Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - contact me Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert Curve
Mad about you, orchestrally.Hooverphonicfeel the vibe, feel the terror, feel the painmore quotes

science: fun



EMBO Practical Course: Bioinformatics and Genome Analysis, 5–17 June 2017.


Color Resources + Tools

Choosing, naming and clustering colors—for everyone

Resources

Color summarizer

The color summarizer generates statistical color summaries of images.

It reports average RGB, HSV, LAB and LCH color components as well as histograms and individual pixel values for these color spaces. Comes with useful web API for all your automation needs.

Yes! I support LCH, which is extremely useful in generating color ramps and, in general, talking about perceptual aspects of color that are intuitive.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My color summarizer reports the representative colors in an image by grouping colors into clusters of similar colors and reporting the average color in each cluster. This is useful in image identification and comparison.

The color summarizer also identifies representative colors in the image by using k-means clustering to group colors into clusters. The centers of each cluster are also reported by name, using my large database of named colors.

Below is an example of a detailed color report of an image—an adorable Fiat 126p I found while it was screaming out its color against the fading background of Havana.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My color summarizer generates statistical color summaries of images, including a poetic list of words used to describe the colors.

Adobe Swatches for Brewer Palettes

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
All the Brewer palettes at a glance.

The Brewer color palettes are an excellent source for perceptually uniform color palettes. I provide Adobe Swatches for all colors in the Brewer Palettes.

I also provide a short talk to help you understand why these palettes are important.

Color Palettes for Color Blindness

Color blindness is a thing. You should worry about it when you're designing and especially when you're encoding information.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Sets of representative hues and tones that are indistinguishable to individuals with different kinds of color blindness. The rectangle below the each color pair shows how the colors appear to someone with color blindness.

I provide some background on color blindness and give options for choosing 7-, 12- and 15-color palettes that are colorblind safe.

Color palette for color blindness. / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
(left) Colors grouped by equivalence of perception in deuteranopes. Each of the two hues is represented in six different brightness and chroma combinations. (right) One of the subsets of colors on the left that are reasonably distinct in both deuteranopia and protanopia. To tritanopes, three of the pairs are difficult to distinguish.

List of Named Colors

Probably the world's largest list of named colors.

With more than 8,300 colors, even a mantis shrimp would be impressed. You can finally imagine a color you can't even imagine and name it!

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Use my list of named colors to name the colors in the Google logo: dodger blue, cinnabar, amber and medium emerland green.

The color name list is hooked into the color summarizer's clustering. You can get a list of words, derived from the color names, that describes an image.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The color summarizer returns words that qualitatively describe the image.

color proportions in country flags

A visual survey of the color proportions in flags of 256 countries.

Color proportions in country flags / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
(right) 256 country flags as concentric circles showing the proportions of each color in the flag. (left) Unique flags sorted by similarity.

Flags are depicted by concentric rings whose thickness is a function of the amount of that color in the flag.

I make the flag color catalog available, as well as similarity scores based on color proportions for each flag pair, so you can run your own analysis.

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news + thoughts

Tabular Data

Tue 11-04-2017
Tabulating the number of objects in categories of interest dates back to the earliest records of commerce and population censuses.

After 30 columns, this is our first one without a single figure. Sometimes a table is all you need.

In this column, we discuss nominal categorical data, in which data points are assigned to categories in which there is no implied order. We introduce one-way and two-way tables and the `\chi^2` and Fisher's exact tests.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Tabular data. Nature Methods 14:329–330.

...more about the Points of Significance column

Happy 2017 `\pi` Day—Star Charts, Creatures Once Living and a Poem

Tue 14-03-2017


on a brim of echo,

capsized chamber
drawn into our constellation, and cooling.
—Paolo Marcazzan

Celebrate `\pi` Day (March 14th) with star chart of the digits. The charts draw 40,000 stars generated from the first 12 million digits.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
12,000,000 digits of `\pi` interpreted as a star catalogue. (details)

The 80 constellations are extinct animals and plants. Here you'll find old friends and new stories. Read about how Desmodus is always trying to escape or how Megalodon terrorizes the poor Tecopa! Most constellations have a story.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Find friends and stories among the 80 constellations of extinct animals and plants. Oh look, a Dodo guardings his eggs! (details)

This year I collaborate with Paolo Marcazzan, a Canadian poet, who contributes a poem, Of Black Body, about space and things we might find and lose there.

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

Data in New Dimensions: convergence of art, genomics and bioinformatics

Tue 07-03-2017

Art is science in love.
— E.F. Weisslitz

A behind-the-scenes look at the making of our stereoscopic images which were at display at the AGBT 2017 Conference in February. The art is a creative collaboration with Becton Dickinson and The Linus Group.

Its creation began with the concept of differences and my writeup of the creative and design process focuses on storytelling and how concept of differences is incorporated into the art.

Oh, and this might be a good time to pick up some red-blue 3D glasses.

BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A stereoscopic image and its interpretive panel of single-cell transcriptomes of blood cells: diseased versus healthy control.

Interpreting P values

Thu 02-03-2017
A P value measures a sample’s compatibility with a hypothesis, not the truth of the hypothesis.

This month we continue our discussion about `P` values and focus on the fact that `P` value is a probability statement about the observed sample in the context of a hypothesis, not about the hypothesis being tested.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Interpreting P values. (read)

Given that we are always interested in making inferences about hypotheses, we discuss how `P` values can be used to do this by way of the Benjamin-Berger bound, `\bar{B}` on the Bayes factor, `B`.

Heuristics such as these are valuable in helping to interpret `P` values, though we stress that `P` values vary from sample to sample and hence many sources of evidence need to be examined before drawing scientific conclusions.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Interpreting P values. Nature Methods 14:213–214.

Background reading

Krzywinski, M. & Altman, N. (2017) Points of significance: P values and the search for significance. Nature Methods 14:3–4.

Krzywinski, M. & Altman, N. (2013) Points of significance: Significance, P values and t–tests. Nature Methods 10:1041–1042.

...more about the Points of Significance column

Snellen Charts—Typography to Really Look at

Sat 18-02-2017

Another collection of typographical posters. These ones really ask you to look.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Snellen charts designed using physical constants, Braille and elemental abundances in the universe and human body.

The charts show a variety of interesting symbols and operators found in science and math. The design is in the style of a Snellen chart and typset with the Rockwell font.