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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: about 2 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 (about 8 years ago)
- Default Branch: devel
- Last Pushed: 2024-01-11T12:51:15.000Z (6 months ago)
- Last Synced: 2024-05-05T01:20:55.546Z (2 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: 285
- Watchers: 6
- Forks: 40
- Open Issues: 56
-
Metadata Files:
- Readme: README.md
Lists
- repo-5916-awesome-genome-visualization - karyoploteR - genome-visualization/karyoploter.png) (Ideogram)
- awesome-genome-visualization - karyoploteR
- Awesome-Bioinformatics-CN - karyoploteR - 可视化染色体/track的R包 (可视化 / 染色体可视化)
README
[](https://travis-ci.org/bernatgel/karyoploteR)
[](http://www.repostatus.org/#active)
# karyoploteR - An R/Biocondutor package to plot arbitrary data along the genome
## 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/)
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.
