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making-figures

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Tips on figure making, plus help with Inkscape and Matplotlib.

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# Tips for making scientific figures

1. [Have a plan](tips/1-1-have-a-plan.md) (start with a sketch)
2. [Design for papers](tips/1-2-design-for-papers.md) (start from a fixed width)
3. [Use vector art where appropriate](https://nbviewer.org/github/MichaelClerx/making-figures/blob/main/tips/1-3-vector-and-raster.ipynb)
4. [Consciously use visual language](https://nbviewer.org/github/MichaelClerx/making-figures/blob/main/tips/1-4-visual-language.ipynb)
5. [Show your workings](https://nbviewer.org/github/MichaelClerx/making-figures/blob/main/tips/1-5-show-your-workings.ipynb)

Disclaimer: I am not an expert on this.
Please use the [issues page](https://github.com/MichaelClerx/making-figures/issues) to tell me I'm wrong, or suggest new things to add!

## References

- A free book on data visualisation, with lots of beautiful examples:
  - [Claus O. Wilke (2019) Fundamentals of Data Visualization](https://clauswilke.com/dataviz)
- General figure making: 
  - [Rolandi, Cheng, Pérez-Kriz (2011) A Brief Guide to Designing Effective Figures for the Scientific Paper](https://doi.org/10.1002/adma.201102518).
- Colour maps:
  - [Nunez, Anderton, Renslow (2018) Optimizing colormaps with consideration for color vision deficiency to enable accurate interpretation of scientific data](https://doi.org/10.1371/journal.pone.0199239)
  - [Rogowitz, Treinish (2017) Why Should Engineers and Scientists Be Worried About Color](https://www.researchgate.net/profile/Ahmed-Elhattab/post/Please-suggest-some-good-3D-plot-tool-Software-for-surface-plot/attachment/5c05ba35cfe4a7645506948e/AS%3A699894335557644%401543879221725/download/Why+Should+Engineers+and+Scientists+Be+Worried+About+Color_.pdf)
  - [Borland, Taylor (2007) Rainbow color map (still) considered harmful](https://doi.org/10.1109/MCG.2007.323435)
- Choosing colours:
  - [Online colourblind simulator](https://www.color-blindness.com/coblis-color-blindness-simulator/) 
  - [Color brewer](https://colorbrewer2.org/)
  - [Seaborn palettes](https://seaborn.pydata.org/tutorial/color_palettes.html)
- Words
  - [What's the difference between a graph, a chart, and a plot](https://english.stackexchange.com/questions/43027/whats-the-difference-between-a-graph-a-chart-and-a-plot)

## Appendix: Making diagrams with Inkscape

E.g. to visualise an experimental set-up or create a graphical abstract.

1. [Getting started](inkscape/2-1-getting-started.md)
2. [Shapes, colours, text, and lines](inkscape/2-2-shapes-colours-lines.md)
3. [More drawing](inkscape/2-3-more-drawing.md)
4. [Paths](inkscape/2-4-paths.md)
5. [Saving and exporting](inkscape/2-5-save-and-export.md)
6. [Annoyances](inkscape/2-6-annoyances.md)

## Appendix: Plotting with Matplotlib

E.g. to plot data or graph functions.

1. [Getting started](https://nbviewer.org/github/MichaelClerx/making-figures/blob/main/matplotlib/3-1-getting-started.ipynb)
2. [Lines and markers](https://nbviewer.org/github/MichaelClerx/making-figures/blob/main/matplotlib/3-2-lines-and-markers.ipynb)
3. [Layout](https://nbviewer.org/github/MichaelClerx/making-figures/blob/main/matplotlib/3-3-layout.ipynb)
4. [Axes, legends, and annotations](https://nbviewer.org/github/MichaelClerx/making-figures/blob/main/matplotlib/3-4-axes-legends-annotations.ipynb)
5. [Raster data](https://nbviewer.org/github/MichaelClerx/making-figures/blob/main/matplotlib/3-5-raster-data.ipynb)
6. [Neat tricks](https://nbviewer.org/github/MichaelClerx/making-figures/blob/main/matplotlib/3-6-neat-tricks.ipynb)

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