Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Oct 1;33(19):3088-3090.
doi: 10.1093/bioinformatics/btx346.

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

Bernat Gel  1 , Eduard Serra  1   2
Affiliations

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

Bernat Gel et al. Bioinformatics. .

Abstract

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.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
(A) The complete human GRCh38 genome. This plot is created with the single command ‘plotKaryotype(genome=“hg38”)’. (B) An example of a figure generated by karyoploteR representing different data types plotted in human chromosomes 1 and 2
See this image and copyright information in PMC

References

    1. Gel B. et al. (2016) regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. Bioinformatics, 32, 289–291. - PMC - PubMed
    1. Hahne F., Ivanek R. (2016) Visualizing genomic data using Gviz and bioconductor. Methods Mol. Biol., 1418, 335–351. - PubMed
    1. Krzywinski M. et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639–1645. - PMC - PubMed
    1. Oróstica K.Y., Verdugo R.A. (2016) ChromPlot: Visualization of genomic data in chromosomal context. Bioinformatics, 32, 2366–2368. - PubMed
    1. Pai S., Ren J. (2014) IdeoViz: Plots data (continuous/discrete) along chromosomal ideogram. R package version 1.8.0.