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https://github.com/euphrasiologist/oxygraphis

An ecological graph library and CLI.
https://github.com/euphrasiologist/oxygraphis

Last synced: 12 days ago
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An ecological graph library and CLI.

Host: GitHub
URL: https://github.com/euphrasiologist/oxygraphis
Owner: Euphrasiologist
License: mit
Created: 2022-08-21T15:17:25.000Z (over 2 years ago)
Default Branch: main
Last Pushed: 2024-12-18T10:45:34.000Z (about 1 month ago)
Last Synced: 2024-12-18T11:42:14.667Z (about 1 month ago)
Language: Rust
Size: 122 KB
Stars: 0
Watchers: 1
Forks: 0
Open Issues: 1
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

# `oxygraphis`

## Introduction

`oxygraphis` is a lightweight small crate, and command line tool to interact with bipartite ecological graphs.

## CLI details

### Install

Currently you will need to clone this repository and build from source. Never fear, just download the rust toolchain. Then:

```bash
# install from crates.io (oxygraphis 0.1.62)
cargo install oxygraphis
# or from this repo
git clone https://github.com/Euphrasiologist/oxygraphis
cd oxygraphis
# install to path.
cargo install --path=.
```

### Interface

Bipartite graphs are the graph of interest. Analyse these graphs directly, or simulate them.

```bash
Usage: oxygraphis [COMMAND]

Commands:
bipartite Generate and analyse bipartite graphs.
simulate Simulate a number of graphs, and return calculations over the samples.
help Print this message or the help of the given subcommand(s)

Options:
-h, --help Print help
-V, --version Print version
```

#### Bipartite graphs

The `bipartite` subcommand.

```bash
Generate and analyse bipartite graphs.

Usage: oxygraphis bipartite [OPTIONS] [COMMAND]

Commands:
interaction-matrix Coerce a bipartite graph into an interaction matrix.
derived-graphs Coerce a bipartite graph into two derived graphs.
modularity Derive the modularity of a bipartite graph.
help Print this message or the help of the given subcommand(s)

Arguments:
An input DSV with three headers only: from, to, and weight.

Options:
-d, --delimiter [] Specify the delimiter of the DSV; we assume tabs.
-p, --plotbp Render an SVG bipartite graph plot.
-q, --plotbp2 Render an SVG bipartite graph plot with proportional node size.
-d, --degrees Return the degrees of a bipartite graph.
-e, --degreedistribution Return the degree distribution of a bipartite graph.
-b, --bivariatedistribution Return the bivariate degree distribution of a bipartite graph.
-h, --help Print help
```

The input must be a delimited file with three columns only:

```txt
from to weight
Sp1 Sp2 1.0
Sp2 Sp3 1.0
Sp1 Sp3 1.0
```

And I guess should be bipartite in structure (i.e. edges only from stratum 1 -> stratum 2). A warning is issued if it isn't, but does not halt the program.

#### Derived graphs

Derived graphs are graphs which show the relationships between species in a stratum.

```bash
Coerce a bipartite graph into two derived graphs.

Usage: oxygraphis bipartite derived-graphs [OPTIONS]

Options:
-p, --plotdg Render an SVG derived graph of a stratum.
-s, --stratum The stratum to display. [default: host] [possible values: host, parasite]
-r, --remove [] Edges with fewer than this number of connections are removed from the graph. [default: 2.0]
-d, --diameter [] The diameter (width and height; plot is square) of the plot. [default: 600.0]
-h, --help Print help
```

#### Interaction matrix

These form the core of some interesting bipartite analyses. Essentially an `n x m` matrix of all possible species-species interactions in the network.

```bash
Coerce a bipartite graph into an interaction matrix.

Usage: oxygraphis bipartite interaction-matrix [OPTIONS]

Options:
--print Print the inner matrix as a TSV. Mainly for debugging.
-p, --plotim Render an SVG interaction matrix plot.
-n, --nodf Compute the NODF number of a *sorted* interaction matrix.
-h, --help Print help
```

#### Modularity

An algorithm operating on the interaction matrix made from a bipartite graph. It attempts to find modules of species-host interactions in a matrix.

```bash
Derive the modularity of a bipartite graph.

Usage: oxygraphis bipartite modularity [OPTIONS]

Options:
-l, --lpawbplus Compute the modularity of a bipartite network using LPAwb+ algorithm.
-d, --dirtlpawbplus Compute the modularity of a bipartite network using DIRTLPAwb+ algorithm.
-m, --modules Compute the modules of a bipartite graph.
-p, --plotmod Plot the interaction matrix of a bipartite network, sorted to maximise modularity.
-h, --help Print help
```

#### Simulations

A subcommand to simulate a number of random graphs (Erdös-Rényi) and execute a calculation on each.

```bash
Simulate a number of graphs, and return calculations over the samples.

Usage: oxygraphis simulate [OPTIONS] --parasitenumber --hostnumber --edgecount

Options:
--parasitenumber
Number of parasite nodes in the graph.
--hostnumber
Number of host nodes in the graph.
-e, --edgecount
Number of edges in the graph.
-n, --nsims []
Number of random samples to make. [default: 1000]
-c, --calculation []
The calculation to make. [default: nodf] [possible values: nodf, lpawbplus, dirtlpawbplus, degree-distribution, bivariate-distribution]
--plot
Plot the simulated bipartite network.
-h, --help
Print help
```

## Oxygraphis..?

*Oxygraphis* is one of only 5-6 genera in the flowering plants which have *graph* included fully in the name. It's in the Ranunculaceae.