latest news

Distractions and amusements, with a sandwich and coffee.

Lips that taste of tears, they say, are the best for kissing.
•
• get cranky
• more quotes

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.

Not a circle in sight in the 2015 `\pi` day art. Try to figure out how up to 612,330 digits are encoded before reading about the method. `\pi`'s transcendental friends `\phi` and `e` are there too—golden and natural. Get it?

This year's `\pi` day is particularly special. The digits of time specify a precise time if the date is encoded in North American day-month-year convention: 3-14-15 9:26:53.

The art has been featured in Ana Swanson's Wonkblog article at the Washington Post—10 Stunning Images Show The Beauty Hidden in `\pi`.

This year's art has a modern Bauhaus style. Sharp edges, lines and solid colors. Potato farms from space. CPUs from up close. If the pieces look like the art of Piet Mondrian, you'd be right.

The digits of `pi` are encoded in something that looks like a treemap. I explain how this is done in the methods section, but before reading it, try to see if you can figure out how it's done.

I briefly experimented with the 4-color theorem in trying to apply color to the treemap, but it turned out to lack interesting stucture. Well, at least some graphs were made.

I experimented with different treemap resolutions. For treemaps that use an outline around each rectangle, I decided to stop at 8 levels, at which 111,469 digits of `pi` can be encoded.

I also made a level 9 treemap without the outlines, which encoded 612,330 digits. When rendered at 20,833 × 20,833 pixels (I needed the image in bitmap form to provide the posters for sale), some regions are essentially a pixel in size, as seen in the 1-1 crop below.

One of my color tools, the `colorsnap`

application snaps colors in an image to a set of reference colors and reports their proportion.

Below is Times Square rendered using the colors of the MTA subway lines.

*Drugs could be more effective if taken when the genetic proteins they target are most active.*

Design tip: rediscover CMYK primaries.

More of my American Scientific Graphic Science designs

Ruben et al. A database of tissue-specific rhythmically expressed human genes has potential applications in circadian medicine *Science Translational Medicine* **10** Issue 458, eaat8806.

We focus on the important distinction between confidence intervals, typically used to express uncertainty of a sampling statistic such as the mean and, prediction and tolerance intervals, used to make statements about the next value to be drawn from the population.

Confidence intervals provide coverage of a single point—the population mean—with the assurance that the probability of non-coverage is some acceptable value (e.g. 0.05). On the other hand, prediction and tolerance intervals both give information about typical values from the population and the percentage of the population expected to be in the interval. For example, a tolerance interval can be configured to tell us what fraction of sampled values (e.g. 95%) will fall into an interval some fraction of the time (e.g. 95%).

Altman, N. & Krzywinski, M. (2018) Points of significance: Predicting with confidence and tolerance *Nature Methods* **15**:843–844.

Krzywinski, M. & Altman, N. (2013) Points of significance: Importance of being uncertain. Nature Methods 10:809–810.

A 4-day introductory course on genome data parsing and visualization using Circos. Prepared for the Bioinformatics and Genome Analysis course in Institut Pasteur Tunis, Tunis, Tunisia.

Data visualization should be informative and, where possible, tasty.

Stefan Reuscher from Bioscience and Biotechnology Center at Nagoya University celebrates a publication with a Circos cake.

The cake shows an overview of a de-novo assembled genome of a wild rice species *Oryza longistaminata*.

The presence of constraints in experiments, such as sample size restrictions, awkward blocking or disallowed treatment combinations may make using classical designs very difficult or impossible.

Optimal design is a powerful, general purpose alternative for high quality, statistically grounded designs under nonstandard conditions.

We discuss two types of optimal designs (D-optimal and I-optimal) and show how it can be applied to a scenario with sample size and blocking constraints.

Smucker, B., Krzywinski, M. & Altman, N. (2018) Points of significance: Optimal experimental design *Nature Methods* **15**:599–600.

Krzywinski, M., Altman, N. (2014) Points of significance: Two factor designs. Nature Methods 11:1187–1188.

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.