Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - contact me Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert CurveMartin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Day 2020 - Piku
Safe, fallen down this way, I want to be just what I am.Cocteau Twinssafe at lastmore quotes

green: color


Scientific graphical abstracts — design guidelines


visualization + design
If you are interested in color, explore my other color tools, Brewer palettes resources, color blindness palettes and math and an exhausting list of 10,000 color names for all those times you couldn't distinguish between tan hide, sea buckthorn, orange peel, west side, sunshade, california and pizzaz.

Designing for Color Blindess

Color choices and transformations for deuteranopia and other afflictions

Here, I help you understand color blindness and describe a process by which you can make good color choices when designing for accessibility.

The opposite of colorblindness is seeing all the colors and I can help you find 1,000 (or more) maximally distinct colors.

You can also delve into the mathematics behind the color blindness simulations and learn about copunctal points (the invisible color!) and lines of confusion.

Download all palettes
plain text, v11 20 May 2020
Download slides
PDF, v11 20 May 2020

In this section, I cover how to make good color choices when considering audiences with color blindness.

With the exception of the 8-color palette, all palettes have been created using a process (read below) that tries to maintain perceptual luminance uniformity in color blind space.

conservative 8-color palettes for color blindness

This 8-color palette is adapted from Nature Method's Points of View: Color blindness by Bang Wong. Note that in that original source the RGB values listed in the table did not exactly correspond to the RGB swatches—probably an RGB vs CMYK conversion mixup.

This palette is suitable for categorical color encoding—the colors do not, as a whole, have a natural order and none is substantially more salient than another.

You can download these colors as plain text list of HEX and RGB values.

An 8-color palette for color blindness. / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An 8-color palette for color blindness, adapted from Wong, B. (2011) Nature Methods 8:441. (zoom, PDF, plain text)

For more tips about designing with color blindness in mind, see Color Universal Design (CUD) — How to make figures and presentations that are friendly to people with color blindess.

using color equivalencies

To people with color blindness, some colors appear the same. This equivalence can be used to identify colors that are distinct to those with normal as well as to those with color blindness.

For a given RGB color we can simulate how it would appear to someone with color blindess and identify groups of RGB colors that appear indistinguishable in color blindness.

Color equivalencies in color blindness for protanopia, deuteranopia and tritanopia. / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Many colors appear the same to people with color blindness. This chart shows the colors that are identical (rows) to those with protanopia, deuteranopia (most common) and tritanopia (zoom)

These equivalencies can be used to construct color palettes—lists of colors that are distinguishable to deuteranopes and those with normal vision.

Since deuteranopia is the most common, this is the condition that I use for color selection.

The exact luminance (perceived brightness) of the simulated color varies depending on the color blindness algorithm. Each row in the squares above should look identical using any color blindness simulation (e.g. Color Oracle, Photoshop, etc) but brightness of the rows may be slightly different than shown here.

12-color palettes for color blindness

This palette maps four colors onto each of the two color dimensions in deuteranopes and four onto greyscale. This palette is very useful for designing transit and subway maps.

Color names are playful selections from my list of 10,000 color names.

You can download these colors as plain text list of HEX and RGB values.

A 12-color palette for color blindness. / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A 12 color palette for color blindness that maps onto each of the color dimensions in deuteranopes. Within each set of four, colors also have reasonably similar greyscale tones. Inset swatches show color alternatives that are indistinguishable from the main swatch for deuternopes. (zoom, PDF, plain text)

15-color palettes for color blindness

You can download these colors as plain text list of HEX and RGB values.

A 15-color palette for color blindness. / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A 15-color palette for color blindness. (zoom, PDF, plain text)

24-color palettes for color blindness

Even more color choices for color blindess, including colors that map onto greys. For these, I don't have RGB/HEX values handy.

You can download these colors as plain text list of HEX and RGB values.

15-color palettes for color blindness / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
15-color palettes designed for each of the three types of color blindness: deuteranopia, protanopia and tritanopia. Palettes are shown as they appear to someone with normal vision as well as to someone affected with each of the three types of color blindness. Each palette contains three groups of swatches, matching to two of the color channels and greys. Within each group colors in the same row map onto the same color. (zoom, PDF)

the last word on color palettes for color blindness

You can create your own color palettes using the figure below.

For a given color blindness type (e.g. deuteranopia) and channel (e.g. blue), the rows represent reasonably uniform steps in LCH luminance of the simulated color and a rich (high chroma) simulation at that luminance.

The last word on color palettes for color blidness. / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Color ramps of 16–19 colors for each color channel for each color blidness type. Color ramps show RGB colors and their color blindness simulation grouped by channels (e.g. greys, blues, yellow). Within a channel, colors are sorted in increasing and roughly equal steps of LCH luminance of the simulated color. At a given luminance, the RGB color whose simulation has the highest chroma is used. (zoom, PDF)

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news + thoughts

Music for the Moon: Flunk's 'Down Here / Moon Above'

Sat 29-05-2021

The Sanctuary Project is a Lunar vault of science and art. It includes two fully sequenced human genomes, sequenced and assembled by us at Canada's Michael Smith Genome Sciences Centre.

The first disc includes a song composed by Flunk for the (eventual) trip to the Moon.

But how do you send sound to space? I describe the inspiration, process and art behind the work.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The song 'Down Here / Moon Above' from Flunk's new album History of Everything Ever is our song for space. It appears on the Sanctuary genome discs, which aim to send two fully sequenced human genomes to the Moon. (more)

Browse the genome discs.

Happy 2021 `\pi` Day—
A forest of digits

Sun 14-03-2021

Celebrate `\pi` Day (March 14th) and finally see the digits through the forest.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 26th tree in the digit forest of `\pi`. Why is there a flower on the ground?. (details)

This year is full of botanical whimsy. A Lindenmayer system forest – deterministic but always changing. Feel free to stop and pick the flowers from the ground.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The first 46 digits of `\pi` in 8 trees. There are so many more. (details)

And things can get crazy in the forest.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A forest of the digits of '\pi`, by ecosystem. (details)

Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day, 2016 `\pi` Day, 2017 `\pi` Day, 2018 `\pi` Day and 2019 `\pi` Day.

Testing for rare conditions

Sun 30-05-2021

All that glitters is not gold. —W. Shakespeare

The sensitivity and specificity of a test do not necessarily correspond to its error rate. This becomes critically important when testing for a rare condition — a test with 99% sensitivity and specificity has an even chance of being wrong when the condition prevalence is 1%.

We discuss the positive predictive value (PPV) and how practices such as screen can increase it.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Testing for rare conditions. (read)

Altman, N. & Krzywinski, M. (2021) Points of significance: Testing for rare conditions. Nature Methods 18:224–225.

Standardization fallacy

Tue 09-02-2021

We demand rigidly defined areas of doubt and uncertainty! —D. Adams

A popular notion about experiments is that it's good to keep variability in subjects low to limit the influence of confounding factors. This is called standardization.

Unfortunately, although standardization increases power, it can induce unrealistically low variability and lead to results that do not generalize to the population of interest. And, in fact, may be irreproducible.

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

Not paying attention to these details and thinking (or hoping) that standardization is always good is the "standardization fallacy". In this column, we look at how standardization can be balanced with heterogenization to avoid this thorny issue.

Voelkl, B., Würbel, H., Krzywinski, M. & Altman, N. (2021) Points of significance: Standardization fallacy. Nature Methods 18:5–6.

Graphical Abstract Design Guidelines

Fri 13-11-2020

Clear, concise, legible and compelling.

Making a scientific graphical abstract? Refer to my practical design guidelines and redesign examples to improve organization, design and clarity of your graphical abstracts.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Graphical Abstract Design Guidelines — Clear, concise, legible and compelling.