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 - Pi Art Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert Curve
I'm not real and I deny I won't heal unless I cry.Cocteau Twinslet it gomore quotes

art: beautiful


Visualizaiton workshop at UBC B.I.G. Research Day. 11 May 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)
VIEW ALL

news + thoughts

Regression diagnostics

Wed 11-05-2016

Residual plots can be used to validate assumptions about the regression model.

Continuing with our series on regression, we look at how you can identify issues in your regression model.

The difference between the observed value and the model's predicted value is the residual, `r = y_i - \hat{y}_i`, a very useful quantity to identify the effects of outliers and trends in the data that might suggest your model is inadequate.

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

We also discuss normal probability plots (or Q-Q plots) and show how these can be used to check that the residuals are normally distributed, which is one of the assumptions of regression (constant variance being another).

Background reading

Altman, N. & Krzywinski, M. (2016) Points of Significance: Analyzing outliers: Influential or nuisance? Nature Methods 13:281-282.

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

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.