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gtrellis

Genomic plot in trellis layout

https://github.com/jokergoo/gtrellis

Science Score: 36.0%

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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    Found 1 DOI reference(s) in README
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    1 of 16 committers (6.3%) from academic institutions
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    Low similarity (11.8%) to scientific vocabulary

Keywords from Contributors

bioconductor-packages genomics gene transcriptomics proteomics bioinformatics bioconductor mass-spectrometry looking-for-maintainer metabolomics
Last synced: 10 months ago · JSON representation

Repository

Genomic plot in trellis layout

Basic Info
Statistics
  • Stars: 41
  • Watchers: 5
  • Forks: 11
  • Open Issues: 0
  • Releases: 0
Created over 11 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License

README.md

Make Genome Level Trellis Graph

R-CMD-check codecov bioc bioc

Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

Citation

Zuguang Gu, et al., gtrellis: an R/Bioconductor package for making genome-level Trellis graphics, 2016. BMC Bioinformatics.

Install

gtrellis is available on Bioconductor, you can install it by:

{r} if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("gtrellis")

If you want the latest version, install it directly from GitHub:

{r} library(devtools) install_github("jokergoo/gtrellis")

Usage

Basic usage is:

```r library(gtrellis)

bed = circlize::generateRandomBed() gtrellislayout(trackylim = range(bed[[4]])) add_track(bed, panel.fun = function(bed) { x = (bed[[2]] + bed[[3]]) / 2 y = bed[[4]] grid.points(x, y, pch = 16, size = unit(1, "mm")) }) ```

There are several tracks with pre-defined graphics:

  • add_points_track()
  • add_lines_track()
  • add_rect_track()
  • add_segments_track()
  • add_heatmap_track()

Layout

gtrellis supports several types of layouts:

One row layout:

Multiple row layout that chromosomes with similar length are arranged in a same column:

Chromosomes in a same row are arranged compactly to the left:

For each chromosome, multiple tracks are supported:

Example

Example figures are:

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
Last Year

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 237
  • Total Committers: 16
  • Avg Commits per committer: 14.813
  • Development Distribution Score (DDS): 0.388
Past Year
  • Commits: 3
  • Committers: 1
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Zuguang Gu j****o@g****m 145
Zuguang Gu z****u@d****e 32
Nitesh Turaga n****a@g****m 14
z.gu z****u@b****8 13
Dan Tenenbaum d****a@f****g 8
Herve Pages h****s@f****g 4
J Wokaty j****y@s****u 4
Bioconductor Git-SVN Bridge b****c@b****g 3
vobencha v****n@r****g 3
Hervé Pagès h****s@f****g 2
d.tenenbaum d****m@b****8 2
vobencha v****a@g****m 2
J Wokaty j****y 2
LiNk-NY m****9@g****m 1
Sonali Arora s****a@f****g 1
s.arora s****a@b****8 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 3 fredhutch.org: 1 roswellpark.org: 1 bioconductor.org: 1 sph.cuny.edu: 1 dkfz.de: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 5
  • Total pull requests: 0
  • Average time to close issues: 8 days
  • Average time to close pull requests: N/A
  • Total issue authors: 4
  • Total pull request authors: 0
  • Average comments per issue: 1.6
  • 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
View more stats
Top Authors
Issue Authors
  • ccwang002 (2)
  • adeschen (1)
  • royfrancis (1)
  • jokergoo (1)
Pull Request Authors
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 30,051 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: gtrellis

Genome Level Trellis Layout

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 30,051 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 13.1%
Downloads: 39.2%
Maintainers (1)
z.gu@dkfz.de
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • GenomicRanges * depends
  • IRanges * depends
  • R >= 3.1.2 depends
  • grid * depends
  • GetoptLong * imports
  • circlize >= 0.4.8 imports
  • grDevices * imports
  • utils * imports
  • Cairo * suggests
  • ComplexHeatmap >= 1.99.0 suggests
  • RColorBrewer * suggests
  • jpeg * suggests
  • knitr * suggests
  • markdown * suggests
  • png * suggests
  • rmarkdown * suggests
  • testthat >= 1.0.0 suggests
  • tiff * suggests