resources
presentations
Let me tell you about something.
lunch break
Distractions and amusements, with a sandwich and coffee.
visualization + design
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
Books
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I have a collection of unpublished Circos posters and thought these might be a good starting point.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.
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.
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.
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.
final image elements
final image
news + thoughts
Mind your p's and q's
In the April Points of Significance Nature Methods column, we continue our and consider what happens when we run a large number of tests.
Observing statistically rare test outcomes is expected if we run enough tests. These are statistically, not biologically, significant. For example, if we run N tests, the smallest P value that we have a 50% chance of observing is 1–exp(–ln2/N). For N = 10k this P value is Pk=10–kln2 (e.g. for 104=10,000 tests, P4=6.9×10–5).
We discuss common correction schemes such as Bonferroni, Holm, Benjamini & Hochberg and Storey's q and show how they impact the false positive rate (FPR), false discovery rate (FDR) and power of a batch of tests.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Comparing Samples — Part II — Multiple Testing Nature Methods 11:215-216. Krzywinski, M. & Altman, N. (2014) Points of Significance: Comparing Samples — Part I — t-tests Nature Methods 11:215-216. Krzywinski, M. & Altman, N. (2013) Points of Significance: Significance, P values and t-tests Nature Methods 10:1041-1042.
Happy Pi Day— go to planet π
Celebrate Pi Day (March 14th) with the art of folding numbers. This year I take the number up to the Feynman Point and apply a protein folding algorithm to render it as a path.
For those of you who liked the minimalist and colorful digit grid, I've expanded on the concept to show stacked ring plots of frequency distributions.
And if spirals are your thing...
Have data, will compare
In the March Points of Significance Nature Methods column, we continue our discussion of t-tests from November (Significance, P values and t-tests).
We look at what happens how uncertainty of two variables combines and how this impacts the increased uncertainty when two samples are compared and highlight the differences between the two-sample and paired t-tests.
When performing any statistical test, it's important to understand and satisfy its requirements. The t-test is very robust with respect to some of its assumptions, but not others. We explore which.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Comparing Samples — Part I Nature Methods 11:215-216.
Krzywinski, M. & Altman, N. (2013) Points of Significance: Significance, P values and t-tests Nature Methods 10:1041-1042.
Circos at British Library Beautiful Science Exhibit
Beautiful Science explores how our understanding of ourselves and our planet has evolved alongside our ability to represent, graph and map the mass data of the time. The exhibit runs 20 February — 26 May 2014 and is free to the public. There is a good Nature blog writeup about it, a piece in The Guardian, and a great video that explains the the exhibit narrated by Johanna Kieniewicz, the curator.
I am privileged to contribute an information graphic to the exhibit in the Tree of Life section. The piece shows how sequence similarity varies across species as a function of evolutionary distance. The installation is a set of 6 30x30 cm backlit panels. They look terrific.
Think outside the bar—box plots
Quick, name three chart types. Line, bar and scatter come to mind. Perhaps you said pie too—tsk tsk. Nobody ever thinks of the box plot.
Box plots reveal details about data without overloading a figure with a full frequency distribution histogram. They're easy to compare and now easy to make with BoxPlotR (try it). In our fifth Points of Significance column, we take a break from the theory to explain this plot type and—I hope— convince you that they're worth thinking about.
The February issue of Nature Methods kicks the bar chart two more times: Dan Evanko's Kick the Bar Chart Habit editorial and a Points of View: Bar charts and box plots column by Mark Streit and Nils Gehlenborg.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Visualizing samples with box plots Nature Methods 11:119-120.