And whatever I do will become forever what I've done.don't rehearsemore quotes

# making poetry out of spam is fun

Visualizaiton workshop at UBC B.I.G. Research Day. 11 May 2016

# Nature Methods: Points of Significance

Points of Significance column in Nature Methods. (Launch of Points of Significance)

## A Statistics Primer and Best Practices

The Points of Significance column was launched in September 2013 as an educational resource to authors and to provide practical suggestions about best practices in statistical analysis and reporting.

This month we launch a new column "Points of Significance" devoted to statistics, a topic of profound importance for biological research, but one that often doesn’t receive the attention it deserves.

The "aura of exactitude" that often surrounds statistics is one of the main notions that the Points of Significance column will attempt to dispel, while providing useful pointers on using and evaluating statistical measures.
—Dan Evanko, Let's Give Statistics the Attention it Deserves in Biological Research

The column is co-authored with Naomi Altman (Pennsylvania State University). Paul Blainey (Broad) is a contributing co-author.

## Free Access

In February 2015, Nature Methods announced that the entire Points of Significance collection will be free.

When Nature Methods launched the Points of Significance column over a year ago we were hopeful that those biologists with a limited background in statistics, or who just needed a refresher, would find it accessible and useful for helping them improve the statistical rigor of their research. We have since received comments from researchers and educators in fields ranging from biology to meteorology who say they read the column regularly and use it in their courses. Hearing that the column has had a wider impact than we anticipated has been very encouraging and we hope the column continues for quite some time.
—Dan Evanko, Points of Significance now free access

Also, in a recent post on the ofschemesandmemes blog, a new statistics collection for biologists was announced.

The pieces range from comments, to advice on very specific experimental approaches, to the entire collection of the Points of Significance columns that address basic concepts in statistics in an experimental biology context. These columns, originally published in Nature Methods thanks to Martin Krzywinski and guest editor Naomi Altman, have already proven very popular with readers and teachers. Finally, the collection presents a web tool to create box plots among other resources.
—Veronique Kiermer, Statistics for biologists—A free Nature Collection

## continuity and consistency

Each column is written with continuity and consistency in mind. Our goal is to never rely on concepts that we have not previously discussed. We do not assume previous statistical knowledge—only basic math. Concepts are illustrated using practical examples that embody the ideas without extraneous complicated details. All of the figures are designed with the same approach—as simple and self-contained as possible.

VIEW ALL

# Analyzing Outliers: Influential or Nuisance?

Fri 08-04-2016

Some outliers influence the regression fit more than others.

This month our column addresses the effect that outliers have on linear regression.

You may be surprised, but not all outliers have the same influence on the fit (e.g. regression slope) or inference (e.g. confidence or prediction intervals). Outliers with large leverage—points that are far from the sample average—can have a very large effect. On the other hand, if the outlier is close to the sample average, it may not influence the regression slope at all.

Nature Methods Points of Significance column: Analyzing Outliers: Influential or Nuisance? (read)

Quantities such as Cook's distance and the so-called hat matrix, which defines leverage, are useful in assessing the effect of outliers.

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.

# Typographical posters of bird songs

Mon 28-03-2016

Chirp, chirp, chirp but much better looking.

The song of the Northern Flicker, Black-capped Chickadee, Olive-sided Flycatcher and Red-eyed Vireo. Sweet to the eye and ear. (details)

If you like these, check out my other typographical art posters.

# Happy 2016 Pi Day—gravity of $\pi$

Mon 14-03-2016

Celebrate $\\pi$ Day (March 14th) with colliding digits in space. This year, I celebrate the detection of gravitational waves at the LIGO lab and simulate the effect of gravity on masses created from the digits of $\\pi$.

1,000 digits of $\pi$ under the influence of gravity. (details)

Some strange things can happen.

44 digits of $\pi$ under the influence of gravity. (details)

The art is featured in the Gravity of Pi article on the Scientific American SA Visual blog.

Check out art from previous years: 2013 $\\pi$ Day and 2014 $\\pi$ Day and 2015 $\\pi$ Day.

# Neural Circuit Diagrams

Sun 13-03-2016

Use alignment and consistency to untangle complex circuit diagrams.

This month we apply the ideas presented in our column about drawing pathways to neural circuit diagrams. Neural circuits are networks of cells or regions, typically with a large number of variables, such as cell and neurotransmitter type.

Nature Methods Points of View column: Neural circuit diagrams. (read)

We discuss how to effectively route arrows, how to avoid pitfalls of redundant encoding and suggest ways to encorporate emphasis in the layout.

Hunnicutt, B.J. & Krzywinski, M. (2016) Points of View: Neural circuit diagrams. Nature Methods 13:189.

Hunnicutt, B.J. & Krzywinski, M. (2016) Points of Viev: Pathways. Nature Methods 13:5.

Wong, B. (2010) Points of Viev: Gestalt principles (part 1). Nature Methods 7:863.

Wong, B. (2010) Points of Viev: Gestalt principles (part 2). Nature Methods 7:941.

# Pathways

Mon 04-01-2016

Apply visual grouping principles to add clarity to information flow in pathway diagrams.

We draw on the Gestalt principles of connection, grouping and enclosure to construct practical guidelines for drawing pathways with a clear layout that maintains hierarchy.

Nature Methods Points of View column: Pathways. (read)

We include tips about how to use negative space and align nodes to emphasizxe groups and how to effectively draw curved arrows to clearly show paths.

Hunnicutt, B.J. & Krzywinski, M. (2016) Points of Viev: Pathways. Nature Methods 13:5.

Wong, B. (2010) Points of Viev: Gestalt principles (part 1). Nature Methods 7:863.

Wong, B. (2010) Points of Viev: Gestalt principles (part 2). Nature Methods 7:941.

# Multiple Linear Regression

Mon 04-01-2016

When multiple variables are associated with a response, the interpretation of a prediction equation is seldom simple.

This month we continue with the topic of regression and expand the discussion of simple linear regression to include more than one variable. As it turns out, although the analysis and presentation of results builds naturally on the case with a single variable, the interpretation of the results is confounded by the presence of correlation between the variables.

By extending the example of the relationship of weight and height—we now include jump height as a second variable that influences weight—we show that the regression coefficient estimates can be very inaccurate and even have the wrong sign when the predictors are correlated and only one is considered in the model.

Nature Methods Points of Significance column: Multiple Linear Regression. (read)

Care must be taken! Accurate prediction of the response is not an indication that regression slopes reflect the true relationship between the predictors and the response.

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.

# Circos and Hive Workshop Workshop—Poznan, Poland

Sun 13-12-2015

Taught how Circos and hive plots can be used to show sequence relationships at Biotalent Functional Annotation of Genome Sequences Workshop at the Institute for Plant Genetics in Poznan, Poland.

Students generated images published in Fast Diploidization in Close Mesopolyploid Relatives of Arabidopsis.

Workshop materials: slides, handout, Circos and hive plot files.

Drawing synteny between modern and ancient genomes with Circos.

Students also learned how to use hive plots to show synteny.

Hive plots are great at showing 3-way sequence comparisons. Here three modern species of Australian Brassicaceae (S. nutans, S. lineare, B. antipoda) are compared based on their common relationships to the ancestral karotype.

Mandakova, T. et al. Fast Diploidization in Close Mesopolyploid Relatives of Arabidopsis The Plant Cell, Vol. 22: 2277-2290, July 2010

# Play the Bacteria Game

Mon 14-12-2015

Nobody likes dusting but everyone should find dust interesting.

Working with Jeannie Hunnicutt and with Jen Christiansen's art direction, I created this month's Scientific American Graphic Science visualization based on a recent paper The Ecology of microscopic life in household dust.

An analysis of dust reveals how the presence of men, women, dogs and cats affects the variety of bacteria in a household. Appears on Graphic Science page in December 2015 issue of Scientific American.

We have also written about the making of the graphic, for those interested in how these things come together.

This was my third information graphic for the Graphic Science page. Unlike the previous ones, it's visually simple and ... interactive. Or, at least, as interactive as a printed page can be.

More of my American Scientific Graphic Science designs

Barberan A et al. (2015) The ecology of microscopic life in household dust. Proc. R. Soc. B 282: 20151139.