resources
presentations
Let me tell you about something.
lunch break
Distractions and amusements, with a sandwich and coffee.
design + visualization
VIZBI 2013 Keynote
Visual Design Principles—Communicating Effectively
This talk happened on Thursday, Mar 21st 2013 at VIZBI 2013 at the Broad Institute in Boston.
How often people speak of art and science as though they were two entirely different things, with no interconnection. An artist is emotional, they think, and uses only his intuition; he sees all at once and has no need of reason. A scientist is cold, they think, and uses only his reason; he argues carefully step by step, and needs no imagination. That is all wrong. The true artist is quite rational as well as imaginative and knows what he is doing; if he does not, his art suffers. The true scientist is quite imaginative as well as rational, and sometimes leaps to solutions where reason can follow only slowly; if he does not, his science suffers. —Isaac Asimov (The Roving Mind)
For more visualization and design resources, see my VIZBI 2012 tutorials, Nature Methods Points of View column, and rant about colors.
presentation video
The video will be posted at vizbi.org.
presentation slides
Slides are available as PDF and keynote (zipped).
A poet is, after all, a sort of scientist, but engaged in a qualitative science in which nothing is measurable. He lives with data that cannot be numbered, and his experiments can be done only once. The information in a poem is, by definition, not reproducible. He becomes an equivalent of scientist, in the act of examining and sorting the things popping in [to his head], finding the marks of remote similarity, points of distant relationship, tiny irregularities that indicate that this one is really the same as that one over there only more important. Gauging the fit, he can meticulously place pieces of the universe together, in geometric configurations that are as beautiful and balanced as crystals. —Lewis Thomas (The Medusa and the Snail: More Notes of a Biology Watcher)
breakout session—making good figures
small, medium and big data visualization
If you're asking how to visualize big data, first make sure you're doing a good job on small and medium data. Each scale requires good design.
to tell many stories
Also consider that there is a very large number of combinations of data sets, hypotheses and possible patterns. Because of this, you cannot expect to use one way to tell many stories. There is no Holy Grail of big data visualization. But there are many good questions to ask and practices to follow that make up a process which can help you get there.
news + thoughts
Before and After—Designing Tiny Figures for Nature Methods
I've posted a writeup about the design and redesign process behind the figures in our Nature Methods Points of Significance column.
I have selected several figures from our past columns and show how they evolved from their draft to published versions.
Clarity, concision and space constraints—we have only 3.4" of horizontal space— all have to be balanced for a figure to be effective.
It's nearly impossible to find case studies of scientific articles (or figures) through the editing and review process. Nobody wants to show their drafts. With this writeup I hope to add to this space and encourage others to reveal their process. Students love this. See whether you agree with my decisions!
Sources of Variation
Past columns have described experimental designs that mitigate the effect of variation: random assignment, blocking and replication.
The goal of these designs is to observe a reproducible effect that can be due only to the treatment, avoiding confounding and bias. Simultaneously, to sample enough variability to estimate how much we expect the effect to differ if the measurements are repeated with similar but not identical samples (replicates).
We need to distinguish between sources of variation that are nuisance factors in our goal to measure mean biological effects from those that are required to assess how much effects vary in the population.
Altman, N. & Krzywinski, M. (2014) Points of Significance: Two Factor Designs Nature Methods 11:5-6.
Background reading
1. Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.
2. Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of variance (ANOVA) and blocking Nature Methods 11:699-700.
3. Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.
Two Factor Designs
We've previously written about how to analyze the impact of one variable in our ANOVA column. Complex biological systems are rarely so obliging—multiple experimental factors interact and producing effects.
ANOVA is a natural way to analyze multiple factors. It can incorporate the possibility that the factors interact—the effect of one factor depends on the level of another factor. For example, the potency of a drug may depend on the subject's diet.
We can increase the power of the analysis by allowing for interaction, as well as by blocking.
Krzywinski, M., Altman, (2014) Points of Significance: Two Factor Designs Nature Methods 11:1187-1188.
Background reading
Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of variance (ANOVA) and blocking Nature Methods 11:699-700.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.
Nested Designs—Assessing Sources of Noise
Sources of noise in experiments can be mitigated and assessed by nested designs. This kind of experimental design naturally models replication, which was the topic of last month's column.
Nested designs are appropriate when we want to use the data derived from experimental subjects to make general statements about populations. In this case, the subjects are random factors in the experiment, in contrast to fixed factors, such as we've seen previously.
In ANOVA analysis, random factors provide information about the amount of noise contributed by each factor. This is different from inferences made about fixed factors, which typically deal with a change in mean. Using the F-test, we can determine whether each layer of replication (e.g. animal, tissue, cell) contributes additional variation to the overall measurement.
Krzywinski, M., Altman, N. & Blainey, P. (2014) Points of Significance: Nested designs Nature Methods 11:977-978.
Background reading
Blainey, P., Krzywinski, M. & Altman, N. (2014) Points of Significance: Replication Nature Methods 11:879-880.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Analysis of variance (ANOVA) and blocking Nature Methods 11:699-700.
Krzywinski, M. & Altman, N. (2014) Points of Significance: Designing Comparative Experiments Nature Methods 11:597-598.