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

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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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