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# pi: beautiful

EMBO Practical Course: Bioinformatics and Genome Analysis, 5–17 June 2017.

# visualization + design

The 2017 Pi Day art imagines the digits of Pi as a star catalogue with constellations of extinct animals and plants. The work is featured in the article Pi in the Sky at the Scientific American SA Visual blog.

# $\pi$ Day 2015 Art Posters

2017 $\pi$ day
2016 $\pi$ approximation day
2016 $\pi$ day
2015 $\pi$ day
2014 $\pi$ approx day
2014 $\pi$ day
2013 $\pi$ day
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.

All art posters are available for purchase.
I take custom requests.

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 $\pi$.

We begin with a square and progressively divide it. At each stage, the digit in $pi$ is used to determine how many lines are used in the division. The thickness of the lines used for the divisions can be attenuated for higher levels to give the treemap some texture.

Representing a number using a tree map. Each digit of the number is used to successively divide a shape, such as a square. (zoom)

This method of encoding data is known as treemapping. Typically, it is used to encode hierarchical information, such as hard disk spac usage, where the divisions correspond to the total size of files within directories.

At each level of the tree map, more digits are encoded. Shown here are tree maps for $pi$ for the first 6 levels of division. (zoom)

This kind of treemap can be made from any number. Below I show 6 level maps for $pi$, $phi$ (Golden ratio) and $e$ (base of natural logarithm).

At each level of the tree map, more digits are encoded. Shown here are tree maps for $pi$ for the first 6 levels of division. (zoom)

The number of digits per level, $n_i$ and total digits, $N_i$ in the tree map for $pi$, $phi$ and $e$ is shown below for levels $i = 1 .. 6$.

$PI PHI e i n_i N_i n_i N_i n_i N_i 1 1 1 1 1 1 1 2 4 5 2 3 3 4 3 15 20 9 12 19 23 4 98 118 59 71 96 119 5 548 666 330 401 574 693 6 2962 3628 1857 2258 3162 3855 7 16616 20244 10041 12299 17541 21396 8 91225 111469 9 500861 612330$

## Dividing the map

In all the treemaps above, the divisions were made uniformly for each rectangle. With uniform division, the lines that divide a shape are evenly spaced. With randomized division, the placement of lines is randomized, while still ensuring that lines do not coincide.

A multiplier, such as $phi$ (Golden Ratio), can be used to control the division. In this case, the first division is made at 1/$phi$ (0.62/0.38 split) and the remaining rectangle (0.38) is further divided at $/$phi$(0.24/0.14 split). The divisions of each shape can be influenced by another number and the level at which the division is performed. (zoom) Using a non-uniform multipler is one way to embed another number in the art. When a multiplier like$phi$is used, divisions at the top levels create very large rectangles. To attenuate this, the effect of the multiplier can be weighted by the level. Regardless of what multiplier is used, the first level is always uniformly divided. Division at subsequent levels incorporates more of the multiplier effect. The orientation of the division can be uniform (same for a layer and alternating across layers), alternating (alternating across and within a layer) or random. This modification has an effect only if the divisions are not uniform. The divisions of each shape can be influenced by another number and the level at which the division is performed. (zoom) ## Adjusting line thickness To emphasize the layers, a different line thickness can be used. When lines are drawn progressively thinner with each layer, detail is controlled and the map has more texture. When all lines have the same thickness, it is harder to distinguish levels. The divisions of each shape can be influenced by another number and the level at which the division is performed. (zoom) You could see this as a challenge! Below I show the treemaps for$pi$,$phi$and$e$with and without stroke modulation. The divisions of each shape can be influenced by another number and the level at which the division is performed. (zoom) When displayed at a low resolution (the image below is 620 pixels across), shapes at higher levels appear darker because the distance between the lines within is close to (or smaller) than a pixel. By matching the line thickness to the image resolution, you can control how dark the smallest divisions appear. The divisions of each shape can be influenced by another number and the level at which the division is performed. (zoom) ## Adding color Adding color can make things better, or worse. Dropping color randomly, without respect for the level structure of the treemap, creates a mess. We can rescue things by increasing the probability that a given rectangle will be made transparent—this will allow the color of the rectangle below to show through. Additionally, by drawing the layers in increasing order, smaller rectangles are drawn on top of bigger ones, giving a sense of recursive subdivision. The divisions of each shape can be influenced by another number and the level at which the division is performed. (zoom) Because the color is assigned randomly, various instances of the treemap can be made. The maps below have the same proportion of colors and transparency (same as the first image in second row in the figure above) and vary only by the random seed to pick colors. Different instances of 5 level$pi$treemaps. The proportion of transparent, white, yellow, red and blue shapes is 20:1:1:1:1. (zoom) ## Coloring using adjacency graph The color assignments above were random. For each shape the probability of choosing a given color (transparent, white, yellow, red, blue) was the same. Color choice for a shape can also be influenced by the color of neighbouring shapes. To do this, we need to create a graph that captures the adjacency relationship between all the shapes at each level. Below I show the first 4 levels of the$pi$treemap and their adjacency graphs. In each graph, the node corresponds to a shape and an edge between nodes indicates that the shapes share a part of their edge. Shapes that touch only at a corner are not considered adjacent. Different instances of 5 level$pi$treemaps. The proportion of transparent, white, yellow, red and blue shapes is 20:1:1:1:1. (zoom) One way in which the graphs can be used is to attempt to color each layer using at most 4 colors. The 4 color theorem tells us that only 4 unique colors are required to color maps such as these in a way that no two neighbouring shapes have the same color. It turns out that the full algorithm of coloring a map with only 4 colors is complicated, but reasonably simple options exist.. For the maps here, I used the DSATUR (maximum degree of saturation) approach. Different instances of 5 level$pi$treemaps. The proportion of transparent, white, yellow, red and blue shapes is 20:1:1:1:1. (zoom) The DSATUR algorithm works well, but does not guarantee a 4-color solution. It performs no backtracking. If you look carefully, one of the rectangles in the 4th layer (top right quadrant in the graph) required a 5th color (shown black). VIEW ALL # news + thoughts # What's wrong with pie charts? Thu 25-05-2017 In this redesign of a pie chart figure from a Nature Medicine article [1], I look at how to organize and present a large number of categories. I first discuss some of the benefits of a pie chart—there are few and specific—and its shortcomings—there are few but fundamental. I then walk through the redesign process by showing how the tumor categories can be shown more clearly if they are first aggregated into a small number groups. (bottom left) Figure 2b from Zehir et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. (2017) Nature Medicine doi:10.1038/nm.4333 # Tabular Data Tue 11-04-2017 Tabulating the number of objects in categories of interest dates back to the earliest records of commerce and population censuses. After 30 columns, this is our first one without a single figure. Sometimes a table is all you need. In this column, we discuss nominal categorical data, in which data points are assigned to categories in which there is no implied order. We introduce one-way and two-way tables and the$\chi^2$and Fisher's exact tests. Altman, N. & Krzywinski, M. (2017) Points of Significance: Tabular data. Nature Methods 14:329–330. # Happy 2017$\pi$Day—Star Charts, Creatures Once Living and a Poem Tue 14-03-2017 on a brim of echo, capsized chamber drawn into our constellation, and cooling. —Paolo Marcazzan Celebrate$\pi$Day (March 14th) with star chart of the digits. The charts draw 40,000 stars generated from the first 12 million digits. 12,000,000 digits of$\pi$interpreted as a star catalogue. (details) The 80 constellations are extinct animals and plants. Here you'll find old friends and new stories. Read about how Desmodus is always trying to escape or how Megalodon terrorizes the poor Tecopa! Most constellations have a story. Find friends and stories among the 80 constellations of extinct animals and plants. Oh look, a Dodo guardings his eggs! (details) This year I collaborate with Paolo Marcazzan, a Canadian poet, who contributes a poem, Of Black Body, about space and things we might find and lose there. Check out art from previous years: 2013$\pi$Day and 2014$\pi$Day, 2015$\pi$Day and and 2016$\pi$Day. # Data in New Dimensions: convergence of art, genomics and bioinformatics Tue 07-03-2017 Art is science in love. — E.F. Weisslitz A behind-the-scenes look at the making of our stereoscopic images which were at display at the AGBT 2017 Conference in February. The art is a creative collaboration with Becton Dickinson and The Linus Group. Its creation began with the concept of differences and my writeup of the creative and design process focuses on storytelling and how concept of differences is incorporated into the art. Oh, and this might be a good time to pick up some red-blue 3D glasses. A stereoscopic image and its interpretive panel of single-cell transcriptomes of blood cells: diseased versus healthy control. # Interpreting P values Thu 02-03-2017 A P value measures a sample’s compatibility with a hypothesis, not the truth of the hypothesis. This month we continue our discussion about$P$values and focus on the fact that$P$value is a probability statement about the observed sample in the context of a hypothesis, not about the hypothesis being tested. Nature Methods Points of Significance column: Interpreting P values. (read) Given that we are always interested in making inferences about hypotheses, we discuss how$P$values can be used to do this by way of the Benjamin-Berger bound,$\bar{B}$on the Bayes factor,$B$. Heuristics such as these are valuable in helping to interpret$P$values, though we stress that$P` values vary from sample to sample and hence many sources of evidence need to be examined before drawing scientific conclusions.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Interpreting P values. Nature Methods 14:213–214.

Krzywinski, M. & Altman, N. (2017) Points of significance: P values and the search for significance. Nature Methods 14:3–4.

Krzywinski, M. & Altman, N. (2013) Points of significance: Significance, P values and t–tests. Nature Methods 10:1041–1042.

# Snellen Charts—Typography to Really Look at

Sat 18-02-2017

Another collection of typographical posters. These ones really ask you to look.

Snellen charts designed using physical constants, Braille and elemental abundances in the universe and human body.

The charts show a variety of interesting symbols and operators found in science and math. The design is in the style of a Snellen chart and typset with the Rockwell font.