Science Score: 36.0%
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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1 of 16 committers (6.3%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (13.4%) to scientific vocabulary
Keywords from Contributors
Repository
Visualize genomic data by Hilbert curve
Basic Info
- Host: GitHub
- Owner: jokergoo
- License: other
- Language: R
- Default Branch: master
- Homepage: http://jokergoo.github.io/HilbertCurve/
- Size: 87.3 MB
Statistics
- Stars: 42
- Watchers: 3
- Forks: 5
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
HilbertCurve 
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:
- greatly improve resolution for the visualization;
- 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. Bioinformatics 2016
Install
The package is at Bioconductor 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.
- Initialize the curve and also map the one-dimensional axis to the curve.
- 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
Owner
- Name: Zuguang Gu
- Login: jokergoo
- Kind: user
- Location: Heidelberg, Germany
- Company: German Cancer Research Center
- Website: http://jokergoo.github.io
- Repositories: 28
- Profile: https://github.com/jokergoo
A bioinformagician
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Zuguang Gu | j****o@g****m | 169 |
| Zuguang Gu | z****u@d****e | 24 |
| Nitesh Turaga | n****a@g****m | 14 |
| z.gu | z****u@b****8 | 9 |
| Dan Tenenbaum | d****a@f****g | 6 |
| J Wokaty | j****y@s****u | 6 |
| d.tenenbaum | d****m@b****8 | 6 |
| Herve Pages | h****s@f****g | 4 |
| Hervé Pagès | h****s@f****g | 3 |
| vobencha | v****n@r****g | 3 |
| vobencha | v****a@g****m | 2 |
| hpages@fhcrc.org | h****s@f****g@b****8 | 2 |
| Sonali Arora | s****a@f****g | 1 |
| Martin Morgan | m****n@f****g | 1 |
| mtmorgan@fhcrc.org | m****n@f****g@b****8 | 1 |
| s.arora | s****a@b****8 | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 4
- Total pull requests: 0
- Average time to close issues: 8 months
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 0.25
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jokergoo (3)
- barracuda156 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 21,411 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: HilbertCurve
Making 2D Hilbert Curve
- Homepage: https://github.com/jokergoo/HilbertCurve https://jokergoo.github.io/HilbertCurve/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/HilbertCurve/inst/doc/HilbertCurve.pdf
- License: MIT + file LICENSE
-
Latest release: 2.2.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.6.0 depends
- grid * depends
- GenomicRanges * imports
- HilbertVis * imports
- IRanges * imports
- circlize >= 0.3.3 imports
- grDevices * imports
- methods * imports
- png * imports
- polylabelr * imports
- utils * imports
- ComplexHeatmap >= 1.99.0 suggests
- GetoptLong * suggests
- RColorBrewer * suggests
- RCurl * suggests
- knitr * suggests
- markdown * suggests
- rmarkdown * suggests
- testthat >= 1.0.0 suggests
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact main composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite