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The Little Book of Smiley Plots: A collection of ancient DNA damage plots and their causes

DOI

This repository contains a examples of different types of ancient DNA damage plots, both valid and invalid, and describes the causes behind them.

Technical guidelines

To add a new plot:

  1. add a new .qmd markdown file (make a copy of template.qmd if you wish)
  2. add the name of the file to the corresponding 'part' in _quarto.yml.
  3. raw deamination plot data file(s) (e.g. from mapDamage or DamageProfiler) for the corresponding plot should be added to the assets/data/ folder in a subfolder named the same as the .qmd file.
  4. new functions for parsing new damage profile tool outputs in assets/src/R/
  5. caricature image should go in assets/images/ in a folder also with the same name as the .qmd, but with the file name the 'name' of the caricature.
  6. bibtex citations should go in references.bib

Artistic guidelines

We want to give the artists of caricatures as much stylistic and creative freedom as possible. The five specifications for the caricatures are:

  1. The perceived 'quality' of the art is not important(!)
  2. They must be a caricature of a face (neither species, nor realism are important - but in most cases do not images of living people)
  3. Must incorporate a damage profiles into it (of those that do not have one in the book already - please assign/leave a comment on the respective GitHub issue!)
  4. Other than gray scale (black, white, shades of grey), can only use three colours: red, blue, and one additional your choice
  5. Must not violate the SPAAM code of conduct(i.e, not contain sexist, racist, homophobic illegal, defamatory, rude, imagery etc.)

Additional recommendations:

  • The image should be shared in vector format (to allow resizing), if possible

Development Guidelines

Once changes to the markdown contents are made, you can preview locally, but you must re-render the book before pushing.

  • To preview: quarto preview . --no-browser --no-watch-inputs
  • To re-render: quarto render --to all
  • Then git commit and push

Warning

If changes are made to R code (e.g. under src/R), you MUST re-render before live previewing! While markdown changes can be updated on the fly, R-code generated images are not updated in real time.
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