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Twenty — minutes — maybe — more.Naomichoose four wordsmore quotes

UCD Computational and Molecular Biology Symposium, Dublin, Ireland. 1-2 Dec 2016.

design + visualization

VIZBI 2013 Keynote

Visual Design Principles—Communicating Effectively

This talk happened on Thursday, Mar 21st 2013 at VIZBI 2013 at the Broad Institute in Boston.

How often people speak of art and science as though they were two entirely different things, with no interconnection. An artist is emotional, they think, and uses only his intuition; he sees all at once and has no need of reason. A scientist is cold, they think, and uses only his reason; he argues carefully step by step, and needs no imagination. That is all wrong. The true artist is quite rational as well as imaginative and knows what he is doing; if he does not, his art suffers. The true scientist is quite imaginative as well as rational, and sometimes leaps to solutions where reason can follow only slowly; if he does not, his science suffers. —Isaac Asimov (The Roving Mind)

For more visualization and design resources, see my VIZBI 2012 tutorials, Nature Methods Points of View column, and rant about colors.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Do not allow encoding or other design choices to hijaack your message. Each element on the page must meaningfully contribute to your figure.

presentation video

The video will be posted at vizbi.org.

presentation slides

Slides are available as PDF and keynote (zipped).

Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
Martin Krzywinski - VIZBI 2013 Keynote - Visual Design Principles
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A poet is, after all, a sort of scientist, but engaged in a qualitative science in which nothing is measurable. He lives with data that cannot be numbered, and his experiments can be done only once. The information in a poem is, by definition, not reproducible. He becomes an equivalent of scientist, in the act of examining and sorting the things popping in [to his head], finding the marks of remote similarity, points of distant relationship, tiny irregularities that indicate that this one is really the same as that one over there only more important. Gauging the fit, he can meticulously place pieces of the universe together, in geometric configurations that are as beautiful and balanced as crystals. —Lewis Thomas (The Medusa and the Snail: More Notes of a Biology Watcher)

breakout session—making good figures

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Sketch notes by the inimitable Francis Rowland from our breakout group. The question was: what do you need to make good figures? (PDF)

small, medium and big data visualization

If you're asking how to visualize big data, first make sure you're doing a good job on small and medium data. Each scale requires good design.

Do not expect to use one way
to tell many stories

Also consider that there is a very large number of combinations of data sets, hypotheses and possible patterns. Because of this, you cannot expect to use one way to tell many stories. There is no Holy Grail of big data visualization. But there are many good questions to ask and practices to follow that make up a process which can help you get there.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Medium data visualization. This is what happens when you show the data (a strategy that works for small data), instead of explaining it. Yup, we need to work on this too. (A) Qi X et al. J Biotech 144:43 (2012) (Saturation-Mutagenesis in Two Positions Distant from Active Site of a Klebsiella pneumoniae Glycerol Dehydratase Identifies Some Highly Active Mutants) (B) Alekseyev, M.A. et al. Genome Res 19:943 (2009) (Breakpoint graphs and ancestral genome reconstructions)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Big data visualization. Yes, data sets are growing but are visual and cognitive abilities are not. There are many data sets, each requiring its own approach. You cannot use one way to tell many stories. Lewis SN et al. PLoS ONE 6:e27175 (2011) (Prediction of Disease and Phenotype Associations from Genome-Wide Association Studies)
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news + thoughts

Happy 2016 `\pi` Approximation, roughly speaking

Sun 24-07-2016

Today is the day and it's hardly an approximation. In fact, `22/7` is 20% more accurate of a representation of `\pi` than `3.14`!

Time to celebrate, graphically. This year I do so with perfect packing of circles that embody the approximation.

By warping the circle by 8% along one axis, we can create a shape whose ratio of circumference to diameter, taken as twice the average radius, is 22/7.

If you prefer something more accurate, check out art from previous `\pi` days: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, and 2016 `\pi` Day.

Logistic Regression

Wed 13-07-2016

Regression can be used on categorical responses to estimate probabilities and to classify.

The next column in our series on regression deals with how to classify categorical data.

We show how linear regression can be used for classification and demonstrate that it can be unreliable in the presence of outliers. Using a logistic regression, which fits a linear model to the log odds ratio, improves robustness.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Logistic regression? (read)

Logistic regression is solved numerically and in most cases, the maximum-likelihood estimates are unique and optimal. However, when the classes are perfectly separable, the numerical approach fails because there is an infinite number of solutions.

Altman, N. & Krzywinski, M. (2016) Points of Significance: Logistic regression. Nature Methods 13:541-542.

Background reading

Altman, N. & Krzywinski, M. (2016) Points of Significance: Regression diagnostics? Nature Methods 13:385-386.

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

Visualizing Clonal Evolution in Cancer

Thu 02-06-2016

Genomic instability is one of the defining characteristics of cancer and within a tumor, which is an ever-evolving population of cells, there are many genomes. Mutations accumulate and propagate to create subpopulations and these groups of cells, called clones, may respond differently to treatment.

It is now possible to sequence individual cells within a tumor to create a profile of genomes. This profile changes with time, both in the kinds of mutation that are found and in their proportion in the overall population.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Ways to present temporal and phylogenetic evolution of clones in cancer. M Krzywinski (2016) Molecular Cell 62:652-656. (read)

Clone evolution diagrams visualize these data. These diagrams can be qualitative, showing only trends, or quantitative, showing temporal and population changes to scale. In this Molecular Cell forum article I provide guidelines for drawing these diagrams, focusing with how to use color and navigational elements, such as grids, to clarify the relationships between clones.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
How to draw clone evolution diagrams better. M Krzywinski (2016) Molecular Cell xxx:xxx-xxx. (read)

I'd like to thank Maia Smith and Cydney Nielsen for assistance in preparing some of the figures in the paper.

Krzywinski, M. (2016) Visualizing Clonal Evolution in Cancer. Mol Cell 62:652-656.

Binning High-Resolution Data

Wed 01-06-2016

Limitations in print resolution and visual acuity impose limits on data density and detail.

Your printer can print at 1,200 or 2,400 dots per inch. At reading distance, your reader can resolve about 200–300 lines per inch. This large gap—how finely we can print and how well we can see—can create problems when we don't take visual acuity into account.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of View column: Binning high-resolution data. (read)

The column provides some guidelines—particularly relevant when showing whole-genome data, where the scale of elements of interest such as genes is below the visual acuity limit—for binning data so that they are represented by elements that can be comfortably discerned.

Krzywinski, M. (2016) Points of view: Binning high-resolution data. Nature Methods 13:463.

...more about the Points of View column