https://github.com/bernatgel/karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
https://github.com/bernatgel/karyoploteR

bioconductor bioinformatics data-visualization genome genomics-visualization plotting-in-r rstats

Last synced: 3 months ago
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karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

• Host: GitHub
• URL: https://github.com/bernatgel/karyoploteR
• Owner: bernatgel
• Created: 2016-06-07T16:32:27.000Z (over 8 years ago)
• Default Branch: devel
• Last Pushed: 2024-01-11T12:51:15.000Z (10 months ago)
• Last Synced: 2024-07-19T01:39:13.110Z (4 months ago)
• Topics: bioconductor, bioinformatics, data-visualization, genome, genomics-visualization, plotting-in-r, rstats
• Language: R
• Homepage: https://bernatgel.github.io/karyoploter_tutorial/
• Size: 3.06 MB
• Stars: 293
• Watchers: 7
• Forks: 42
• Open Issues: 58
• Metadata Files:
  • Readme: README.md

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README

        
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# karyoploteR - An R/Biocondutor package to plot arbitrary data along the genome

![karyoploteR Example](https://raw.githubusercontent.com/bernatgel/karyoploter_tutorial/master/docs/Examples/MultipleDataTypes/images/Figure-1.png

 "Example of plot created with karyoploteR")

## Description

[karyoploteR](http://bioconductor.org/packages/karyoploteR) is an R package to 

plot data along the genome using a karyotype style plot.

It is entirely based on R base graphics and inspired by the R base graphics API. 

It includes functions to plot primitive graphic elements such as points, lines,

rectangles, text, etc mapped into the genome plot coordinates and higher 

level functions to plot a heatmap, the regions in a GenomicRanges object

or the cumulative coverage of such regions.

Data positioning and track configuration has been inspired by Circos and does

not explicitly understands the concept of track. Thus, it is possible to freely specify 

where to plot the data and to create plots with multiple independent tracks or

overlapping representations.

It is highly configurable and in addition to the parametrization of the 

different data plotting functions, it is possible to specify custom functions 

for every plotting action from the basic chromosome bands to the chromosome labels

or base numbers as well as creating completely new plotting functions.

## How to use it

Documentation ([vignette](http://bioconductor.org/packages/devel/bioc/vignettes/karyoploteR/inst/doc/karyoploteR.pdf) and [user manual](http://bioconductor.org/packages/devel/bioc/manuals/karyoploteR/man/karyoploteR.pdf)) is available at the karyoploteR's 

Bioconductor landing page at [http://bioconductor.org/packages/karyoploteR](http://bioconductor.org/packages/karyoploteR)

## Tutorial and Examples

In addition to the documentation above, a short tutorial and some examples can be found at [https://bernatgel.github.io/karyoploter_tutorial/](https://bernatgel.github.io/karyoploter_tutorial/)

## Citing karyoploteR

karyoploteR has been developed by [Bernat Gel](https://twitter.com/bernatgel) and [Eduard Serra](mailto:[email protected]) at [IGTP](http://www.germanstrias.org/)

Hereditary Cancer Group.

If you use karyoploteR in your research, please cite the [Bioinformatics paper](https://academic.oup.com/bioinformatics/article/3857734/karyoploteR-an-R-Bioconductor-package-to-plot) describing it:

Bernat Gel & Eduard Serra. (2017). *karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data*. Bioinformatics, 31–33. [doi:10.1093/bioinformatics/btx346](https://doi.org/10.1093/bioinformatics/btx346)

## A few example plots created with karyoploteR

These images are all created with karyoploteR and are part of the documented 

examples in the [karyoploteR's tutorial and examples page](https://bernatgel.github.io/karyoploter_tutorial/).

Click on them to see how the code needed to create them.