plot_variant_list: Plot known variants list

In seqCAT: High Throughput Sequencing Cell Authentication Toolkit

Description

Plot a genotype grid from a list of known variants

Usage

plot_variant_list(variant_list, legend = TRUE, legend_size = 22,
  text_size = 14, palette = c("#4e8ce4", "#a6c6f2", "#999999",
  "#cccccc"))

Arguments

variant_list	The data containing the variants (dataframe)
legend	Show a legend for the genotype colours (boolean)
legend_size	Size of the legend (numeric).
text_size	Text size for axes and legend (numeric).
palette	Nucleotide colour palette (4-element character vector)

Details

This function creates publication-ready plots from lists of known variants, taking a dataframe containing all the genotypes (on "A1/A2" format) for each sample (columns) and variant (row names).

Value

A ggplot2 graphical object.

Examples

# Load test variant list
data(test_variant_list)

# Plot each variant's genotype per sample
genotype_grid <- plot_variant_list(test_variant_list)

seqCAT documentation built on Nov. 8, 2020, 7:36 p.m.