Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - contact me Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Lumondo Photography
This love loves love. It's a strange love, strange love.Liz Fraserwatch

visualization: exciting



Circos at British Library Beautiful Science exhibit—Feb 20–May 26


visualization + design

Getting into Visualization of Large Biological Data Sets

The 20 imperatives of information design

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.

If you are interested in guidelines for data encoding and visualization in biology, see our Visualization Principles Vizbi 2012 Tutorial and Nature Methods Points of View column by Bang Wong.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Getting into Visualization of Large Biological Data Sets. M Krzywinski, I Birol, S Jones, M Marra (poster presentation) (PDF)


The 20 imperatives of information design


ENSURE LEGIBILITY AND FOCUS ON THE MESSAGE

Create legible visualizations with a strong message. Make elements large enough to be resolved comfortably. Bin dense data to avoid sacrificing clarity.

Distinguish between exploration and communication.

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.

Do not exceed resolution of visual acuity.

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.

Use no more than ~500 scale intervals.

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.

Show variation with statistics.

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.

Do not draw small elements to scale.

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.

Aggregate data for focused theme.

A strong visual message has no uncertainty in its interpretation. Focus on a single theme by aggregating unnecessary detail.

Show density maps and outliers.

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.

Consider whether showing the full data set is useful.

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.

USE EFFECTIVE VISUAL ENCODINGS TO ORGANIZE INFORMATION.

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.

Use the simplest encoding.

Choose concise encodings over elaborate ones.

Help the reader judge accurately.

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.

Use encodings that are robust and comparable.

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.

Crop scale to reveal fine structure in data.

Biological data sets are typically high-resolution (changes at base pair level can meaningful), sparse (distances between changes are orders of magnitude greater than the affected areas) and connect distant regions by adjacency relationships (gene fusions and other rearrangements). It is difficult to take these properties into account on a fixed linear scale, the kind used by traditional genome browsers. To mitigate this, crop and order axis segments arbitrarily and apply a scale adjustment to a segment or portion thereof.

Use perceptual palettes.

Selecting perceptually favorable colors is difficult because most software does not support the required color spaces. Brewer palettes exist for the full range of colors to help us make useful choices. Qualitative palettes have no perceived order of importance. Sequential palettes are suitable for heat maps because they have a natural order and the perceived difference between adjacent colors is constant. Twin hue diverging palettes, are useful for two-sided quantitative encodings, such as immunofluorescence and copy number.

Never use hue to encode magnitude.

Hue does not communicate relative change in values because we perceive hue categorically (blue, green, yellow, etc). Changes within one category have less perceptual impact than transitions between categories. For example, variations across the green/yellow boundary are perceived to be larger than variations across the same sized hue interval in other parts of the spectrum.

USE EFFECTIVE DESIGN PRINCIPLES TO EMPHASIZE AND COMMUNICATE PATTERNS.

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.

Reduce unnecessary variation.

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.

Encapsulate details.

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.

Use consistent alignment. Center on theme.

Establish equivalence using consistent alignment. Awkward callouts can be avoided if elements are logically placed.

Respect natural hierarchies.

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.

Palette for color blindness / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
This 15-color palette provides good discrimination for common color blindness types. Individuals with tritanopia cannot distinguish colors marked with ● and ◥. (hires)

Be aware of the luminance effect.

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.

Be aware of color blindness.

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.

news + thoughts

Mind your p's and q's

Sat 29-03-2014

In the April Points of Significance Nature Methods column, we continue our and consider what happens when we run a large number of tests.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Comparing Samples — Part II — Multiple Testing. (read)

Observing statistically rare test outcomes is expected if we run enough tests. These are statistically, not biologically, significant. For example, if we run N tests, the smallest P value that we have a 50% chance of observing is 1–exp(–ln2/N). For N = 10k this P value is Pk=10kln2 (e.g. for 104=10,000 tests, P4=6.9×10–5).

We discuss common correction schemes such as Bonferroni, Holm, Benjamini & Hochberg and Storey's q and show how they impact the false positive rate (FPR), false discovery rate (FDR) and power of a batch of tests.

Krzywinski, M. & Altman, N. (2014) Points of Significance: Comparing Samples — Part II — Multiple Testing Nature Methods 11:215-216.

Krzywinski, M. & Altman, N. (2014) Points of Significance: Comparing Samples — Part I — t-tests Nature Methods 11:215-216.

Krzywinski, M. & Altman, N. (2013) Points of Significance: Significance, P values and t-tests Nature Methods 10:1041-1042.

Happy Pi Day— go to planet π

Fri 21-03-2014

Celebrate Pi Day (March 14th) with the art of folding numbers. This year I take the number up to the Feynman Point and apply a protein folding algorithm to render it as a path.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Digits of Pi form landmass and shoreline. (details)

For those of you who liked the minimalist and colorful digit grid, I've expanded on the concept to show stacked ring plots of frequency distributions.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Frequency distribution of digits of Pi in groups of 6 up to the Feynman Point. (details)

And if spirals are your thing...

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Frequency distribution of digits of Pi in groups of 4 up to digit 4,988. (details)

Have data, will compare

Fri 07-03-2014

In the March Points of Significance Nature Methods column, we continue our discussion of t-tests from November (Significance, P values and t-tests).

We look at what happens how uncertainty of two variables combines and how this impacts the increased uncertainty when two samples are compared and highlight the differences between the two-sample and paired t-tests.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Comparing Samples — Part I. (read)

When performing any statistical test, it's important to understand and satisfy its requirements. The t-test is very robust with respect to some of its assumptions, but not others. We explore which.

Krzywinski, M. & Altman, N. (2014) Points of Significance: Comparing Samples — Part I Nature Methods 11:215-216.

Krzywinski, M. & Altman, N. (2013) Points of Significance: Significance, P values and t-tests Nature Methods 10:1041-1042.

Circos at British Library Beautiful Science Exhibit

Thu 06-03-2014

Beautiful Science explores how our understanding of ourselves and our planet has evolved alongside our ability to represent, graph and map the mass data of the time. The exhibit runs 20 February — 26 May 2014 and is free to the public. There is a good Nature blog writeup about it, a piece in The Guardian, and a great video that explains the the exhibit narrated by Johanna Kieniewicz, the curator.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circos at the British Library Beautiful Science exhibit. (about exhibit)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Mailed invitation to the exhibit features my science art. (zoom)

I am privileged to contribute an information graphic to the exhibit in the Tree of Life section. The piece shows how sequence similarity varies across species as a function of evolutionary distance. The installation is a set of 6 30x30 cm backlit panels. They look terrific.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circos Circles of Life installation at Beautiful Science exhibit at the British Library. (zoom)

Think outside the bar—box plots

Fri 31-01-2014

Quick, name three chart types. Line, bar and scatter come to mind. Perhaps you said pie too—tsk tsk. Nobody ever thinks of the box plot.

Box plots reveal details about data without overloading a figure with a full frequency distribution histogram. They're easy to compare and now easy to make with BoxPlotR (try it). In our fifth Points of Significance column, we take a break from the theory to explain this plot type and—I hope— convince you that they're worth thinking about.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Visualizing samples with box plots. (read)

The February issue of Nature Methods kicks the bar chart two more times: Dan Evanko's Kick the Bar Chart Habit editorial and a Points of View: Bar charts and box plots column by Mark Streit and Nils Gehlenborg.

Krzywinski, M. & Altman, N. (2014) Points of Significance: Visualizing samples with box plots Nature Methods 11:119-120.