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https://github.com/vaporised/lolliprot
An R package for drawing lollipop plots of proteins using genetic variant data.
https://github.com/vaporised/lolliprot
bioinformatics lollipop-plot r
Last synced: about 1 month ago
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An R package for drawing lollipop plots of proteins using genetic variant data.
- Host: GitHub
- URL: https://github.com/vaporised/lolliprot
- Owner: vaporised
- License: apache-2.0
- Created: 2023-05-01T02:38:36.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-02-07T08:07:27.000Z (11 months ago)
- Last Synced: 2024-02-08T07:37:17.913Z (11 months ago)
- Topics: bioinformatics, lollipop-plot, r
- Language: R
- Homepage:
- Size: 97.7 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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
```R
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
```R
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
```R
devtools::install_github("vaporised/lolliprot")