lolliprot

R package for drawing lollipop plots of proteins using genetic variant data.

Lolliplots show sites of amino acid changes, given a VCF file and a gene symbol.

Pre-processing

All variants to be plotted should be in one VCF file. If variants across multiple VCFs should be plotted, merge them first. This can be done using the ./extdata/merged.sh file.

Usage

plot_lolliprot(vcf_path, gene_symbol, remove_mnv = TRUE, to_pdf = FALSE, width = 16, height = 6)

Arguments

vcf_path: Path to the VCF file containing variants to be plotted.
gene_symbol: Gene symbol of the gene to be plotted.
remove_mnv: If multinucleotide variants should be omitted when plotting. Defaults to TRUE.
to_pdf: If a PDF of the plot should be created instead in ./lolliprot_output. Defaults to FALSE.
width: Width of the PDF. Defaults to 16.
height: Height of the PDF. Defaults to 6.

Notes

The canonical transcript is used for plotting. Protein domains are represented as grey boxes. The GRCh38 assembly is used for reference.

Examples

example_path <- system.file("extdata", "example.vcf", package="lolliprot")

# Plot with the multinucleotide variant
plot_lolliprot(vcf_path = example_path, gene_symbol = "DNMT3A", remove_mnv = FALSE)

# Plot without the multinucleotide variant
plot_lolliprot(vcf_path = example_path, gene_symbol = "DNMT3A")

# Create a PDF
plot_lolliprot(vcf_path = example_path, gene_symbol = "DNMT3A", to_pdf = TRUE, width = 15, height = 5)

Installation

devtools::install_github("vaporised/lolliprot")