resources
visualizations
presentations
lunch break
Distractions and amusements, with a sandwich and coffee.
data visualization + art
Art of the Personalized Oncogenomics Program
Nature uses only the longest threads to weave her patterns, so that each small piece of her fabric reveals the organization of the entire tapestry.
— Richard Feynman
Art is Science in Love
— E.F. Weisslitz
what do the circles mean?
The legend can be printed at 4" × 6". The bitmap resolution is 600 dpi.
a case for a visual case summary
For every case, we sequence the DNA to study the genome structure and the RNA to discover which genes are expressed and to what extent. The analysis is quite complex and brings together many steps: sequence alignment, structural variation detection, expression profiling, pathway analysis and so on. Every case is "summarized" by a lengthy report, such as the one below, which can run to over 40 pages.
One of the goals of the 5-year anniversary art was to represent the cases in a way to clearly show their number, classification as well as diversity. There are many metrics that can be used and I decided to choose the case's correlation to other cancer types.
correlation to TCGA cancer database
For every POG case, the gene expression of 1,744 key genes is compared to that of 1,000's of cases in the TCGA database of cancer samples. For a given cancer type in the TCGA database (e.g. BRCA), we visualize the correlations using box plots. The box plot is ideal for showing the distribution of values in a sample.
The 10 largest Spearman correlation coefficients for the case shown above are
case corr type tissue ----------------------------------------------- POG661 0.436 BRCA Breast POG661 0.371 PRAD Urologic POG661 0.295 OV Gynecologic POG661 0.257 UCEC Gynecologic POG661 0.244 LUAD Thoracic POG661 0.235 CESC_CAD Gynecologic POG661 0.225 MB_Adult Central Nervous System POG661 0.222 KICH Urologic POG661 0.219 THCA Endocrine POG661 0.208 UCS Gynecologic
In the figure below I show how the final encoding of the correlations is done. First, the top three correlations are taken—using more generates a busy look and diminishes visual impact. The correlations are encoded as concentric rings.
Because in most cases the differences in the top 3 correlations are relatively small, differences are emphasized by non-linearly scaling the encoding (the correlations are first scaled `r^3`).
The type face is Proxima Nova. The colors for each tissue source are
Gastrointestinal ● 234,62,144
Breast ● 237,75,51
Thoracic ● 242,130,56
Gynecologic ● 253,188,61
Soft tissue ● 244,217,59
Skin ● 193,216,51
Urologic ● 114,197,49
Hematologic ● 29,166,68
Head and neck ● 43,168,224
Endocrine ● 71,82,178
Central nervous system ● 127,65,146
Other ● 150,150,150
news + thoughts
Predicting with confidence and tolerance
I abhor averages. I like the individual case. —J.D. Brandeis.We focus on the important distinction between confidence intervals, typically used to express uncertainty of a sampling statistic such as the mean and, prediction and tolerance intervals, used to make statements about the next value to be drawn from the population.
Confidence intervals provide coverage of a single point—the population mean—with the assurance that the probability of non-coverage is some acceptable value (e.g. 0.05). On the other hand, prediction and tolerance intervals both give information about typical values from the population and the percentage of the population expected to be in the interval. For example, a tolerance interval can be configured to tell us what fraction of sampled values (e.g. 95%) will fall into an interval some fraction of the time (e.g. 95%).
Altman, N. & Krzywinski, M. (2018) Points of significance: Predicting with confidence and tolerance Nature Methods 15:843–844.
Background reading
Krzywinski, M. & Altman, N. (2013) Points of significance: Importance of being uncertain. Nature Methods 10:809–810.
4-day Circos course
A 4-day introductory course on genome data parsing and visualization using Circos. Prepared for the Bioinformatics and Genome Analysis course in Institut Pasteur Tunis, Tunis, Tunisia.
Oryza longistaminata genome cake
Data visualization should be informative and, where possible, tasty.
Stefan Reuscher from Bioscience and Biotechnology Center at Nagoya University celebrates a publication with a Circos cake.
The cake shows an overview of a de-novo assembled genome of a wild rice species Oryza longistaminata.
Optimal experimental design
Customize the experiment for the setting instead of adjusting the setting to fit a classical design.The presence of constraints in experiments, such as sample size restrictions, awkward blocking or disallowed treatment combinations may make using classical designs very difficult or impossible.
Optimal design is a powerful, general purpose alternative for high quality, statistically grounded designs under nonstandard conditions.
We discuss two types of optimal designs (D-optimal and I-optimal) and show how it can be applied to a scenario with sample size and blocking constraints.
Smucker, B., Krzywinski, M. & Altman, N. (2018) Points of significance: Optimal experimental design Nature Methods 15:599–600.
Background reading
Krzywinski, M., Altman, N. (2014) Points of significance: Two factor designs. Nature Methods 11:1187–1188.
Krzywinski, M. & Altman, N. (2014) Points of significance: Analysis of variance (ANOVA) and blocking. Nature Methods 11:699–700.
Krzywinski, M. & Altman, N. (2014) Points of significance: Designing comparative experiments. Nature Methods 11:597–598.
The Whole Earth Cataloguer
All the living things.An illustration of the Tree of Life, showing some of the key branches.
The tree is drawn as a DNA double helix, with bases colored to encode ribosomal RNA genes from various organisms on the tree.
All living things on earth descended from a single organism called LUCA (last universal common ancestor) and inherited LUCA’s genetic code for basic biological functions, such as translating DNA and creating proteins. Constant genetic mutations shuffled and altered this inheritance and added new genetic material—a process that created the diversity of life we see today. The “tree of life” organizes all organisms based on the extent of shuffling and alteration between them. The full tree has millions of branches and every living organism has its own place at one of the leaves in the tree. The simplified tree shown here depicts all three kingdoms of life: bacteria, archaebacteria and eukaryota. For some organisms a grey bar shows when they first appeared in the tree in millions of years (Ma). The double helix winding around the tree encodes highly conserved ribosomal RNA genes from various organisms.
Johnson, H.L. (2018) The Whole Earth Cataloguer, Sactown, Jun/Jul, p. 89
Why we can't give up this odd way of typing
All fingers report to home row.An article about keyboard layouts and the history and persistence of QWERTY.
My Carpalx keyboard optimization software is mentioned along with my World's Most Difficult Layout: TNWMLC. True typing hell.
McDonald, T. (2018) Why we can't give up this odd way of typing, BBC, 25 May 2018.