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Distractions and amusements, with a sandwich and coffee.

Sun is on my face ...a beautiful day without you.
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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.

The video will be posted at vizbi.org.

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)

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.

Do not expect to use one way

to tell many stories

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.

*It is important to understand both what a classification metric expresses and what it hides.*

We examine various metrics use to assess the performance of a classifier. We show that a single metric is insufficient to capture performance—for any metric, a variety of scenarios yield the same value.

We also discuss ROC and AUC curves and how their interpretation changes based on class balance.

Altman, N. & Krzywinski, M. (2016) Points of Significance: Classifier evaluation. *Nature Methods* **13**:603-604.

Today is the day and it's hardly an approximation. In fact, `22/7` is 20% more accurate of a representation of `\pi` than `3.14`!

Time to celebrate, graphically. This year I do so with perfect packing of circles that embody the approximation.

By warping the circle by 8% along one axis, we can create a shape whose ratio of circumference to diameter, taken as twice the average radius, is 22/7.

If you prefer something more accurate, check out art from previous `\pi` days: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, and 2016 `\pi` Day.

*Regression can be used on categorical responses to estimate probabilities and to classify.*

The next column in our series on regression deals with how to classify categorical data.

We show how linear regression can be used for classification and demonstrate that it can be unreliable in the presence of outliers. Using a logistic regression, which fits a linear model to the log odds ratio, improves robustness.

Logistic regression is solved numerically and in most cases, the maximum-likelihood estimates are unique and optimal. However, when the classes are perfectly separable, the numerical approach fails because there is an infinite number of solutions.

Altman, N. & Krzywinski, M. (2016) Points of Significance: Logistic regression. *Nature Methods* **13**:541-542.

Altman, N. & Krzywinski, M. (2016) Points of Significance: Regression diagnostics? *Nature Methods* **13**:385-386.

Altman, N. & Krzywinski, M. (2015) Points of Significance: Multiple Linear Regression *Nature Methods* **12**:1103-1104.

Altman, N. & Krzywinski, M. (2015) Points of significance: Simple Linear Regression *Nature Methods* **12**:999-1000.

Genomic instability is one of the defining characteristics of cancer and within a tumor, which is an ever-evolving population of cells, there are many genomes. Mutations accumulate and propagate to create subpopulations and these groups of cells, called clones, may respond differently to treatment.

It is now possible to sequence individual cells within a tumor to create a profile of genomes. This profile changes with time, both in the kinds of mutation that are found and in their proportion in the overall population.

Clone evolution diagrams visualize these data. These diagrams can be qualitative, showing only trends, or quantitative, showing temporal and population changes to scale. In this Molecular Cell forum article I provide guidelines for drawing these diagrams, focusing with how to use color and navigational elements, such as grids, to clarify the relationships between clones.

I'd like to thank Maia Smith and Cydney Nielsen for assistance in preparing some of the figures in the paper.

Krzywinski, M. (2016) Visualizing Clonal Evolution in Cancer. Mol Cell 62:652-656.