om_var_pie_stats: Transform variants summary to plot data for ggplot

In bioShaun/omplotr: store plot functions & themes for onmath projects

Transform variants summary to plot data for ggplot

Description

Transform variants summary to plot data for ggplot

Usage

om_var_pie_stats(stats_name, stats_dir, impact_map_file,
  stats_prefix = "all_sample", varRegion_order = NULL)

Arguments

stats_name	type of summary file
stats_dir	directory of summary file
impact_map_file	snpeff effect impact file
stats_prefix	prefix of summary file
varRegion_order	plot order of variant region

Examples

stats_names <- om_const_reseq_variant[['var_file_labs']][1:2]
stats_dir <- system.file("extdata", "variant_stats", package = "omplotr")
impact_map_file <- system.file("extdata", "variant_stats", "snpeff_varEffects.csv", package = "omplotr")
test_pie_stats <- lapply(stats_names, om_var_pie_stats, stats_dir=stats_dir, impact_map_file=impact_map_file)
head(test_pie_stats[[1]], 4)

bioShaun/omplotr documentation built on June 11, 2025, 7:48 a.m.