
#'
#' Adds a geom_point layer to the output of \code{\link{mito_plot}} showing
#' mitochondrial variants contained in the given VCF file.
#'
#' @param vcf_file Path of the input VCF file
#' @param show_loci_names Show labels of loci names on the genome (default = TRUE)
#' @param show_loci_legend Show legend for locus type colours (default = TRUE)
#' @param show_var_labels Show labels with the position for each variant (default = FALSE)
#' @param title Set plot title (default = "")
#' @param save_plot Save the current plot to a file (default = FALSE)
#' @param save_to Path or filename to which the current plot will be saved (default = "mitoviz_plot.png")
#' @param verbose Show messages returned by the \code{vcfR} package functions (default = FALSE)
#'
#' @return p ggplot2 polar plot variants on the human mitochondrial genome
#'
#' @import vcfR
#' @import ggplot2
#'
#' @export

plot_vcf <- function(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) {
    vcf <- read.vcfR(vcf_file, verbose = verbose)
    vcf_tidy <- vcfR2tidy(vcf, verbose = verbose)
    if ("gt_HF" %in% colnames(vcf_tidy$gt)) {
        vcf_df <- data.frame("POS" = vcf_tidy$fix$POS, "REF" = vcf_tidy$fix$REF,
                            "ALT" = vcf_tidy$fix$ALT, "SAMPLE" = vcf_tidy$gt$Indiv,
                            "GT" = vcf_tidy$gt$gt_GT, "HF" = vcf_tidy$gt$gt_HF,
                            stringsAsFactors = F)
        # don't want to remove these variants, maybe I'll show them differently
        # vcf_df <- vcf_df[!(vcf_df$HF %in% c("0.0", "0")), ]
    } else {
        vcf_df <- data.frame("POS" = vcf_tidy$fix$POS, "REF" = vcf_tidy$fix$REF,
                            "ALT" = vcf_tidy$fix$ALT, "SAMPLE" = vcf_tidy$gt$Indiv,
                            "GT" = vcf_tidy$gt$gt_GT, "HF" = 0.5,
                            stringsAsFactors = F)
        # don't want to remove these variants, maybe I'll show them differently
        # vcf_df <- vcf_df[!(vcf_df$GT %in% c("0/0", "0")), ]
    }
    p <- plot_df(vcf_df, show_loci_names = show_loci_names,
                 show_loci_legend = show_loci_legend,
                 show_var_labels = show_var_labels, title = title,
                 save_plot = save_plot, save_to = save_to)
    return(p)
}