Choosing Plotting Symbols

In this months column, Bang and I consider how to choose effective plotting symbols in the Points of View column Plotting Symbols.

▲ Nature Methods Points of View column: Plotting Symbols. (download, more about Points of View)

Choose symbols that overlap without ambiguity and communicate relationships in data.

Figure Design and Writing — Two Goals, One Process

This month I look at how creating effective figures is similar to the process of writing well in the Points of View column Elements of Visual Style.

▲ Nature Methods Points of View column: Elements of Visual Style. (download, more about Points of View)

Using Strunk's Elements of Style as an example of writing guidelines, I look how these can be translated to creating figures.

VIZBI 2013 Keynote—Visual Design Principles

When we create figures, we must communicate and design. In my talk I discuss some of the rules that turn graphical improvisation into a structured and reproducible process.

▲ Try to focus on a spot in these posters that celebrate Pi day. (download talk)

The fractal tree was created with OneZoom, which received the best poster award at the conference.

Happy Pi Day— 3.14

Celebrate Pi Day (March 14th) with a funky modern posters. Transcend, don't repeat, yourself and watch the dots shimmer.

▲ Try to focus on a spot in these posters that celebrate Pi day. (download posters)

The posters were inspired by the beautiful AIDS posters by Elena Miska.

For the Love of Type

I am always drawn to type and periodically I must do something about it.

If you were a type, what type would you be? Me, Gill Sans on weekdays and Perpetua on the weekend.

▲ Finding intrigue and consensus within and among letters. (typography posters)

Return of Nature Methods Points of View

I take over from Bang Wong as primary contributor to the Points of View column, a monthly advice and opinion piece about data visualization and information and figure design in molecular biology.

▲ Nature Methods Points of View column returns. (read more, Nature Methods blog)

Nature Encode Explorer

▲ Nature uses Circos motif on cover and interactive ENCODE data explorer. (read more)

Nature's special issue dedicated to the Encode Project uses the Circos motif on its cover as well as the interactive Encode Explorer, which is available as an app at iTunes.

Bloomberg Businessweek Design Conference

Together with Alberto Cairo, and then in conversation with Sam Grobart, I presented about science and design at Bloomberg's Businessweek Design Conference in San Francisco.

▲ Science loves design, but doesn't always know it. (download talk)

ICDM2012 Keynote — Needles in Stacks of Needles

My ICDM2012 keynote on genomics and data mining: Needles in Stacks of Needles.

▲ Computers compute but humans are ultimately responsible for identifying what is relevant and useful. (abstract, download talk, ICDM2012)

Genome Research cover

Creating strings of genome jewelery. Read about how it was done.

▲ Cover image accompanying Spark: A navigational paradigm for genomic data exploration. Genome Research 22 (11). (details, Genome Research)

The design accompanies Cydney Nielsen's Spark manuscript, which appeared in Genome Research.

Biovis 2012 — Getting into Visualization of Large Biological Data Sets

Guidelines for data encoding and visualization in biology, presented presented at Biovis 2012 (Visweek 2012).

▲ 20 imperatives of information design. (Krzywinski et al biovis2012)

2012 Presidential Debates — a Lexical Analysis

Building on the method I used to analyze the 2008 debates, I look at the 2012 Debates between Obama and Romney, lexically speaking. Obama speaks to "folks", while Romney fearmongers with "kill" and "hurt".

▲ Analysis of word usage by parts of speech for Obama and Romney reveals insight into each candidate.

Trends in Genetics cover

Making things round, not square. Read about how it was done.

▲ Nature and human life are as various as our several constitutions. Who shall say what prospect life offers to another? —Henry David Thoreau

A Circos-based design for the cover of the human genetics special issue of Trends in Genetics (Trends in Genetics October 2012, 28 (10)).

Schloss Dagstuhl - Visualization: communicating, clearly

My talk — Visualization: communicating, clearly from the Biological Data Visualization seminar at Schloss Dagstuhl.

Science needs words

And usually, really long and funny ones.

▲ Scientists love new words, when the old ones aren't long enough.

My neologisms were picked up by James Gorman of the New York Times in an article Ome, the sound of the scientific universe expanding.

PNAS cover

Biology or astrophysics? Read about how it was done.

▲ Hint: biology.

The image was published on the cover of PNAS (PNAS 1 May 2012; 109 (18))

the art of numbers

Numerology is bogus but art based on numbers has a beautiful random quality. Oh, and none of the metaphysical baggage.

▲ Distribution of the first 3,422, 13,689 and 123,201 digits of π.

▲ Progression and transition probabilities of digits in e, φ and π.

accidental similarity number

The quantity formed by the overlap of two or more numbers.

▲ The accidental similarity number of π, φ and e.

the 4ness of pi

How much 4ness does π have?

▲ The iness of each digit of π generalizes 4ness. It measures the similarity of the digit to its neighbours.

Compare the iness of π to that of the other famous transcendental number, e, and the mysterious but attractive Golden Ratio, φ.

▲ The iness of e and φ.

ASCII Illustration—Outer Space, Sequence and Typography

I have found a way to combine my curiosity about space, fear of large sequence assemblies and love of typography in a single illustration. Inspired by typographical portraits, I wanted to automate representing an image with multiple font weights, while sampling characters from a quote or debate transcripts.

▲ Part of the Pioneer plaque rendered with the sequence of human chromosome 1, using 4 layers of sizes (17pt, 33pt, 59pt and 93pt) and 8 weights of Gotham.

Tangering Tango—Color of 2012

If you made widgets, you could be justified in campaigning a widget of the year. Business acumen suggests it should be one of your widgets. Pantone has done exactly that, naming their 17-1463 color (tangerine tango), as color of the year 2012.

▲ Tangerine Tango - Pantone's color of the year.

I prefer green—green jive.

▲ Green Jive - My own color of the year.

World's Most Expensive Photograph

I really like the world's most expensive photograph, Rhein II by Andreas Gursky. Cautious use of the word "expensive" should be practised — in this case, merely meaning that only one person saw the $4.3 million price tag. Others saw lower prices, or no price tag at all.

▲ Rhein II by Andreas Gursky. $4.3 million.

Here's my own attempt at such compositions.

▲ Near Jokulsarlon on the way to Hofn, Iceland.

Adobe Swatches for Brewer Palettes

I could not find Illustrator swatch files for this awesome color resource, so I created them myself.

▲ Brewer palettes are ideal for information design. Download Illustrator swatch files (.ase .ai).

If you're interested in color and design and don't know about Brewer palettes, see my presentation.

Global Visualization of Google Searches by Language

World-wide Google searches, categorized by one of 21 languages, are visualized with WebGL, available from Chrome Experiments. The data offers some fascinating insights such as (a) in what two places in the US are Google searches in Chinese are performed? (b) what are the most remote locations are from which Google searches were detected? (c) Why is Istanbul the 3rd top location for searches? Why is Miami in the top 10?

▲ Global visualization of google searches by language reveals English dominates (42% searches) with Spanish a distant second (14%) and German and French third (7% each).

Download geotagged data.

PSA Genomics Workshop Slides

Designing effective visualizations in the biological sciences.

▲ Neither communication nor design are purely subjective.

Circos and Hive Plots: Challenging visualization paradigms in genomics and network analysis.

▲ Neither communication nor design are purely subjective.

Tor tor & Loa Loa — 546 Organisms with Same Genus and Species

In a recent conversation, I was challenged to name as many organisms with the same genus and species as I could. Neither a biologist, and especially not a taxonomist, my responses were limited to organisms with sequenced genomes I had come across in the literature. Immediately to mind sprung Gallus gallus (chicken) and ... nothing else. Well, that was embarrassing.

I was suddently taken up by the urge to find all instances of this occurrence. Using resources at the NCBI Taxonomy Browser I downloaded the NCBI taxonomy table which contains 1,097,405 entries in the names.dmp file (not all of these are unique genus/species combinations).

To my suprise I discovered that my performance in this challenge was beyond dysmal. In fact, there are 380 genuses which contain organisms that have the same genus and species name. Most of them (317) include a single organism, but some have many. For example the genus Salamandra has 14 organisms with the species salamandra, including Salamandra salamandra, Salamandra salamandra crespoi and Salamandra salamandra morenica. The genus Regulus has 13 organisms, including Regulus regulus azoricus, Regulus regulus japonensis and Regulus regulus regulus (these are all Goldcrests).

In total, there are 546 unique entries, when organisms with a unique subspecies name are considered distinct. If subspecies is not considered, the number of organisms with the same genus as species (i.e., regardless of subspecies) is 383. Here are organisms whose genus/species name is shorter than 6 letters (82 entries).

Shortest Species/Genus Duplicates (82, 5 letters or less)

Longest Species/Genus Duplicates (5, 14 letters or more)

Coccothraustes coccothraustes

Labiostrongylus labiostrongylus

Macrobilharzia macrobilharzia

Macropostrongylus macropostrongylus

Xanthocephalus xanthocephalus

The nematode worm Macropostrongylus macropostrongylus has the honour of being the longest genus/species duplicate organism. Given this distinction, it is surprising that Pubmed returns only 2 papers that refer to it.

Dataset

Download the full list. The number next to each ENTRY field is the NCBI Taxonomy ID for the organism. In a small number of cases there are ambiguities in parsing the data file (e.g. Troglodytes cf. troglodytes PS-2, Troglodytes sp. troglodytes PS-1). I left these in.

Visual Acuity and Sequence Visualization

Visual acuity limits of the human eye restrict the resolution at which we can comfortably visualize data.

In this short guide, I explain why dividing a scale into no more than 500 divisions is a good idea.

▲ Visualizing 1.5 Mb (S. cerevisiae chrIV) in a 183 mm wide figure (size limit in Nature for double column figures) restricts scale division to 2.9 kb to ensure comfortable reading.

2011 EMBO Journal Cover Contest

For the EMBO Journal 2011 Cover Contest, I prepared two entries, one for the scientific category and one for the non-scientific category.

▲ The non-scientific entry is abstract photo of fiber optics. The scientific entry was an information graphic showing a hive panel of genomic annotations in human, mouse and dog genomes. The hive panel is based on the use of the newly introduced hive plot.

The 2011 winners have been announced. My non-scientific entry (photo of fiber optics) received honourable mention and was included in the Favourites of the Jury gallery.

New Circos Domains

Until now, Circos did not have its own domain name, having been served from the lengthy and boring http://mkweb.bcgsc.ca/circos.

Recently, I was surprised to find out that the following domains were available

• circos.ca
• genomevisualization.com
• genomevisualization.org
• genomevisualization.net

All these now point to the Circos site.

ee spammings - beautiful language of spam poetry

ee spammings are spam edited into a format reminiscent of the poetry of ee cummings. Unwanted solicitations for questionable endeavours and products suddenly turn into heady words of the new literature. Art suddenly freed from the husk of spam.

Literature 2.0 — from unlikely origins.

Here's one example that emphasizes that today is ok.

i got 
to touch you

i like us 
and know the more. 

believe
       recontact 
me

today ok!
but matters

waiting for
           happy

I now have over 20 ee spammings — enjoy them all.

Neologisms - New Words, Much Needed

What do inconversible, mystific, postpetizer, prenopsis and suscitate have in common?

They are words that don't exist, but should. Learn new words.

Hive Plot Ads

Download large ads: 00 01 02 03 04

World's Most Popular Questions
Today's Zeitgeist

What are the world's top questions?

Using Google's autocomplete feature, I have tabulated the world's most popular questions. By combining a interrogative term, such as what, who or why, with a term from a related set, such as do I, can I, and can't I, it is possible to sample the space of questions and obtain the most popular for a given start word combination.

I have tabulated the most popular questions by category.

Science

What kind of questions about science are people asking? From the Career & Education section,

• Can biology lead to new theorems?
• Can physics explain miracles?
• Can math be fun?
• Can science and religion coexist?
• Can history repeat itself?
• Can psychology be morally neutral?

Curios

What are the strangest questions? I'll let you explore, but these have me wondering:

• Has the world gone mad or is it me?
• Why can't I hold all these limes?
• What happens if I make a formal commitment to Satan?
• Why can't I sell my kidney?
• Who is the most powerful Jedi?
• Can Jesus microwave a burrito?
• Where is the hardest part of your head?

Circos Table Browser

Circos can be used to visualize tabular data, such as spreadsheets.

1,000s of tables have already been visualized. Has yours?

648 Ratios

Hive plots are excellent at visualizing ratios. They're not just an anti-hairball network visualization agent.

Below are visualized 3 x 8 x 27 = 648 (axes, ribbons, plots) ratios visualized.

The image above compares the relative ratios of region annotations in human, mouse and dog genomes.

Cáceres Creativa - Model and Strategy for Urban Innovation

Cáceres is a small city of 100,000 inhabitants in western Spain, where the city government is promoting Cáceres Creativa, a project to build citizens collaboratively sustainable future for the city based on activating the creative capacity of the population.

The project has been published as a book (excerpt), which provides a basis for working with city residents and businesses in this collaborative design.

Circos proved useful in showing the complex relationships that are established in such an environment is a city which combines flows of energy and resources, physical items and intellectual concepts. The online Circos tableviewer was used to generate the images.

Storage Cluster

Taking photos of inanimate objects is rewarding. Your subject doesn't complain, nor move, and a coffee break fits naturally into the workflow at any time. In this case, the inanimate object is over 3 Pb (3,000 Tb) of storage composed of a variety of Netapp appliances.

Using three gelled Hensel Integras (500 Ws monoheads — here I'm using only the modelling light for illumination along with red, blue and green filters) (lighting details), I spent some time getting to know the components up close.

See more photos.

All photos by Martin Krzywinski (Lumondo Photography).

Genesis 1.0

Our new compute cluster has been released to the user community.

This cluster consists of 420 compute nodes each with 12 cores and 48GB RAM, totaling 5,040 cores and 20TB RAM. Each node has 160GB local /tmp space and all nodes are tied together over an Inifiniband 40Gbs network.

The nodes all have access to a dedicated storage system over the Infiniband Network running GPFS with a total 700TB of usable scratch space. The filesystem is served by 8 IBM x3850 servers. All nodes are running CentOS5.4 and are using open source Grid Engine 6.2u5 as their scheduler.

Lighting details and more photos.

All photos by Martin Krzywinski (Lumondo Photography).

1 First the server room was expanded 2 It was empty and without racks, and the lights were dim. Sysadmins scurried about and unpacked equipment 3 The circuit was closed and there were electrons 4 IT staff were pleased and accounts were handed out to users 5 Who had work they called "important" 6 But which the IT staff merely called "jobs".

Photo

Periodically, I take my camera, point it at things. Here, I'll share a favourite from my creations.

This image — I will keep the subject a mystery — gives me the same feeling as some of the Hubble images. For this shot, I didn't need to reach orbit.

Other images in this series are available on flickr.

I also like geometry and lines. This shot is a tense composition of the Hancock Building at Copley Square in Boston.

and an assortment of baggage carts at St Pancreas station (London) which catches the eye.

I like to collect time in a photo, be it uniformly as in this diptych of street and traffic lights from a moving car

or blended, as in this skyline of Vancouver showing the flow of time from 5.30pm to 9.30pm.

WIZARD — Longest English Reverse Complement

DNA is composed of two strands, which are complementary. Given a sequence, its reverse complement is created by swapping A/T and G/C and writing the remapped sequence backwards (e.g. ATGC is first remapped to TACG and then reversed to GCAT).

Consider the corresponding concept applied to English words (or any language, for that matter). First, construct the complementarity map, which assigns to the nth letter of the alphabet the N-n letter, given an alphabet of N letters.

abcdefghijklmnopqrstuvwxyz
||||||||||||||||||||||||||
zyxwvutsrqponmlkjihgfedcba

For example, a becomes z, b becomes y, and so on. To create a reverse complement of a word, apply this mapping and then reverse the new word (e.g. 'dog' is remapped to 'wlt' and then reversed to obtain 'tlw').

So far, that's not very exciting.

But consider the question: What is the longest English word that is a palindrome under this set of rules (reverse complementarity). In other words, it's the same forward and backward after complementing the letters. Clearly "dog" is not such a palindrome since its reverse complement is "tlw".

The answer? wizard and hovels.

wizard
||||||
draziw -> 'wizard' backwards

It's an amazingly fitting answer, since a wizard is someone with special powers.

A few interesting 4-letter words that are their own reverse complement palindromes are bevy, grit, trig and wold. Common surnames that match are Ghrist, Elizarov and Prawdzik. Female first name Zola and male first name Iver are also reverse complement palindromes, as are trolig (Norwegian for 'likely', as well as an IKEA curtain product) and aviverez (2nd person plural future of 'aviver', French for 'brighten').

I've scanend a very large word list (4,138,000 unique English and foreign words) and identified 108 reverse complement palindromes. If you find a new entry longer than 6 letters, let me know.

Typefaces that are worth it

Finding just the right font is hard work. There are so many to choose from. Or are there?

If the type face is not on this list, don't use it (except Bodoni &mdash I hate Bodoni &mdash don't use it). If you need a shorter list, consult the quintissential 15 serif and 15 sans-serif fonts.

You'll notice a rotating image of type faces at the top of this page. Here's the full list.

I love Gotham and have used it in visualization projects. It's more rational than Helvetica and still enjoys a freshness that has evapourated from Helvetica after near-ubiquitous use. Don't get me wrong, there is still not enough Helvetica in the world, but more Gotham would be nice.

Paper

Anyone who has met me, quickly learns that I have a personal and antagonistic relationship with Comic Sans, the type face that shouldn't have been.

In a recent article in the journal Cognition, Fortune favours the bold (and the italicized): Effects of disfluence on educational outcomes, Diemand-Yauman et al. suggest that rendering educational materials in a hard-to-read font, and thereby recruiting the effects of the disfluency ("the subjective experience of difficulty associated with cognitive operations"), improves retention of material.

Regardless whether the effect is real, there must be better ways to improve education than through bad design.

Kittens

Surely you like kittens. So don't hurt your audience.

Side Interest Spawns Brazilian Fashion Line

In a cosmically improbable confluence of multidisciplinary pursuits, my work on keyboard layouts, which as one of its fruits has produced the TNWMLC keyboard layout — the most difficult for English typing — has been incorporated into the eponymously named Brazilian fashion line by Julia Valle.

Spatter of Network Communities

Looking into network data sets for the linear layout project, I found pretty hairballs which make a juicy spatter pattern.