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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Published on: December 7, 2021

karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data.

Bernat Gel¹, Eduard Serra^1,2

¹Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer - Germans Trias i Pujol Research Institute (PMPPC-IGTP), Campus Can Ruti, Badalona, Spain.

Bioinformatics (Oxford, England)

|June 3, 2017

Summary

karyoploteR is a new R/Bioconductor package for creating customizable linear genome plots. It enables flexible visualization of genomic data and annotations for any species.

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Area of Science:

Bioinformatics
Genomics
Data Visualization

Background:

Data visualization is essential for exploring and interpreting genomic data.
Existing tools lack customizable non-circular whole-genome plotting capabilities for diverse species.

Purpose of the Study:

To develop a flexible R/Bioconductor package for creating customizable linear genome plots.
To enable visualization of genomic annotations and experimental data along chromosomal representations.

Main Methods:

Developed karyoploteR, an R/Bioconductor package.
Utilized R base graphics principles for plot creation.
Implemented a main function for base karyoplots and additional functions for data integration and customization.

Main Results:

karyoploteR allows creation of linear chromosomal representations for any genome.
The package supports plotting genomic annotations and experimental data.
Highly customizable plots can be generated with freedom in data positioning and representation.

Conclusions:

karyoploteR provides a versatile solution for non-circular whole-genome visualization.
The package enhances the exploration and interpretation of genomic data across species.