> For the complete documentation index, see [llms.txt](https://time-series-features.gitbook.io/research-resources/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://time-series-features.gitbook.io/research-resources/advice/making-figures.md).

# Making figures

#### General

* Generate figures algorithmically as much as possible, as clear scripts in an open code repository.
* Know the difference between vector and bitmap graphics, and output your figures appropriately.
* Aesthetic touch-ups can be made after exporting your figure, for vector graphics ([Adobe Illustrator](https://www.adobe.com/products/illustrator.html), [Affinity Designer](https://affinity.serif.com/en-gb/), or the free [Inkscape](https://inkscape.org/)) or bitmap graphics ([Adobe Photoshop](https://www.adobe.com/au/products/photoshop.html), or the free [GIMP](https://www.gimp.org/)).
* Label your axes clearly, with units of measurement in parentheses.
* If using python, the typical pipeline outputs to svg and then does post-processing in Inkscape. You may find this [scour](https://github.com/scour-project/scour) package useful for cleaning up the svg files.

[Here](https://drive.google.com/file/d/1LouVvISCRlWkItZgzoHcgoU5Q1VyHT4U/view) is a great presentation by Dan Larremore on how to present data clearly.

#### Color palettes

You should select the color palette for your figures carefully, with a priority towards making the key pieces of science that you're trying to communicate as clear as possible. Be especially wary of common forms of [colorblindness](https://davidmathlogic.com/colorblind/), and giving some thought to how readable figures are in greyscale. There are tools for [simulating different types of colorblindness](https://www.color-blindness.com/coblis-color-blindness-simulator/).

When using a continuous color scale, avoiding the colormap [`jet`](https://jakevdp.github.io/blog/2014/10/16/how-bad-is-your-colormap/) will prevent incurring the wrath of passionate [jet fighters](https://github.com/smsaladi/jetfighter), who will direct you to [automatically 'fix'](https://fixthejet.ecrlife.org/) your colormap.

* If you love a good :rainbow: rainbow :rainbow:, the [turbo colormap](https://gist.github.com/mikhailov-work/ee72ba4191942acecc03fe6da94fc73f) is a solid alternative to jet.
* Pick from some [classics](http://colorbrewer2.org/).
* Here is a good way to select [nice color palettes](https://learnui.design/tools/data-color-picker.html).
* Algorithmically [make your own](http://vrl.cs.brown.edu/color).
* Another [algorithmic one](https://medialab.github.io/iwanthue/).
* Another way to [make your own](https://jdherman.github.io/colormap/).

#### Plotting distributions

For data exploration, you should always avoid plots that make assumptions about the distribution of values (like those that plot the mean plus/minus standard deviation). Alternatives include violin plots:

* Violin Plots: [Matlab Code](https://github.com/bastibe/Violinplot-Matlab).


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation by asking a question.

Perform an HTTP GET request on the following URL with the `ask` and `goal` query parameters:

```
GET https://time-series-features.gitbook.io/research-resources/advice/making-figures.md?ask=<question>&goal=<user_goal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is what the user is ultimately trying to achieve, the reason they need the answer. Sharing it helps GitBook give you a better, more relevant answer. A goal is most helpful when it describes the outcome the user wants rather than restating the question. For example, with `ask=how do I create an API token`, a goal like `automate deployments from our CI pipeline` lets GitBook tailor the answer to that use case.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.