Distractions and amusements, with a sandwich and coffee.
This video series focuses on relevant and practical concepts in scientific data visualization. Our aim is to make you think more clearly about visual presentation and to make you a better communicator.
Each video in the series presents fundamental ideas and is designed to provide constraints and guidance to your thoughts about communicating your data. The purpose of scientific data visualization is not merely to inform but also to answer and generate hypotheses.
Though few firm rules exist when it comes to how to achieve clarity—whatever the communication medium—we must meet core requirements such as consistency, redundancy and appropriate mapping between relevant and salience. We present these essential topics using biological data as examples. But if you're not a biologist, don't worry. Instead, think about the data structure rather than meaning and you'll be fine.
Each video is about 15 minutes long and comes with a slide deck of the images used in the video, exercise and suggested solutions.
Download all course materials.
Make it easy to answer relevant questions.
When you think of data visualization, the first ideas that come to mind are a scatter plot, or a bar char, a box plot or a network diagram. These are all data encodings—methods that relate data values to the positions, sizes and shapes of the lines or symbols that appear on the screen or in a figure. There are many data encodings—which do you choose?
watch | PDF slides
Intuitively encode role and relevance.
Shapes and glyphs are really important. They make up the heart of a lot of data plots. Your default should be the circle. If you need different shapes, try to map the classes as intuitively as possible onto the shapes. Use less prominent symbols for data that are less relevant (such as reference data included for context).
watch | PDF slides
Use it for emphasis and visual separation.
Color is one of the most exciting ways in which you can completely screw over your visualization. What can start off as a great diagram can be absolutely ruined by a lack of color judgment. When using color, ask yourself—do I need it? Try to work around it using grey tones from Brewer palettes. If you succeed, you’re in a perfect place to use spot color, sparingly, for emphasis.
watch | PDF slides
Don't make errors in error bars.
Knowing the limits of your knowledge is very important. In biology, it’s important to be able to sample the extent of biological variation. And so being able to show this and other forms of variation in measurements or any computed values in visualizations is very important—it addresses reproducibility and your capacity to make statistical inference. Often this is done with error bars. Ironically, there’s a lot of error associated with the use of and interpretation of error bars.
watch | PDF slides
Organize and clarify.
Design plays a large role in data visualization. Think of design as choreography for the page. In our context it’s not merely driven by aesthetic, but function. Although there’s always room for aesthetic—gently applied—and I really encourage you to find your own and continue to refine it. But always remember, be understood before being articulate. Be legible before being attractive! Your goal here isn’t to make inroads on the global stage of aesthetic studies. Become a good visual explainer. It’s harder … and more worth doing.
watch | PDF slides
No data, no ink.
Data-to-ink ratio, taken to the extreme: if there is no data to show, no ink should be used. The idea of “no data to show” may correspond to a variety of scenarios. There may be sincerely no data to show—no values were collected. Or, there are no significant changes to see. Where possible, you should use empty space to indicate lack of data or lack of change in data. You should never be distracted by something that isn’t relevant and empty space is not distracting—it really just provides contrast to adjacent elements, which presumably correspond to actual data or actionable data.
watch | PDF slides
Respect type and use it to establish hierarchy.
Open up a journal or your favourite text book. Find a figure. There’s probably some labels in there. Maybe it’s a multi-panel figure and the labels are the titles. Maybe there are some callouts that tell you what the parts are. If it’s a plot there are probably axis labels and tick labels and maybe a legend with some labels. There’s usually several informational layers in the image, each with their own labels. These labels should reflect that these layers are different. They should also reflect the relative importance of these layers.
watch | PDF slides
Creating a visualization for Scientific American Graphic Science: from start to finish.
Let’s now look at the process of designing a visualization from scratch—from the encoding all the way to design. This was a graphic I did for the June 2015 issue of Scientific American. It appeared on the Graphic Science page.
watch | PDF slides
My poster showing the genome structure and position of mutations on all SARS-CoV-2 variants appears in the March/April 2022 issue of American Scientist.
An accompanying piece breaks down the anatomy of each genome — by gene and ORF, oriented to emphasize relative differences that are caused by mutations.
My cover design on the 11 April 2022 Cancer Cell issue depicts depicts cellular heterogeneity as a kaleidoscope generated from immunofluorescence staining of the glial and neuronal markers MBP and NeuN (respectively) in a GBM patient-derived explant.
LeBlanc VG et al. Single-cell landscapes of primary glioblastomas and matched explants and cell lines show variable retention of inter- and intratumor heterogeneity (2022) Cancer Cell 40:379–392.E9.
Browse my gallery of cover designs.
My cover design on the 4 April 2022 Nature Biotechnology issue is an impression of a phylogenetic tree of over 200 million sequences.
Konno N et al. Deep distributed computing to reconstruct extremely large lineage trees (2022) Nature Biotechnology 40:566–575.
Browse my gallery of cover designs.
My cover design on the 17 March 2022 Nature issue depicts the evolutionary properties of sequences at the extremes of the evolvability spectrum.
Vaishnav ED et al. The evolution, evolvability and engineering of gene regulatory DNA (2022) Nature 603:455–463.
Browse my gallery of cover designs.
Celebrate `\pi` Day (March 14th) and finally hear what you've been missing.
“three one four: a number of notes” is a musical exploration of how we think about mathematics and how we feel about mathematics. It tells stories from the very beginning (314…) to the very (known) end of π (...264) as well as math (Wallis Product) and math jokes (Feynman Point), repetition (nn) and zeroes (null).
The album is scored for solo piano in the style of 20th century classical music – each piece has a distinct personality, drawn from styles of Boulez, Feldman, Glass, Ligeti, Monk, and Satie.
Each piece is accompanied by a piku (or πku), a poem whose syllable count is determined by a specific sequence of digits from π.
Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day, 2018 `\pi` Day, 2019 `\pi` Day, 2020 `\pi` Day and 2021 `\pi` Day.