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EMBO Practical Course: Bioinformatics and Genome Analysis, 5–17 June 2017.


data visualization + science communication

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Essentials of Data Visualization. An 8-part video mini-series on how to think about drawing data. In collaboration with University of Sydney.

Insights into Data Visualization: 8-part mini-series

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.

Resources

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.

Episodes

1 Data Encoding

Make it easy to answer relevant questions.

watch | PDF | 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?

2 Shapes and Symbols

Intuitively encode role and relevance.

watch | PDF | 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).

3 Color

Use it for emphasis and visual separation.

watch | PDF | 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.

4 Uncertainty

Don't make errors in error bars.

watch | PDF | 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.

5 Design

Organize and clarify.

watch | PDF | 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.

6 Nothing

No data, no ink.

watch | PDF | 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.

7 Labels

Respect type and use it to establish hierarchy.

watch | PDF | 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.

8 Process

Creating a visualization for Scientific American Graphic Science: from start to finish.

watch | PDF | 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.