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

Bioinformatics. 2017 Oct 1;33(19):3088-3090. doi: 10.1093/bioinformatics/btx346.


Motivation: Data visualization is a crucial tool for data exploration, analysis and interpretation. For the visualization of genomic data there lacks a tool to create customizable non-circular plots of whole genomes from any species.

Results: We have developed karyoploteR, an R/Bioconductor package to create linear chromosomal representations of any genome with genomic annotations and experimental data plotted along them. Plot creation process is inspired in R base graphics, with a main function creating karyoplots with no data and multiple additional functions, including custom functions written by the end-user, adding data and other graphical elements. This approach allows the creation of highly customizable plots from arbitrary data with complete freedom on data positioning and representation.

Availability and implementation: karyoploteR is released under Artistic-2.0 License. Source code and documentation are freely available through Bioconductor (http://www.bioconductor.org/packages/karyoploteR) and at the examples and tutorial page at https://bernatgel.github.io/karyoploter_tutorial.

Contact: bgel@igtp.cat.

MeSH terms

  • Computer Graphics
  • Genome
  • Genomics / methods*
  • Software*