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Visualizaiton workshop at UBC B.I.G. Research Day. 11 May 2016


visualization + design

Creating the Genome Research November 2012 Cover

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Cover image accompanying Spark: A navigational paradigm for genomic data exploration. Genome Research 22 (11). (zoom, Genome Research)

The Genome Research cover design takes a fun and illustrative approach to visualization. It's both art and science — in a 4:1 ratio.

The cover image accompanies the article by Cydney Nielsen from our visualization group, describing her Spark tool for visualization epigenetics data.

Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, et al. (2012) Spark: A navigational paradigm for genomic data exploration. Genome Res 22: 2262-2269.

Instead of a literal depiction of output from Spark, the final design presents what appears to be necklaces of the kind of tiles that Spark uses for its visual presentation. I took a chance that Genome Research had a sense of humor. Luckily, they did and accepted the design for the cover.

Colored tiles are playfully suspended on vertical strings to illustrate how Spark, presented in this issue, uses clustering to group genomic regions (tiles) with similar data patterns (colored heatmaps) and facilitates genome-wide data exploration.Genome Research 22 (11)

The image was published on the November 2012 issue of cover of Genome Research.

Tools

Illustrator CS5, and a cup (or two) of Galileo coffee from a Rancilio Epoca.

Other Covers

I had two other covers published this year: the PNAS cover accompanied our manuscript about mouse vasculature development and the Trends in Genetics cover was commissioned.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Cover image accompanying our article on mouse vasculature development. Biology turns astrophysical. PNAS 1 May 2012; 109 (18) (zoom, how it was made, PNAS)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Cover image for the human genetics special issue. Trends in Genetics October 2012, 28 (10) (lowres, hires, how it was made, Trends in Genetics)

source of design

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
To lower this computational barrier, particularly in the early data exploration phases, Spark was developed as an interactive pattern discovery and visualization tool for epigenomic data. (Spark)

Thinking about design ideas for the cover, I looked to the kind of visual motifs that Spark used for inspiration. Immediately the colorful tiles, which represent clustered data tracks, stood out.

Spark's output is very stylized, colorful and high contrast. It was important to preserve this aesthetic in the design. I also wanted to incorporate the idea of clustering in the design, as well as the concept that the clusters represented data from different parts of the genome.

While it was not important to illustrate how Spark organizes and analyzed data explicitly — in fact, I wanted these aspects to be subtle — it was important that the cover illustration had connections to Spark at several levels.

Spark

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Many genomics techniques produce measurements that have both a value and a position on a reference genome, for example ChIP-sequencing.

Spark was created by Cydney Nielsen, who works with me at the Genome Sciences Center. It is designed to mitigate the difficulties arising from the fact that genome-wide data is typically scattered across thousands of points of interest.

Genome browsers integrate diverse data sets by plotting them as vertically stacked tracks across a common genomic x-axis. Genome browsers are designed for viewing local regions of interest (e.g. an individual gene) and are frequently used during the initial data inspection and exploration phases.

Most genome browsers support zooming along the genome coordinate. This type of overview is not always useful because it produces a summary across a continuous genomic range (e.g. chromosome 1) and not across the subset of regions that are of interest (e.g. genes on chromosome 1). Spark addresses this shortcoming and provides a way to help answer questions like: What are the common data patterns across genes start sites in my data set?

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Spark's approach to analysis and display of epigenetic data.

Spark's visualization is driven by clustering data tracks (e.g. ChIP-seq coverage) from across equivalent regions (e.g. gene start sites). The clustered tracks are displayed as heatmaps, with each row being a data track and each column a windowed region of the genome.

early comps

With fond memories of Monte Carlo simulations from my physics days, I set out to simulate some realistic-looking, but entirely synthetic, Spark cluster tiles.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A collection of synthetic Spark tiles, each 7x20.

My first idea was a design which would show these tiles falling, perhaps accumulating on a pile on the ground. Quick prototypes of this idea were disappointing. The tiles appeared flimsy and too complex, while the image was largely empty. I spent several hours messing around with the rotation and pseudo-3D layout, but could not find anything that was satisfying.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Spark tiles, falling.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Early attempt at a design. Meh.

I thought to do this right would require a proper simulation within a 3D system.

refining the design

To address the fact that the tiles felt flimsy and overly complicated and the design lacked depth, I simplified the tile simulation to generate 5x5 tiles. These simpler representations still embodied how Spark displayed data, but did so minimally.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A second attempt at simulating Spark clusters.

To keep with the idea that the clusters come from different regions of the genome, I thought of arranging them along line segments. Unlike the design in which the tiles were falling, this constrained the layout significantly and allowed me to play with the design to make it look like the clusters were draped over it. By casting a light shadow behind each string of tiles, a subtle 3D effect could be achieved while still keeping the design within a plane.

There are 11 orientations of tiles created by rotating a thin square around the vertical axis with a slight forward tilt. There are 5 rotations to the left and right at angles 10, 26, 46, 66 and 80 degrees. The rotation was achieved using Illustrator's Extrude and Bevel 3D filter.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Layout of tiles.
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Rotated tiles with Spark clusters.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Flight and Fall by Rachel Nottingham. (artist's site)

The layout and rotation of the tiles was inspired by Flight and Fall by Rachel Nottingham, a mobile of paper birds.

I wanted to keep the layout of the spark tiles pleasant, without being too organized. I find this to be a difficult balance to achieve — natural randomness is deceptively difficult to create by hand.

final image

Four different versions of the design were submitted to Genome Research. I was happiest with the treatment in which the tiles maintained their color and the Spark clusters were projected as tones of white. This designed felt more solid and punchy — I feel like you can reach out and touch one of those strings.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Final Spark cover designs. The top left one was chosen by Genome Research.
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news + thoughts

Analyzing Outliers: Influential or Nuisance?

Fri 08-04-2016

Some outliers influence the regression fit more than others.

This month our column addresses the effect that outliers have on linear regression.

You may be surprised, but not all outliers have the same influence on the fit (e.g. regression slope) or inference (e.g. confidence or prediction intervals). Outliers with large leverage—points that are far from the sample average—can have a very large effect. On the other hand, if the outlier is close to the sample average, it may not influence the regression slope at all.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Analyzing Outliers: Influential or Nuisance? (read)

Quantities such as Cook's distance and the so-called hat matrix, which defines leverage, are useful in assessing the effect of outliers.

Background reading

Altman, N. & Krzywinski, M. (2015) Points of Significance: Multiple Linear Regression Nature Methods 12:1103-1104.

Altman, N. & Krzywinski, M. (2015) Points of significance: Simple Linear Regression Nature Methods 12:999-1000.

...more about the Points of Significance column

Typographical posters of bird songs

Mon 28-03-2016

Chirp, chirp, chirp but much better looking.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The song of the Northern Flicker, Black-capped Chickadee, Olive-sided Flycatcher and Red-eyed Vireo. Sweet to the eye and ear. (details)

If you like these, check out my other typographical art posters.

Happy 2016 Pi Day—gravity of `\pi`

Mon 14-03-2016

Celebrate `\\pi` Day (March 14th) with colliding digits in space. This year, I celebrate the detection of gravitational waves at the LIGO lab and simulate the effect of gravity on masses created from the digits of `\\pi`.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
1,000 digits of `\pi` under the influence of gravity. (details)

Some strange things can happen.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
44 digits of `\pi` under the influence of gravity. (details)

The art is featured in the Gravity of Pi article on the Scientific American SA Visual blog.

Check out art from previous years: 2013 `\\pi` Day and 2014 `\\pi` Day and 2015 `\\pi` Day.

Neural Circuit Diagrams

Sun 13-03-2016

Use alignment and consistency to untangle complex circuit diagrams.

This month we apply the ideas presented in our column about drawing pathways to neural circuit diagrams. Neural circuits are networks of cells or regions, typically with a large number of variables, such as cell and neurotransmitter type.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of View column: Neural circuit diagrams. (read)

We discuss how to effectively route arrows, how to avoid pitfalls of redundant encoding and suggest ways to encorporate emphasis in the layout.

Hunnicutt, B.J. & Krzywinski, M. (2016) Points of View: Neural circuit diagrams. Nature Methods 13:189.

background reading

Hunnicutt, B.J. & Krzywinski, M. (2016) Points of Viev: Pathways. Nature Methods 13:5.

Wong, B. (2010) Points of Viev: Gestalt principles (part 1). Nature Methods 7:863.

Wong, B. (2010) Points of Viev: Gestalt principles (part 2). Nature Methods 7:941.

...more about the Points of View column

Pathways

Mon 04-01-2016

Apply visual grouping principles to add clarity to information flow in pathway diagrams.

We draw on the Gestalt principles of connection, grouping and enclosure to construct practical guidelines for drawing pathways with a clear layout that maintains hierarchy.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of View column: Pathways. (read)

We include tips about how to use negative space and align nodes to emphasizxe groups and how to effectively draw curved arrows to clearly show paths.

Hunnicutt, B.J. & Krzywinski, M. (2016) Points of Viev: Pathways. Nature Methods 13:5.

background reading

Wong, B. (2010) Points of Viev: Gestalt principles (part 1). Nature Methods 7:863.

Wong, B. (2010) Points of Viev: Gestalt principles (part 2). Nature Methods 7:941.

...more about the Points of View column