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https://github.com/jokergoo/hilbertcurve
Visualize genomic data by Hilbert curve
https://github.com/jokergoo/hilbertcurve
Last synced: 8 days ago
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Visualize genomic data by Hilbert curve
- Host: GitHub
- URL: https://github.com/jokergoo/hilbertcurve
- Owner: jokergoo
- License: other
- Created: 2015-06-30T16:13:22.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2024-10-08T18:21:12.000Z (30 days ago)
- Last Synced: 2024-10-15T11:11:18.340Z (23 days ago)
- Language: R
- Homepage: http://jokergoo.github.io/HilbertCurve/
- Size: 87.3 MB
- Stars: 40
- Watchers: 4
- Forks: 5
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# HilbertCurve 
[](https://github.com/jokergoo/HilbertCurve/actions)
[](https://codecov.io/github/jokergoo/HilbertCurve)
[](https://bioconductor.org/packages/stats/bioc/HilbertCurve/)
[](http://bioconductor.org/packages/devel/bioc/html/HilbertCurve.html)
[Hilbert curve](https://en.wikipedia.org/wiki/Hilbert_curve) is a type of space-filling curves
that fold one dimensional axis into a two dimensional space, but with still keeping the locality.
It has advantages to visualize data with long axis in following two aspects:
1. greatly improve resolution for the visualization;
2. easy to visualize clusters because generally data points in the cluster will also be close in the Hilbert curve.
This package aims to provide an easy and flexible way to visualize data through Hilbert curve.
The implementation and example figures are based on following sources:
- http://mkweb.bcgsc.ca/hilbert/
- http://corte.si/posts/code/hilbert/portrait/index.html
- http://bioconductor.org/packages/devel/bioc/html/HilbertVis.html
### Citation
Zuguang Gu, et al., [HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data.](https://doi.org/10.1093/bioinformatics/btw161)
Bioinformatics 2016
### Install
The package is at [Bioconductor](http://bioconductor.org/packages/devel/bioc/html/HilbertCurve.html) now
and you can install the newest version by:
```r
library(devtools)
install_github("jokergoo/ComplexHeatmap") # in order to get the newest version of ComplexHeatmap
install_github("jokergoo/HilbertCurve")
```
### Usage
Basically, there are two steps to make a Hilbert curve.
1. Initialize the curve and also map the one-dimensional axis to the curve.
2. add low-level graphics by `hc_points()`, `hc_segments()`, ... by giving the positions of the graphics.
```r
hc = HilbertCurve(1, 100, level = 4)
hc_points(hc, ...)
hc_segments(hc, ...)
hc_rect(hc, ...)
hc_text(hc, ...)
```
There is another 'pixel' mode which provides a high resolution for visualizing genomic data by the Hilbert curve.
```r
hc = HilbertCurve(1, 100000000000, level = 10)
hc_layer(hc, ...) # this can be repeated several times to add multiple layers on the curve
hc_png(hc, ...)
```
### Examples
Rainbow color spectrum:
Chinese dynasty:
GC percent and genes on chromosome 1:
Association between H3K36me3 histone modification and gene bodies:
Methylation on chromosome 1:
Copy number alterations in 22 chromosomes:
### License
MIT @ Zuguang Gu