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circlize

Circular visualization in R

https://github.com/jokergoo/circlize

Science Score: 20.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    1 of 9 committers (11.1%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (18.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Circular visualization in R

Basic Info
Statistics
  • Stars: 986
  • Watchers: 26
  • Forks: 149
  • Open Issues: 65
  • Releases: 0
Created about 13 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Code of conduct

README.md

circlize: circular visualization in R

R-CMD-check CRAN CRAN Codecov test coverage

Circular layout is an efficient way for the visualization of huge amounts of information. Here the circlize package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of this package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, circlize gives users more convenience and freedom to design figures for better understanding complex patterns behind multi-dimensional data.

Citation

Zuguang Gu, et al., circlize Implements and enhances circular visualization in R. Bioinformatics (Oxford, England) 2014. PubMed

Documentation

The full documentations are available at https://jokergoo.github.io/circlize_book/book/ and the online website is at https://jokergoo.github.io/circlize/.

Blog posts

There are the following blog posts focusing on specific topics.

Examples

See https://jokergoo.github.io/circlize_examples/.

circlize_example

Install

The package can be installed from CRAN:

r install.packages("circlize")

or directly from GitHub:

r devtools::install_github("jokergoo/circlize")

Basic design

Since most of the figures are composed of points, lines and polygons, we just need to implement functions for drawing points, lines and polygons, then the plots will not be restricted in any specific types.

Current there are following low-level graphic functions:

  • circos.points()
  • circos.lines()
  • circos.segments()
  • circos.rect()
  • circos.polygon()
  • circos.text()
  • circos.axis()
  • circos.raster()
  • circos.arrow()
  • circos.raster()
  • circos.barplot()
  • circos.boxplot()
  • circos.link(), This maybe the unique feature for circos layout to represent relationships between elements.

For drawing points, lines and text through the whole track (among several sectors), the following functions are available:

  • circos.trackPoints()
  • circos.trackLines()
  • circos.trackText()

Draw circular heatmaps

  • circos.heatmap()

Functions to arrange the circular layout:

  • circos.track()
  • circos.update()
  • circos.nested()
  • circos.par()
  • circos.info()
  • circos.clear()

Theoretically, you are able to draw most kinds of circular plots by the above functions.

For specific use in Genomics, we also implement functions which add graphics in genome scale.

Functions to initialize circular plot with genomic coordinates:

  • circos.initializeWithIdeogram()
  • circos.genomicInitialize()

Functions to arrange genomic circular layout:

  • circos.genomicTrack()

Functions to add basic graphics in genomic scale:

  • circos.genomicPoints()
  • circos.genomicLines()
  • circos.genomicText()
  • circos.genomicRect()
  • circos.genomicLink()

Functions with specific purpose:

  • circos.genomicIdeogram()
  • circos.genomicHeatmap()
  • circos.genomicLabels()
  • circos.genomicDensity()
  • circos.genomicRainfall()

Finally, function that draws Chord diagram:

  • chordDiagram()

License

MIT @ Zuguang Gu

Owner

  • Name: Zuguang Gu
  • Login: jokergoo
  • Kind: user
  • Location: Heidelberg, Germany
  • Company: German Cancer Research Center

A bioinformagician

GitHub Events

Total
  • Issues event: 7
  • Watch event: 38
  • Issue comment event: 3
  • Pull request event: 1
  • Fork event: 9
Last Year
  • Issues event: 7
  • Watch event: 38
  • Issue comment event: 3
  • Pull request event: 1
  • Fork event: 9

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 850
  • Total Committers: 9
  • Avg Commits per committer: 94.444
  • Development Distribution Score (DDS): 0.016
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Zuguang Gu j****o@g****m 836
David Gabbé d****e 4
Zuguang Gu j****o@d****e 3
cola-recount2 z****u@d****e 2
Robert Redd r****1@g****m 1
Guy Abel g****l@g****m 1
Darío Hereñú m****a@g****m 1
joker j****r@j****) 1
Pan, Calvin C****n@m****u 1
Committer Domains (Top 20 + Academic)
mednet.ucla.edu: 1 joker-thinkpad-x230.(none): 1 dfkz.de: 1 dkfz-vpn111.inet.dkfz-heidelberg.de: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 136
  • Total pull requests: 3
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 115
  • Total pull request authors: 2
  • Average comments per issue: 2.08
  • Average comments per pull request: 2.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 9
  • Pull requests: 2
  • Average time to close issues: 14 days
  • Average time to close pull requests: N/A
  • Issue authors: 8
  • Pull request authors: 1
  • Average comments per issue: 0.22
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jokergoo (11)
  • komalsrathi (4)
  • elcortegano (2)
  • nfancy (2)
  • zhipengliu92 (2)
  • rbutleriii (2)
  • ShixiangWang (2)
  • jonaskohh (2)
  • ms-gx (2)
  • ghs101 (2)
  • nzx9581 (1)
  • medbenamine (1)
  • testorialessandro (1)
  • elpavlos (1)
  • endrebak (1)
Pull Request Authors
  • kullrich (2)
  • cbrueffer (1)
Top Labels
Issue Labels
enhancement (4)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 27,664 last-month
  • Total docker downloads: 76,101
  • Total dependent packages: 65
  • Total dependent repositories: 294
  • Total versions: 46
  • Total maintainers: 1
cran.r-project.org: circlize

Circular Visualization

  • Versions: 46
  • Dependent Packages: 65
  • Dependent Repositories: 294
  • Downloads: 27,664 Last month
  • Docker Downloads: 76,101
Rankings
Stargazers count: 0.3%
Forks count: 0.4%
Dependent repos count: 1.0%
Average: 1.4%
Dependent packages count: 1.6%
Docker downloads count: 2.2%
Downloads: 2.7%
Maintainers (1)
z.gu@dkfz.de
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.0.0 depends
  • graphics * depends
  • GlobalOptions >= 0.1.2 imports
  • colorspace * imports
  • grDevices * imports
  • grid * imports
  • methods * imports
  • shape * imports
  • stats * imports
  • utils * imports
  • ComplexHeatmap >= 2.0.0 suggests
  • bezier * suggests
  • covr * suggests
  • dendextend >= 1.0.1 suggests
  • gridBase * suggests
  • knitr * suggests
  • markdown * suggests
  • png * suggests
  • rmarkdown * suggests
.github/workflows/R-CMD-check.yaml actions
  • 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