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https://github.com/biosustain/shu

Multi-dimensional, trans-omics metabolic maps.
https://github.com/biosustain/shu

metabolism systems-biology visualization

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Multi-dimensional, trans-omics metabolic maps.

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README 

        
# shu






[![my badge](https://badgen.net/badge/docs/latest/blue?icon=book)](https://biosustain.github.io/shu/docs/index.html)

[![wasm](https://img.shields.io/github/deployments/biosustain/shu/github-pages)](https://biosustain.github.io/shu)

[![wasm](https://img.shields.io/crates/v/shu.svg)](https://crates.io/crates/shu)



## What?



App to plot multidimensional data to a metabolic map. Metabolic maps are graphs with metabolites

as nodes and reactions as edges.



For a **quick start**, we provide a web application at https://biosustain.github.io/shu. There

are example maps and data available at https://github.com/biosustain/shu_case_studies, that

can be load with the buttons at the top-right.



For a more comprehensive guide, visit the [documentation](https://biosustain.github.io/shu/docs/plotting.html).



> Paper to cite: https://doi.org/10.1093/bioinformatics/btae140



## Why?



[Escher](https://escher.github.io/#/) is great. In fact, the format

of the map is exactly the same as escher's. However, escher only allows for plotting 2 (+2 with tooltips)

kinds of data: reaction data and metabolite data. **Shu** attempts to provide ways of plotting at least

6:



- [x] Reaction sizes.

- [x] Reaction colors.

- [x] Reaction right sides.

- [x] Reaction left sides.

- [x] Metabolite sizes.

- [x] Metabolite colors.



(+2 with hovers):

- [x] Hover reactions.

- [x] Hover metabolites.



with special focus on being able to plot **distributions** (not just points) and **n-conditions**. Escher also has the

distinction between color and size, it is simply that they are not independently accessible from the GUI.



## How to use



Shu is distributed both through a web app (preview build at https://biosustain.github.io/shu) and as standalone

native application. To use the latter, download the [latest release for your operating system](https://github.com/biosustain/shu/releases/latest), unpack if necessary and run it as executable.



Documentation for the rust crate and the python API will be made available once they are published. In the meantime, a preview

of the python documentation can be found at https://biosustain.github.io/shu/docs.



### Building from source (latest master commit)



Install [cargo](https://doc.rust-lang.org/cargo/getting-started/installation.html) and run



```bash

git clone https://github.com/biosustain/shu.git

cd shu

cargo install --path .

```



This may possibly require extra dependencies. Check the bevy setup, **shu** uses `lld`

to fasten linking times.



## API design

 

Shu follows a Grammar of Graphics design like [ggplot](https://ggplot2.tidyverse.org/) or [plotnine](https://plotnine.readthedocs.io/en/stable/index.html).

See the [python API](ggshu/README.rst) for the full analogy. The particular implementation

is an Entity Component System in [bevy](https://bevyengine.org/):



* Each aesthetic is a *component* (`Gsize`, `Gcolor`, etc.) containing its data (see [`src/aesthetics.rs`](src/aesthetics.rs)). Identifiers are stored in the `Aesthetic` *component*.

* *Entities* with `Aesthetic`, other aes components and Geom component (`GeomArrow`, `GeomMetabolite`, etc. in [`src/geom.rs`](src/geom.rs)) are

processed and plotted by a *system* (in [`src/aesthetics.rs`](src/aesthetics.rs)).

* The accepted aesthetics for a given geom are made explicit in the *queries* of the *systems*.



Data handling (`df`, ad `map_file`) lives in [`src/data.rs`](src/data.rs) and

[`src/escher.rs`](src/escher.rs) and the GUI componets lives in [`src/gui.rs`](src/gui.rs).



## License



Copyright 2023 The Novo Nordisk Foundation Center for Biosustainability.



Licensed under either of



- Apache License, Version 2.0, ([LICENSE-APACHE](LICENSE-APACHE) or http://www.apache.org/licenses/LICENSE-2.0)

- MIT license ([LICENSE-MIT](LICENSE-MIT) or http://opensource.org/licenses/MIT)



at your option.



### Contribution



Unless you explicitly state otherwise, any contribution intentionally submitted

for inclusion in the work by you, as defined in the Apache-2.0 license, shall

be dual licensed as above, without any additional terms or conditions.