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Twenty — minutes — maybe — more.Naomichoose four wordsmore quotes

circles: exciting



DNA on 10th — street art, wayfinding and font


visualization + design

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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)

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
EMBO Journal, May 2009, 28(9). Cover design by Martin Krzywinski. (EMBO)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Genome Research, April 2008, 18(4). Cover design by Ryan Morin (Genome Research)

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

Books

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

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An old Circos poster. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Refining color palettes. (zoom)

final image elements

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

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

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Masks showing the locations of smaller vignettes. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An 8 x 8 tableviewer image with outlined ribbons. (zoom)

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Thoreau quote: Nature and human life are as various as our several constitutions. Who shall say what prospect life offers to another? (zoom)

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Background and midground elements. (zoom)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Background and foreground elements. (zoom)

final image

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Final image with all the layers. (Trends in Genetics October 2012, 28 (10)) (zoom)
VIEW ALL

news + thoughts

Quantile regression

Sat 01-06-2019
Quantile regression robustly estimates the typical and extreme values of a response.

Quantile regression explores the effect of one or more predictors on quantiles of the response. It can answer questions such as "What is the weight of 90% of individuals of a given height?"

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Quantile regression. (read)

Unlike in traditional mean regression methods, no assumptions about the distribution of the response are required, which makes it practical, robust and amenable to skewed distributions.

Quantile regression is also very useful when extremes are interesting or when the response variance varies with the predictors.

Das, K., Krzywinski, M. & Altman, N. (2019) Points of significance: Quantile regression. Nature Methods 16:451–452.

Background reading

Altman, N. & Krzywinski, M. (2015) Points of significance: Simple linear regression. Nature Methods 12:999–1000.

Analyzing outliers: Robust methods to the rescue

Sat 30-03-2019
Robust regression generates more reliable estimates by detecting and downweighting outliers.

Outliers can degrade the fit of linear regression models when the estimation is performed using the ordinary least squares. The impact of outliers can be mitigated with methods that provide robust inference and greater reliability in the presence of anomalous values.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Analyzing outliers: Robust methods to the rescue. (read)

We discuss MM-estimation and show how it can be used to keep your fitting sane and reliable.

Greco, L., Luta, G., Krzywinski, M. & Altman, N. (2019) Points of significance: Analyzing outliers: Robust methods to the rescue. Nature Methods 16:275–276.

Background reading

Altman, N. & Krzywinski, M. (2016) Points of significance: Analyzing outliers: Influential or nuisance. Nature Methods 13:281–282.

Two-level factorial experiments

Fri 22-03-2019
To find which experimental factors have an effect, simultaneously examine the difference between the high and low levels of each.

Two-level factorial experiments, in which all combinations of multiple factor levels are used, efficiently estimate factor effects and detect interactions—desirable statistical qualities that can provide deep insight into a system.

They offer two benefits over the widely used one-factor-at-a-time (OFAT) experiments: efficiency and ability to detect interactions.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Two-level factorial experiments. (read)

Since the number of factor combinations can quickly increase, one approach is to model only some of the factorial effects using empirically-validated assumptions of effect sparsity and effect hierarchy. Effect sparsity tells us that in factorial experiments most of the factorial terms are likely to be unimportant. Effect hierarchy tells us that low-order terms (e.g. main effects) tend to be larger than higher-order terms (e.g. two-factor or three-factor interactions).

Smucker, B., Krzywinski, M. & Altman, N. (2019) Points of significance: Two-level factorial experiments Nature Methods 16:211–212.

Background reading

Krzywinski, M. & Altman, N. (2014) Points of significance: Designing comparative experiments.. Nature Methods 11:597–598.

Happy 2019 `\pi` Day—
Digits, internationally

Tue 12-03-2019

Celebrate `\pi` Day (March 14th) and set out on an exploration explore accents unknown (to you)!

This year is purely typographical, with something for everyone. Hundreds of digits and hundreds of languages.

A special kids' edition merges math with color and fat fonts.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
116 digits in 64 languages. (details)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
223 digits in 102 languages. (details)

Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day and 2018 `\pi` Day.

Tree of Emotional Life

Sun 17-02-2019

One moment you're :) and the next you're :-.

Make sense of it all with my Tree of Emotional life—a hierarchical account of how we feel.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A section of the Tree of Emotional Life.