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data visualization + art
Art of the Personalized Oncogenomics Program
Nature uses only the longest threads to weave her patterns, so that each small piece of her fabric reveals the organization of the entire tapestry.
— Richard Feynman
cancer is the difference of differences
As individuals, we all have slightly different genomes. If you compare the genomes of two people, you will find about 3 million base pair differences, which is about 0.1% of the genome.
This variation exists not only within the population but potentially also, to a lesser extent, among our cells, which number around 40 trillion. That's roughly 10,000 cells for each base in your 3 billion base genome. And each has a role to play.
| POG cases, by tissue type | |||
|---|---|---|---|
| n | % | ||
| Gastrointestinal ● | 141 | 25 | |
| Breast ● | 138 | 25 | |
| Thoracic ● | 57 | 10 | |
| Gynecologic ● | 45 | 8.3 | |
| Soft tissue ● | 44 | 8.1 | |
| Skin ● | 11 | 2.0 | |
| Urologic ● | 8 | 1.5 | |
| Hematologic ● | 7 | 1.3 | |
| Head and neck ● | 6 | 1.1 | |
| Endocrine ● | 5 | 0.9 | |
| Central nervous system ● | 5 | 0.9 | |
| Other ● | 78 | 14 | |
| ALL | 545 | ||
One consequence of this complexity and variation is that changes in the genome (through mutation or other processes) can have very different effects, depending on both the change and the genome. Cancer is a phenomena in which cells' ability to organize themselves as they divide is altered due to changes in the genome. It is an incredibly complex biological phenomenon—considering all the genomes in the population and all the possible changes that may arise, there is truly an inexhaustible number of ways in which the genome can break.
classifying cancer
Cancers are classified according to their site of origin, such as lung, breast, liver, or colon. This is a coarse grouping—within each group there are many subtypes with differences in response to treatment and overall behaviour.
diversities among clinical cases
The design of the POG art highlights the diversity and similarity among cases. The diversity is what makes the study of cancer difficult and the similarities are what makes inference possible.
Each case is represented by three concentric rings. The width of each ring represents the extent to which the case is similar (as measured by correlation) to cancers of the type encoded by the color of the ring (see Methods).
remixes
In additional to the posters, I've created remixes for your desktop at 4k resolution.
Ride to Conquer Cancer — Data-powered, Human-driven
This year, the cyclists in the Ride to Conquer Cancer will not only have the chance to raise money for research (as they've always done) but also do so while wearing data (as they've never done before).
You can purchase your own data-powered and human-driven cycling jersey.
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news + thoughts
Music for the Moon: Flunk's 'Down Here / Moon Above'
The Sanctuary Project is a Lunar vault of science and art. It includes two fully sequenced human genomes, sequenced and assembled by us at Canada's Michael Smith Genome Sciences Centre.
The first disc includes a song composed by Flunk for the (eventual) trip to the Moon.
But how do you send sound to space? I describe the inspiration, process and art behind the work.
Happy 2021 `\pi` Day—
A forest of digits
Celebrate `\pi` Day (March 14th) and finally see the digits through the forest.
This year is full of botanical whimsy. A Lindenmayer system forest – deterministic but always changing. Feel free to stop and pick the flowers from the ground.
And things can get crazy in the forest.
Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day, 2018 `\pi` Day and 2019 `\pi` Day.
Testing for rare conditions
All that glitters is not gold. —W. Shakespeare
The sensitivity and specificity of a test do not necessarily correspond to its error rate. This becomes critically important when testing for a rare condition — a test with 99% sensitivity and specificity has an even chance of being wrong when the condition prevalence is 1%.
We discuss the positive predictive value (PPV) and how practices such as screen can increase it.
Altman, N. & Krzywinski, M. (2021) Points of significance: Testing for rare conditions. Nature Methods 18:224–225.
Standardization fallacy
We demand rigidly defined areas of doubt and uncertainty! —D. Adams
A popular notion about experiments is that it's good to keep variability in subjects low to limit the influence of confounding factors. This is called standardization.
Unfortunately, although standardization increases power, it can induce unrealistically low variability and lead to results that do not generalize to the population of interest. And, in fact, may be irreproducible.
Not paying attention to these details and thinking (or hoping) that standardization is always good is the "standardization fallacy". In this column, we look at how standardization can be balanced with heterogenization to avoid this thorny issue.
Voelkl, B., Würbel, H., Krzywinski, M. & Altman, N. (2021) Points of significance: Standardization fallacy. Nature Methods 18:5–6.
Graphical Abstract Design Guidelines
Clear, concise, legible and compelling.
Making a scientific graphical abstract? Refer to my practical design guidelines and redesign examples to improve organization, design and clarity of your graphical abstracts.
"This data might give you a migrane"
An in-depth look at my process of reacting to a bad figure — how I design a poster and tell data stories.
