Designing genome visualizations with IdeogramJS

This presentation discusses how to make compelling interactive graphics for genomics using Ideogram.js (https://github.com/eweitz/ideogram), a tool for chromosome visualization on the web.

It discusses a range of use cases, and shows you how to: depict clinical variants, compare your genes to a plant’s, show where BRCA1 is, visualize genome alignments, see how cancer wreaks genomic havoc, explore how space flight affects gene expression, and more.

Design considerations are also discussed, including layout, annotations, labels, and legends.

Transcript

1. Eric Weitz Broad Institute of MIT and Harvard 2020-04-24 https://github.com/eweitz/ideogram Designing genome visualizations with Ideogram.js
2. Outline
3. What is an ideogram?
4. Human genome as karyotype
5. Human genome as ideogram
6. Parts of a chromosome
7. p arm q arm Parts of a chromosome
8. Parts of a chromosome
9. Ideograms are widely used
10. Outline
11. Ideogram.js • • • •
12. Ideogram.js is a reusable component • • • • • •
13. Ideogram.js in React
14. Ideogram.js in Jupyter Notebooks
15. Outline
16. Show the human genome https://eweitz.github.io/ideogram/human
17. https://eweitz.github.io/ideogram/mouse View genome on phone or tablet
18. See any of 100+ eukaryotic genomes https://eweitz.github.io/ideogram/eukaryotes
19. Where do these genes from species A exist in species B?
20. Customize layout
21. Visualize genome alignments
22. Explore differential expression across the genome
23. Use Terra to learn how to run Ideogram data pipeline https://app.terra.bio/#workspaces/degenome/degenome/notebooks/launch/degenome-tutorial.ipynb
24. Compare chromosomal events across cancer samples
25. Inform clinicians and patients about genetics ACMG 59 genes. Red: BRCA1. Purple: highly-weighted genes from NCBI Gene.
26. Load BED files
27. Show gene location
28. More use cases, live examples, source code: https://eweitz.github.io/ideogram
29. Outline
30. Geometry and orientation
31. Multiple rows for space-efficient layout
32. Annotations: tracks, layout, color, shape
33. Labels and legends
34. Thank you! • • • •