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Here we are now at the middle of the fourth large part of this talk.Pepe Deluxeget nowheremore quotes

hitchens: exciting


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


visualization + design

Christopher Hitchens—Out of Letters

ASCII Art

The images shown here were created as part of my ASCII Art project, which extends ASCII art to include

  • proportionally spaced fonts
  • a variety of font weights in a single image
  • both tone and structure of the image to select characters
  • fixed strings to render an image in legible text

Applying the code to images of Hitchens was motivated by my own deep love of Hitchens and a typographic portrait of Christopher Hitchens, created out of Gill Sans letters by Miles Chic at Capilano University.

This adds to my growing shrines to Hitchens, including Merry Hitchmas! and hitchslap t-shirts.

Christopher Hitchens in Letters and Words

All images are generated using Gotham, with up to 8 weights (Extra Light to Ultra). Each image includes size and characters used for the image. I give the absolute type size, though only useful to know in relative terms to the size of the image and other images drawn with the same method. The color of text in each layer is the same—black— but font weight may vary.

Some images are generated using more than one layer of ASCII. In some cases the characters used in each layer are different.

basic ascii

As the font size is reduced, greater detail and contrast can be achieved.

Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 43pt set: . x 8 : * @ - \ | _space_ / (source from Christian Witkin/Twelve/Grand Central Publishing) (zoom, source)
Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 29pt set: . x 8 : * @ - \ | _space_ / (source from Christian Witkin/Twelve/Grand Central Publishing) (zoom, source)
Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 17pt set: . x 8 : * @ - \ | _space_ / (source from Christian Witkin/Twelve/Grand Central Publishing) (zoom, source)
Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 11pt set: . x 8 : * @ - \ | _space_ / (source from Christian Witkin/Twelve/Grand Central Publishing) (zoom, source)

By setting the image with a fixed string, such as a short quote or longer body of text, detail is lost but the ASCII representation takes on more meaning.

Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 11pt set: godisnotgreat (source from Christian Witkin/Twelve/Grand Central Publishing) (zoom, source)
Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 29pt set: godisnotgreat (source from Christian Witkin/Twelve/Grand Central Publishing) (zoom, source)
Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 11pt set: Hitchslap 11 (source from Christian Witkin/Twelve/Grand Central Publishing) (zoom, source)
Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 5 layers (11pt -6deg, 17pt 6deg, 29pt -3deg, 43pt 3deg, 59pt 0deg) set: godisnotgreat (source from Christian Witkin/Twelve/Grand Central Publishing) (zoom, source)
Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 7pt set: . x 8 : * @ - \ | _space_ / (source from Gasper Tringale) (zoom, source)

multi-layered ascii art

Images take on detail when multiple rotated layers of text is used. Each of the images below is composed of more than one layer, starting with a 2-layer image which uses the uppercase alphabet at 0 and 90 degrees.

Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 2 layers (0deg, 90deg) set: A-Z (source from HBO) (zoom, source)

Meaning can be added to the image by using different text in each layer. In the examples below, I set the same image using the pair "Godisnotgreat" (at 0 degrees) and "religionpoisonseverything" (at 90 degrees). In the second example, I use the unlikely combination of "Jesus" and "Mohammad"—inspired by Jesus and Mo.

Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 2 layers set: Godisnotgreat. 0deg Relionpoisonseverything. 90deg (source from HBO) (zoom, source)
Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 2 layers set: Jesus 0deg Mohammad 90deg (source from HBO) (zoom, source)

When rotated layers contain punctuation, very high level of detail can be achieved.

Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 2 layers set: . : - + * _space_ 0deg / 90deg (zoom, source)

The image below is made out of layers that contain only forward (/) and back (\) slashes.

Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 2 layers set: \ / (zoom, source)

The image below is made using only the period character in three layers rotated at -45, 0 and 45 degrees. Although the image looks like a pixelated version of the original—it is more than that. It is a typeset representation that uses 8 weights of Gotham. Character spacing between periods is informed by font metrics.

Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 2 layers set: . (zoom, source)
Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 2 layers set: 8 X x | ^ : . - = + ' " @ \ / | * ~ , # (source from The Australian) (zoom, source)

hitchens at the podium

The three images below show the difference between using a variety of punctuation characters and setting an image using a block of text. The first image uses "8 X x" and common punctuation.

Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 11pt set: 8 X x | ^ : . - = + ' " @ \ / | * ~ , # (zoom, source)

I use hitchslap 9 for the first image below, and all the hitchslaps for the second image. When setting an image in using a block of text, the choice of character at any position is fixed and only the font weight is allowed to vary. When the text is relatively short (e.g. hitchslap 9 is 544 characters and is repeated 50 times in the image), rivers of space appear in the image.

Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 11pt set: Hitchslap 9 (zoom, source)
Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 11pt set: all Hitchslaps (zoom, source)

In both cases, the image is very recognizable.

recursive ascii art

When an image of text is set with the text itself, you have recursive ASCII art. Below is hitchslap 2, set with itself. In the image, the font is Gotham and the text used to asciify the image is also Gotham.

It makes ordinary moral people, compels them, forces them, in some cases orders them do disgusting wicked unforgivable things. There's no expiation for the generations of misery and suffering that religion has inflicted in this way and continues to inflict. And I still haven't heard enough apology for it. — Christopher Hitchens

The quote is 307 characters long and is repeated 391 times in the image.

Christopher Hitchens - ASCII Art / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Christopher Hitchens ASCII Art. method: Gotham font, 8 weights, 11pt set: Hitchslap 2 (source from hitchslap 2) (zoom, source)

In principle, the process of asciifying text with text can be repeated, by using the asciified image as input for asciification with progressively smaller text.

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news + thoughts

Ensemble methods: Bagging and random forests

Mon 16-10-2017
Many heads are better than one.

We introduce two common ensemble methods: bagging and random forests. Both of these methods repeat a statistical analysis on a bootstrap sample to improve the accuracy of the predictor. Our column shows these methods as applied to Classification and Regression Trees.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Ensemble methods: Bagging and random forests. (read)

For example, we can sample the space of values more finely when using bagging with regression trees because each sample has potentially different boundaries at which the tree splits.

Random forests generate a large number of trees by not only generating bootstrap samples but also randomly choosing which predictor variables are considered at each split in the tree.

Krzywinski, M. & Altman, N. (2017) Points of Significance: Ensemble methods: bagging and random forests. Nature Methods 14:933–934.

Background reading

Krzywinski, M. & Altman, N. (2017) Points of Significance: Classification and regression trees. Nature Methods 14:757–758.

...more about the Points of Significance column

Classification and regression trees

Mon 16-10-2017
Decision trees are a powerful but simple prediction method.

Decision trees classify data by splitting it along the predictor axes into partitions with homogeneous values of the dependent variable. Unlike logistic or linear regression, CART does not develop a prediction equation. Instead, data are predicted by a series of binary decisions based on the boundaries of the splits. Decision trees are very effective and the resulting rules are readily interpreted.

Trees can be built using different metrics that measure how well the splits divide up the data classes: Gini index, entropy or misclassification error.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Classification and decision trees. (read)

When the predictor variable is quantitative and not categorical, regression trees are used. Here, the data are still split but now the predictor variable is estimated by the average within the split boundaries. Tree growth can be controlled using the complexity parameter, a measure of the relative improvement of each new split.

Individual trees can be very sensitive to minor changes in the data and even better prediction can be achieved by exploiting this variability. Using ensemble methods, we can grow multiple trees from the same data.

Krzywinski, M. & Altman, N. (2017) Points of Significance: Classification and regression trees. Nature Methods 14:757–758.

Background reading

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

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

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

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Model Selection and Overfitting. Nature Methods 13:703-704.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of Significance: Regularization. Nature Methods 13:803-804.

...more about the Points of Significance column

Personal Oncogenomics Program 5 Year Anniversary Art

Wed 26-07-2017

The artwork was created in collaboration with my colleagues at the Genome Sciences Center to celebrate the 5 year anniversary of the Personalized Oncogenomics Program (POG).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
5 Years of Personalized Oncogenomics Program at Canada's Michael Smith Genome Sciences Centre. The poster shows 545 cancer cases. (left) Cases ordered chronologically by case number. (right) Cases grouped by diagnosis (tissue type) and then by similarity within group.

The Personal Oncogenomics Program (POG) is a collaborative research study including many BC Cancer Agency oncologists, pathologists and other clinicians along with Canada's Michael Smith Genome Sciences Centre with support from BC Cancer Foundation.

The aim of the program is to sequence, analyze and compare the genome of each patient's cancer—the entire DNA and RNA inside tumor cells— in order to understand what is enabling it to identify less toxic and more effective treatment options.

Principal component analysis

Thu 06-07-2017
PCA helps you interpret your data, but it will not always find the important patterns.

Principal component analysis (PCA) simplifies the complexity in high-dimensional data by reducing its number of dimensions.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Principal component analysis. (read)

To retain trend and patterns in the reduced representation, PCA finds linear combinations of canonical dimensions that maximize the variance of the projection of the data.

PCA is helpful in visualizing high-dimensional data and scatter plots based on 2-dimensional PCA can reveal clusters.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Principal component analysis. Nature Methods 14:641–642.

Background reading

Altman, N. & Krzywinski, M. (2017) Points of Significance: Clustering. Nature Methods 14:545–546.

...more about the Points of Significance column