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. 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.

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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

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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.