pl_curves
Python script for drawing Pareto–Lorenz curves for bacterial abundance data.
Science Score: 77.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
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Links to: nature.com, zenodo.org -
✓Committers with academic emails
2 of 4 committers (50.0%) from academic institutions -
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.9%) to scientific vocabulary
Repository
Python script for drawing Pareto–Lorenz curves for bacterial abundance data.
Basic Info
Statistics
- Stars: 3
- Watchers: 1
- Forks: 2
- Open Issues: 0
- Releases: 3
Metadata Files
readme.md
Introduction
A program for graphically describing the evenness of bacterial communities using Pareto–Lorenz (PL) curves, by plotting the cumulative relative abundance against the cumulative proportion of each taxonomical bins (based on e.g. T-RFs , OTUs). The more the plotted line deviates from the 1:1 line (45° diagonal), the lower the evenness of the community.
For each sample individually, empty bins are removed and the remaining bins are sorted in decreasing order of relative abundance. The cumulative relative abundance (range 0-1) and cumulative proportion of bins (range 0-1) are calculated and the data plotted so that the first (left most) data point represents the contribution of the bin with the highest relative abundance. Data for all samples in the imported data set are plotted on the same graph, to facilitate comparisons between samples.
The program also calculates the Gini-coefficient for each community, which describes the evenness of a community as the ratio of the area between the PL curve and the equality line and the whole triangular area above the equality line. The Gini coefficient ranges from 0 (perfect evenness) to 1 (perfect unevenness). The reported Gini coefficient has been corrected for the number of taxonomical units in the sample by multiplying the ratio with n/(n-1).
This implements the method described in the following papers:
Possible interactions between bacterial diversity, microbial activity and supraglacial hydrology of cryoconite holes in Svalbard" by Arwyn Edwards, Alexandre M Anesio, Sara M Rassner, Birgit Sattler, Bryn Hubbard, William T Perkins, Michael Young & Gareth W Griffith in The ISME Journal volume 5, pages 150–160 (2011) https://www.nature.com/articles/ismej2010100
and
Can the Bacterial Community of a High Arctic Glacier Surface Escape Viral Control?" by Sara M. E. Rassner, Alexandre M. Anesio, Susan E. Girdwood, Katherina Hell, Jarishma K. Gokul, David E. Whitworth and Arwyn Edwards in Frontiers in Microbiology 21 June 2016 https://doi.org/10.3389/fmicb.2016.00956
Citing this software
If you are using this software in an academic paper then please cite it. A machine readable citation.cff file and BibTex (citation.bib) file can also be found in this repository.
Colin Sauze and Sara Rassner, 2019, "PA script for generating Pareto–Lorenz (PL) curves", https://doi.org/10.5281/zenodo.2628856
Build Status
This software is automatically tested by Github Actions after each build. Its current status is shown below:
Owner
- Name: Colin Sauze
- Login: colinsauze
- Kind: user
- Location: Aberystwyth/Liverpool, UK
- Company: National Oceanography Centre
- Website: https://colinsauze.github.io/
- Repositories: 95
- Profile: https://github.com/colinsauze
Senior Research Software Engineer at the UK's National Oceanography Centre.
Citation (CITATION.bib)
@software{plcurves,
author = {Colin Sauze and Sara Rassner},
title = {A script for generating Pareto–Lorenz (PL) curves},
doi = {10.5281/zenodo.7783405},
url = {https://github.com/colinsauze/pl_curves},
version = {1.2},
date = {2023-03-29},
}
GitHub Events
Total
Last Year
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Colin Sauze | c****s@a****k | 113 |
| WYVERN2742 | 3****2 | 13 |
| matt✨ | 4****l | 1 |
| Ed Bennett | e****t@s****k | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 2
- Total pull requests: 2
- Average time to close issues: over 1 year
- Average time to close pull requests: 4 months
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 0.5
- Merged pull requests: 2
- 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
- fjebaker (1)
- colinsauze (1)
Pull Request Authors
- mhmatthall (1)
- WYVERN2742 (1)
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Dependencies
- codecov *
- flake8 *
- matplotlib <=3.3.4
- pandas <=1.2.3
- pytest <=6.2.2
- pytest-cov *
- actions/checkout v2 composite
- actions/setup-python v2 composite
- codecov/codecov-action v1 composite