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 Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert Curve
Thoughts rearrange, familiar now strange.Holly Golightly & The Greenhornes break flowers

Visualization Tour, Melbourne, October 9–20, 2014

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)

news + thoughts

Replication—Quality over Quantity

Tue 02-09-2014

It's fitting that the column published just before Labor day weekend is all about how to best allocate labor.

Replication is used to decrease the impact of variability from parts of the experiment that contribute noise. For example, we might measure data from more than one mouse to attempt to generalize over all mice.

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

It's important to distinguish technical replicates, which attempt to capture the noise in our measuring apparatus, from biological replicates, which capture biological variation. The former give us no information about biological variation and cannot be used to directly make biological inferences. To do so is to commit pseudoreplication. Technical replicates are useful to reduce the noise so that we have a better chance to detect a biologically meaningful signal.

Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.

Background reading

Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of variance (ANOVA) and blocking Nature Methods 11:699-700.

Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.

...more about the Points of Significance column

Monkeys on a Hilbert Curve—Scientific American Graphic

Tue 19-08-2014

I was commissioned by Scientific American to create an information graphic that showed how our genomes are more similar to those of the chimp and bonobo than to the gorilla.

I had about 5 x 5 inches of print space to work with. For 4 genomes? No problem. Bring out the Hilbert curve!

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Our genomes are much more similar to the chimp and bonobo than to the gorilla. And, we're practically still Denisovans. (details)

To accompany the piece, I will be posting to the Scientific American blog about the process of creating the figure. And to emphasize that the genome is not a blueprint!

As part of this project, I created some Hilbert curve art pieces. And while exploring, found thousands of Hilbertonians!

Happy Pi Approximation Day— π, roughly speaking 10,000 times

Wed 13-08-2014

Celebrate Pi Approximation Day (July 22nd) with the art of arm waving. This year I take the first 10,000 most accurate approximations (m/n, m=1..10,000) and look at their accuracy.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Accuracy of the first 10,000 m/n approximations of Pi. (details)

I turned to the spiral again after applying it to stack stacked ring plots of frequency distributions in Pi for the 2014 Pi Day.

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

Analysis of Variance (ANOVA) and Blocking—Accounting for Variability in Multi-factor Experiments

Mon 07-07-2014

Our 10th Points of Significance column! Continuing with our previous discussion about comparative experiments, we introduce ANOVA and blocking. Although this column appears to introduce two new concepts (ANOVA and blocking), you've seen both before, though under a different guise.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Analysis of variance (ANOVA) and blocking. (read)

If you know the t-test you've already applied analysis of variance (ANOVA), though you probably didn't realize it. In ANOVA we ask whether the variation within our samples is compatible with the variation between our samples (sample means). If the samples don't all have the same mean then we expect the latter to be larger. The ANOVA test statistic (F) assigns significance to the ratio of these two quantities. When we only have two-samples and apply the t-test, t2 = F.

ANOVA naturally incorporates and partitions sources of variation—the effects of variables on the system are determined based on the amount of variation they contribute to the total variation in the data. If this contribution is large, we say that the variation can be "explained" by the variable and infer an effect.

We discuss how data collection can be organized using a randomized complete block design to account for sources of uncertainty in the experiment. This process is called blocking because we are blocking the variation from a known source of uncertainty from interfering with our measurements. You've already seen blocking in the paired t-test example, in which the subject (or experimental unit) was the block.

We've worked hard to bring you 20 pages of statistics primers (though it feels more like 200!). The column is taking a month off in August, as we shrink our error bars.

Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of Variance (ANOVA) and Blocking Nature Methods 11:699-700.

Background reading

Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.

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.

...more about the Points of Significance column