jamesxx/ionio-illustrate

A Typst package for rendering and annotating mass spectrometric data

The ionio-illustrate package

This package implements a Cetz chart-like object for displying mass spectrometric data in Typst documents. It allows for individually styled mass peaks, callouts, titles, and mass callipers.

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Getting Started

To make use of the ionio-illustrate package, you'll need to add it to your project like shown below. Make sure you are importing a version that supports your end goal.

#import "@preview/ionio-illustrate:0.3.0": *

Then, load in your mass spectrum data and pass it through to the package like so. Data should be 2D array, and by default the mass-charge ratio is in the first column, and the relative intensities are in the second column.

#let data = csv("isobutelene_epoxide.csv")

#let ms = mass-spectrum(massspec, args: (
  size: (12,6),
  range: (0,100),
)) 

#figure((ms.display)())

There are many ways to further enhance your spectrum, please check out the manual to find out how.

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Roadmap

• Pass style options through to the plot (tracker: #1)
• Better placement of text depending on plot size
• Improve default step on axes
• Add support for callouts that are not immediately above their assigned peak
  • Automatically detect when two annotations are too close, and display accordingly
• Move to new Typst type system (waiting on upstream)
• Add in function for displaying skeletal structure of chemical
• Optional second axis for absolute intensity
• Add additional display functions
  • Figure out function signature for multiple data sets
  • Overlayed and shifted
  • Horizontal reflection
    • How to update existing extras?

See the open issues for a full list of proposed features (and known issues).

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Contributing

Contributions are what make the open source community such an amazing place to learn, inspire, and create. Any contributions you make are greatly appreciated.

If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement". Don't forget to give the project a star! Thanks again!

1. Fork the Project
2. Create your Feature Branch (git checkout -b feature/AmazingFeature)
3. Commit your Changes (git commit -m 'Add some AmazingFeature')
4. Push to the Branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

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License

Distributed under the MIT License. See LICENSE for more information.

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Gallery

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ionio-illustrate's Issues

`dual-reflection` display mode

Tracking issue for dual display mode. Current objectives are:

• Handle data input
• Handle how axes are calculated
• Handle plot-extra functions
  • Pass additional option, maybe automatically somehow? Store state on #ms?
  • Adjust labels to account for vertical space on reflected pane.
  • Adjust callipers

Style Tracker

This issue will track the progress towards allowing styling on the graph components using Cetz style dictionaries.

Tracking chart:

• Styling for axes
• Styling for all peaks
• Styling for specific peaks
• Styling for peak annotations
• Styling for mass callipers

`add-callout` does not respect `size`

If there are callouts outside of the x-axis range, they are still rendered when they should be culled.

Better error when range does not contain content

Throws a cetz error when it could be better handled in the library