Martin Krzywinski, Inanc Birol, Steven Jones, Marco Marra
Presented at Biovis 2012 (Visweek 2012). Content is drawn from my book chapter Visualization Principles for Scientific Communication (Martin Krzywinski & Jonathan Corum) in the upcoming open access Cambridge Press book Visualizing biological data - a practical guide (Seán I. O'Donoghue, James B. Procter, Kate Patterson, eds.), a survey of best practices and unsolved problems in biological visualization. This book project was conceptualized and initiated at the Vizbi 2011 conference.
Create legible visualizations with a strong message. Make elements large enough to be resolved comfortably. Bin dense data to avoid sacrificing clarity.
Use exploratory tools (e.g. genome browsers) to discover patterns and validate hypotheses. Avoid using screenshots from these applications for communication – they are typically too complex and cluttered with navigational elements to be an effective static figure.
Our acuity is ~50 cycles/degree or about 1/200 (0.3 pt) at 10 inches. Ensure the reader can comfortably see detail by limiting resolution to no more than 50% of acuity. Where possible, elements that require visual separation should be at least 1 pt part.
Ensure data elements are at least 1 pt on a two-column Nature figure (6.22 in), 4 pixels on a 1920 horizontal resolution display, or 2 pixels on a typical LCD projector. These restrictions become challenges for large genomes.
Data on large genomes must be downsampled. Depict variation with min/max plots and consider hiding it when it is within noise levels. Help the reader notice significant outliers.
Map size of elements onto clearly legible symbols. Legibility and clarity are more important than precise positioning and sizing. Discretize sizes and positions to facilitate making meaningful comparisons.
A strong visual message has no uncertainty in its interpretation. Focus on a single theme by aggregating unnecessary detail.
Establishing context is helpful when emergent patterns in the data provide a useful perspective on the message. When data sets are large, it is difficult to maintain detail in the context layer because the density of points can visually overwhelm the area of interest. In this case, consider showing only the outliers in the data set.
The reader’s attention can be focused by increasing the salience of interesting patterns. Other complex data sets, such as networks, are shown more effectively when context is carefully edited or even removed.
Match the visual encoding to the hypothesis. Use encodings specific and sensitive to important patterns. Dense annotations should be independent of the core data in distinct visual layers.
Choose concise encodings over elaborate ones.
Accuracy and speed in detecting differences in visual forms depends on how information is presented. We judge relative lengths more accurately than areas, particularly when elements are aligned and adjacent. Our judgment of area is poor because we use length as a proxy, which causes us to systematically underestimate.
In addition to being transparent and predictable, visualizations must be robust with respect to the data. Changes in the data set should be reflected by proportionate changes in the visualization. Be wary of force-directed network layouts, which have low spatial autocorrelation. In general, these are neither sensitive nor specific to patterns of interest.
Well-designed figures illustrate complex concepts and patterns that may be difficult to express concisely in words. Figures that are clear, concise and attractive are effective – they form a strong connection with the reader and communicate with immediacy. These qualities can be achieved with methods of graphic design, which are based on theories of how we perceive, interpret and organize visual information.
The reader does not know what is important in a figure and will assume that any spatial or color variation is meaningful. The figure’s variation should come solely from data or act to organize information.
Including details not relevant to the core message of the figure can create confusion. Encapsulation should be done to the same level of detail and to the simplest visual form. Duplication in labels should be avoided.
When the data set embodies a natural hierarchy, use an encoding that emphasizes it clearly and memorably. The use hierarchy in layout (e.g. tabular form) and encoding can significantly improve a muddled figure.
Color is a useful encoding – the eye can distinguish about 450 levels of gray, 150 hues, and 10-60 levels of saturation, depending on the color – but our ability to perceive differences varies with context. Adjacent tones with different luminance values can interfere with discrimination, in interaction known as the luminance effect.
In an audience of 8 men and 8 women, chances are 50% that at least one has some degree of color blindness. Use a palette that is color-blind safe. In the palette below the 15 colors appear as 5-color tone progressions to those with color blindness. Additional encodings can be achieved with symbols or line thickness.
I have designed 15-color palettes for color blindess for each of the three common types of color blindness.
One of my color tools, the
colorsnap application snaps colors in an image to a set of reference colors and reports their proportion.
Below is Times Square rendered using the colors of the MTA subway lines.
Drugs could be more effective if taken when the genetic proteins they target are most active.
Design tip: rediscover CMYK primaries.
Ruben et al. A database of tissue-specific rhythmically expressed human genes has potential applications in circadian medicine Science Translational Medicine 10 Issue 458, eaat8806.
We focus on the important distinction between confidence intervals, typically used to express uncertainty of a sampling statistic such as the mean and, prediction and tolerance intervals, used to make statements about the next value to be drawn from the population.
Confidence intervals provide coverage of a single point—the population mean—with the assurance that the probability of non-coverage is some acceptable value (e.g. 0.05). On the other hand, prediction and tolerance intervals both give information about typical values from the population and the percentage of the population expected to be in the interval. For example, a tolerance interval can be configured to tell us what fraction of sampled values (e.g. 95%) will fall into an interval some fraction of the time (e.g. 95%).
Altman, N. & Krzywinski, M. (2018) Points of significance: Predicting with confidence and tolerance Nature Methods 15:843–844.
Krzywinski, M. & Altman, N. (2013) Points of significance: Importance of being uncertain. Nature Methods 10:809–810.
A 4-day introductory course on genome data parsing and visualization using Circos. Prepared for the Bioinformatics and Genome Analysis course in Institut Pasteur Tunis, Tunis, Tunisia.
Data visualization should be informative and, where possible, tasty.
Stefan Reuscher from Bioscience and Biotechnology Center at Nagoya University celebrates a publication with a Circos cake.
The cake shows an overview of a de-novo assembled genome of a wild rice species Oryza longistaminata.