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
Mad about you, orchestrally.Hooverphonicfeel the vibe, feel the terror, feel the painmore quotes

numbers: fun


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


visualization + design

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 2016 Pi Day art imagines the digits of Pi as physical masses collapsing under gravity and is featured in the article The Gravity of Pi at the Scientific American SA Visual blog.

`\pi` Day 2016 Art Posters


Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2015 `\pi` day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` approx day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2013 `\pi` day

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circular `\pi` art

On March 14th celebrate Pi Day. Hug `\pi`—find a way to do it.

For those who favour `\tau=2\pi` will have to postpone celebrations until July 26th. That's what you get for thinking that `\pi` is wrong.

If you're not into details, you may opt to party on July 22nd, which is `\pi` approximation day (`\pi` ≈ 22/7). It's 20% more accurate that the official Pi day!

Finally, if you believe that `\pi = 3`, you should read why `\pi` is not equal to 3.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
All art posters are available for purchase.
I take custom requests.

This year's `\pi` day art collection celebrates not only the digit but also one of the fundamental forces in nature: gravity.

In February of 2016, for the first time, gravitational waves were detected at the Laser Interferometer Gravitational-Wave Observatory (LIGO).

The signal in the detector was sonified—a process by which any data can be encoded into sound to provide hints at patterns and structure that we might otherwise miss—and we finally heard what two black holes sound like. A buzz and chirp.

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

this year's theme music

All the art was processed while listening to Roses by Coeur de Pirate, a brilliant female French-Canadian songwriter, who sounds like a mix of Patricia Kaas and Lhasa. The lyrics Oublie-moi (Forget me) are fitting with this year's theme of gravity.

Mais laisse-moi tomber, laisse-nous tomber
Laisse la nuit trembler en moi
Laisse-moi tomber, laisse nous tomber
Cette fois

But let me fall, let us fall
Let the night tremble in me
Let me fall, let us fall
This time

The Einstein-`\pi` connection

The number `\pi` appears in the fundamental equation of general relativity, which relates gravity (left side) to energy and momentum (right side).

`R_{\mu \nu} - \tfrac{1}{2} Rg_{\mu\nu} = 8 \pi G T_{\mu \nu}`

The reason why `\pi` appears has to do with the need to include the surface area of the sphere, `4 \pi r^2` in the mathematics. This is very nicely described in Sean Carrol's article Einstein and `\pi`.

The gravity of `\pi`

Let's make the digits of `\pi` into masses, throw them into space, and watch gravity make them collide and orbit each other. Read about the details of the simulation and look at the posters.


Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
The first 14 digits of `\pi` generate various orbits as the digits are assigned mass and subject to gravity. (BUY ARTWORK)

As the number of digits is increased, more elaborate patterns arise. Here is one simulation using 100 digits.


Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
Things can get a little crazy with mor digits. Here, 153 digits are used. (BUY ARTWORK)

How about 1000 digits? In this simulation the masses are similar and they all collide within the circle.


Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
The first 1000 digits of `\pi` collapse into a single mass. (BUY ARTWORK)

Pi Day 2016 Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca buy artwork
The first 3 digits of `\pi` collapse into a single mass. 49 times. (BUY ARTWORK)

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.

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