What do the trees know.sway, sway, swaymore quotes

# circles: exciting

DNA on 10th — street art, wayfinding and font

# visualization + design

Cover image for the human genetics special issue. Trends in Genetics October 2012, 28 (10) (lowres, hires, Trends in Genetics)

# Creating the Trends in Genetics October 2012 Cover

Lately, I've been making a lot of square things round. So when Rhiannon Macrae, the Editor of Trends in Genetics, requested a Circos-like cover image for the human genetics special edition of the journal, I started drawing circles.

The image was published on the cover of Trends in Genetics human genetics special issue (Trends in Genetics October 2012, 28 (10)).

## Tools

Circos, Circos tableviewer, Illustrator CS5, and a cup (or two) of Galileo coffee from a Rancilio Epoca.

## Other Covers

Circos has appeared on covers of journals and books. Some of the images were designed by me and others were drawn from papers published in the issue.

### Journals

Cover of Blood, 2 Aug 2012, 120(5). Figure from Egan, J. B., C. X. Shi, et al. (2012). Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides. Blood 120(5): 1060-1066. (Blood)
Genomics, Aug 2012, 100(2). Figure from Katapadi, V. K., M. Nambiar, et al. (2012). Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility. Genomics 100(2): 72-80. (Genomics)
Science Translational Medicine, December 2010, 2(61). Figure from Lo, Y. M., K. C. Chan, et al. (2010). Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med 2(61): 61ra91 (Science Translational Medicine)

EMBO Journal, May 2009, 28(9). Cover design by Martin Krzywinski. (EMBO)
Nature Biotechnology, November 2009, 27(11). Figure from Cho, B. K., K. Zengler, et al. (2009). The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol 27(11): 1043-1049. (Nature Biotechnology)
Genome Research, April 2008, 18(4). Cover design by Ryan Morin (Genome Research)

American Scientist, September/October 2007. Cover design by Martin Krzywinski — how it was done. (American Scientist)

### Books

iGenetics, 3rd ed. by Peter Russell (Benjamin Cummings). Cover design by Martin Krzywinski. (iGenetics)
Building Bioinformatics Solutions with Perl, R and MySQL (Oxford University Press). Cover design by Martin Krzywinski. (Building Bioinformatics Solutions)
Designing Universal Knowledge by Gerlinde Schuller (Lars Müller Publishers) (Designing Universal Knowledge)

Chromosomes — art book of film stills, David Cronenberg. Contribution to book design by Martin Krzywinski. (Chromosomes)

## source of design

I have a collection of unpublished Circos posters and thought these might be a good starting point. Rhiannon and I narrowed the choice down to the black-and-white design that showed sequenced organisms. We also liked the complex style of a panel of hundreds of Circos images generated with the tableviewer.

An old Circos poster. (zoom)
A panel of images generated from the Circos tableviewer. (zoom)

The idea would be that the foreground would be more artistic and stylized, while the background was more technical and complex. I have thousands of images available from the tableviewer (e.g. huge 15,129 image matrix).

Rhiannon also wanted to include the quote by Henry David Thoreau, "Nature and human life are as various as our several constitutions. Who shall say what prospect life offers to another?" This reminded me of a similar but more tragic line from Shakespeare's Julius Caesar, "How many ages hence shall this our lofty scene be acted over in states unborn and accents yet unknown!"

## early comps

In the early comps we played around with the idea of using non-genomics elements in the image, such as coins. We thought that we could use the variety of color and shape of the coins to communicate the idea of genetic diversity. However, after wrestling with how to do this effectively the concept was scrapped — the idea of using coins felt both arcane and arbitrary.

First set of comps. (zoom)

I decided to go with a warm brown color scheme. It's not a color I use a lot of, which makes me think that I should try to do more with it.

Deep brown provides great contrast for saturated colors, though I had to be careful not to make the image look too kitchy with an excess of colour variation. In some of the early comps shown above, two or more different color palettes were used (e.g. grey/red/blue and false color) and this lowered to overall visual cohesion of the image.

It's always a good idea to add variety to design. After all, without any variety we'd be left with a blank page. Ok, so variety is good, but too much variety is very bad, and can make you wish for that blank page again. Think about this: one kind of variety already provides variety! A variety of variety (I run the risk of recursing myself ad infinitum) can not only compete for attention but resonate destructively (that's design-speak for "turn into visual mush").

## refining the design

Everyone liked the combination of bright colors and dark background. This is an approach I favour too, which has worked well on other covers.

Experimenting with an organic look. (zoom)

Briefly I experimented with various brush and pencil filters to give the image a more hand-drawn and organic look. Most of the illustrations I generate are very digital — blocks of solid colors and high-contrast shapes — and I thought a departure from this look could work in this case. However, like with the coins, this path didn't produce anything productive.

Refining color palettes. (zoom)

## final image elements

The background is created from a matrix of about 1,400 individual Circos images created by the user community using the tableviewer. (zoom)
The main element is a Circos image of a 15 x 15 table, also created with the tableviewer. (zoom)

A watermark made up from elements in a tableviewer image that show aggregate statistics for each row and column. (zoom)
A multi-crop zoom of the main element shown above. This version is colored for punch. (zoom)

Masks showing the locations of smaller vignettes. (zoom)
An 8 x 8 tableviewer image with outlined ribbons. (zoom)

Thoreau quote: Nature and human life are as various as our several constitutions. Who shall say what prospect life offers to another? (zoom)

Background and midground elements. (zoom)
Background and foreground elements. (zoom)

## final image

Final image with all the layers. (Trends in Genetics October 2012, 28 (10)) (zoom)
VIEW ALL

# Scientific data visualization: Aesthetic for diagrammatic clarity

Mon 13-01-2020

The scientific process works because all its output is empirically constrained.

My chapter from The Aesthetics of Scientific Data Representation, More than Pretty Pictures, in which I discuss the principles of data visualization and connect them to the concept of "quality" introduced by Robert Pirsig in Zen and the Art of Motorcycle Maintenance.

# Yearning for the Infinite — Aleph 2

Mon 18-11-2019

Discover Cantor's transfinite numbers through my music video for the Aleph 2 track of Max Cooper's Yearning for the Infinite (album page, event page).

Yearning for the Infinite, Max Cooper at the Barbican Hall, London. Track Aleph 2. Video by Martin Krzywinski. Photo by Michal Augustini. (more)

I discuss the math behind the video and the system I built to create the video.

# Hidden Markov Models

Mon 18-11-2019

Everything we see hides another thing, we always want to see what is hidden by what we see.
—Rene Magritte

A Hidden Markov Model extends a Markov chain to have hidden states. Hidden states are used to model aspects of the system that cannot be directly observed and themselves form a Markov chain and each state may emit one or more observed values.

Hidden states in HMMs do not have to have meaning—they can be used to account for measurement errors, compress multi-modal observational data, or to detect unobservable events.

Nature Methods Points of Significance column: Hidden Markov Models. (read)

In this column, we extend the cell growth model from our Markov Chain column to include two hidden states: normal and sedentary.

We show how to calculate forward probabilities that can predict the most likely path through the HMM given an observed sequence.

Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of significance: Hidden Markov Models. Nature Methods 16:795–796.

Altman, N. & Krzywinski, M. (2019) Points of significance: Markov Chains. Nature Methods 16:663–664.

# Hola Mundo Cover

Sat 21-09-2019

My cover design for Hola Mundo by Hannah Fry. Published by Blackie Books.

Hola Mundo by Hannah Fry. Cover design is based on my 2013 $\pi$ day art. (read)

Curious how the design was created? Read the full details.

# Markov Chains

Tue 30-07-2019

You can look back there to explain things,
but the explanation disappears.
You'll never find it there.
Things are not explained by the past.
They're explained by what happens now.
—Alan Watts

A Markov chain is a probabilistic model that is used to model how a system changes over time as a series of transitions between states. Each transition is assigned a probability that defines the chance of the system changing from one state to another.

Nature Methods Points of Significance column: Markov Chains. (read)

Together with the states, these transitions probabilities define a stochastic model with the Markov property: transition probabilities only depend on the current state—the future is independent of the past if the present is known.

Once the transition probabilities are defined in matrix form, it is easy to predict the distribution of future states of the system. We cover concepts of aperiodicity, irreducibility, limiting and stationary distributions and absorption.

This column is the first part of a series and pairs particularly well with Alan Watts and Blond:ish.

Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of significance: Markov Chains. Nature Methods 16:663–664.