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lunch break
Distractions and amusements, with a sandwich and coffee.
visualization + design
`pi` Day 2013 Art Posters
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.
2013 was the first year in which I made `\pi` day art. It was a year of dots and love.
René Hansen has created an interactive version of this year's posters! Why not go to the Feynman point directly!
shimmering dots
The posters explore the relationship between adjacent digits in `\pi`, which are encoded by color using the scheme shown above. The design appears to shimmer due to the luminance effect. In some versions of the poster, adjacent identical (or similar) digits are connected by lines.
The recipe for each poster is included in its figure legend. It gives the color of the `i`th outer and inner circles. `\pi_i` is used to represent the `i`th digit of `\pi`. For example, the recipe
`\pi_i` / `\pi_{i+1}`
corresponds to the case where outer circle color encodes the `i`th digit and the inner circle color encodes the next digit `i+1`th. In this scheme, inner and outer circles of adjacent positions have the same color.
The posters were generated automatically with a Perl script that generated SVG files. Post processing and layout was done in Illustrator. If you are interested in depicting your favourite number this way, let me know.
The design was inspired by the beautiful AIDS posters by Elena Miska.
love in `\pi`—you can find it here
I calculated `pi` to 13,099,586 digits and then I found love.
It's fun to look for digits or look for words in `\pi`.
Just don't get carried away. Because `\pi` is likely normal in base 10, all words and all patterns appear in it, somewhere.
I wanted to know the first time that "love" appears in `\pi`. When encoded using the scheme a=0, b=1, ..., z=25, "love" is the digit sequence 1114214.
This sequence appears first at position 13,099,586 (...892199163111142148187311392...). And, of course, infinitely many times after that.
Curiously, "hate" (0700194) appears well before love, at digit 514,717. In the first 200,000,000 digit "hate" appears 23 times, 6 times more than "love".
If you use the scheme a=1, b=2, ..., z=26, then "love" becomes 1215225. This is first seen at 6,317,696 (...610311912912152256606850141...).
news + thoughts
Find and snap to colors in an image
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.
Colors used by the New York MTA subway lines.
Take your medicine ... now
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.
Predicting with confidence and tolerance
I abhor averages. I like the individual case. —J.D. Brandeis.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.
Background reading
Krzywinski, M. & Altman, N. (2013) Points of significance: Importance of being uncertain. Nature Methods 10:809–810.
4-day Circos course
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.
Oryza longistaminata genome cake
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.
Optimal experimental design
Customize the experiment for the setting instead of adjusting the setting to fit a classical design.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.
Background reading
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.