diff --git a/assets/docs/FigureTitleLegend.docx b/assets/docs/FigureTitleLegend.docx new file mode 100644 index 0000000..c29d79e Binary files /dev/null and b/assets/docs/FigureTitleLegend.docx differ diff --git a/assets/images/figures.jpg b/assets/images/figures.jpg new file mode 100644 index 0000000..70424ee Binary files /dev/null and b/assets/images/figures.jpg differ diff --git a/assets/slides/Making_model_figures_workshop.pptx b/assets/slides/Making_model_figures_workshop.pptx new file mode 100644 index 0000000..8594c19 Binary files /dev/null and b/assets/slides/Making_model_figures_workshop.pptx differ diff --git a/figures.qmd b/figures.qmd new file mode 100644 index 0000000..88f70a0 --- /dev/null +++ b/figures.qmd @@ -0,0 +1,62 @@ +--- +title: "Preparing Thesis Figures" +image: ./assets/images/figures.jpg +description: | + How to prepare figures for your thesis +number-sections: true +about: + template: marquee + links: + - icon: twitter + text: Twitter + href: https://twitter.com/scompbiol + - icon: github + text: Github + href: https://github.com/sipbs-compbiol + - icon: envelope + text: Email + href: mailto:leighton.pritchard@strath.ac.uk +html: + anchor-sections: true +--- + +## Figure Preparation checklist + +1. Determine what message you want the reader to take from your figure, and the most effective way of conveying that point +2. Remove any extraneous or distracting data that distracts from the main message of your figure (taking care not to make the figure misleading by doing so) +3. Determine how large the figure needs to be: how much space will it take up on a page? +4. Will it be easy for your reader to see key details if the figure is this size? +5. Check that the figure is clear and not pixellated: will your reader be able to see all the important details? Is the resolution good enough? + - You should always prepare figures in _vector format_ (i.e. PDF, PS, or SVG) where possible to avoid pixellation issues. +6. Check that the colour scheme you have chosen is colour-blind friendly and not visually jarring +7. Check that any fonts used are legible at the size printed +8. Figure titles should give a concise "take-home message" conveying the result(s) shown in the figure +9. Figure legends should give enough detail about the experiment for the reader to understand what was done (the figure should be able to stand on its own) + +- [Dr Feeney's guidance on writing good figure titles and legends (with examples)](./assets/docs/FigureTitleLegend.docx) + +## A guide to figure preparation + +- Refer back to the [Data presentation and figure preparation](https://sipbs-compbiol.github.io/BM432/notebooks/04-data_presentation_workshop.html) (BM432 workshop 6 materials) as needed. +- [Points of View](https://protocolsmethods.springernature.com/posts/43650-data-visualization-a-view-of-every-points-of-view-column) - _In my opinion the definitive guide to graphic design for scientific figures - LP_ +- [Making model figures](./Making_model_figures_workshop.pptx) (slides used in our regular meeting discussion) +- [Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002128) - _A compelling case for why you should **never** use bar graphs, and especially not dynamite plots - LP_ +- [Read Ten Simple Rules for Better Figures](https://doi.org/10.1371/journal.pcbi.1003833) - _Yet another excellent "Ten Simple Rules…" article - LP_ +- [Digital Images Are Data: And Should Be Treated as Such](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4210356/) - _It's natural to think of images as being "neutral" in some way, but they are not - LP_ +- [Ten common statistical mistakes to watch out for when writing or reviewing a manuscript](https://elifesciences.org/articles/48175) - _Another "Ten Simple Rules…" article - LP_ +- [Fundamentals of graphic design---essential tools for effective visual science communication](https://www.facetsjournal.com/doi/10.1139/facets-2018-0049) - _A good, short summary of graphic design principles relevant to scientific communication - LP_ +- [11 Graphic Design Tips to Create Images Like a Pro](https://blog.snappa.com/graphic-design-tips/) - _Economical advice for powerful graphic design - LP_ + +## Other Useful Resources + +- [Biorender](https://www.biorender.com/) - _Useful clipart and images for building your own figures - LP_ +- [ImageJ Basics](https://imagej.nih.gov/ij/docs/pdfs/ImageJ.pdf) - _The standard open source image analysis software - LP_ +- [Coblis --- Color Blindness Simulator](https://www.color-blindness.com/coblis-color-blindness-simulator/) - _It's kind to consider the needs of others, so always check your images for colourblindness accessibility - LP_ +- [Data visualization with ggplot2 :: Cheat Sheet](https://rstudio.github.io/cheatsheets/html/data-visualization.html?_gl=1*yq93b*_ga*NDg4Mzg2NDQ4LjE2OTI4ODYzNzY.*_ga_2C0WZ1JHG0*MTY5MzIyOTcyMy41LjAuMTY5MzIyOTcyMy4wLjAuMA..) - _`ggplot` is an amazing way to generate powerful graphs, though there can be a learning curve, especially if you don't yet know `R` - LP_ + +## Dr Feeney's pet peeves for figures + +- [Why You *Must* Plot Your Growth Data On a Semi-log Graph](https://schaechter.asmblog.org/schaechter/2018/07/why-you-must-plot-your-growth-data-on-semi-log-graph-paper.html) - _TBH, this is trivial to do now in most graphic packages, so there's no excuse - LP_ +- Make sure you include a scale on any images that need them (e.g., micrographs, phylogenetic trees) +- By convention, figure titles and legends are presented **below** the corresponding figure, while table titles are presented **above** the corresponding table. +- Make sure your text is formatted correctly within your figure (e.g., species names should be italicized, gene and protein names should be formatted correctly)