Linear genome/mutation visualizer

[atc3]

Intro

When we implement the 3D PDB viewer with a mutation heatmap, it would be good to have some sort of 2D visualization of mutations – mutations that are either lineage defining, or if possible, a continuous scale of mutation frequency mapped along some sort of 2D representation of the genome.

For reference here is what our 3D viewer will eventually look like:

Examples

Here are some attempts by others to map mutations onto a 2D representation of the genome:

New York Times Variant Tracker

The biggest problem with this visualization is that it doesn't fit entirely on my screen – I have to zoom out to capture all of it.

outbreak.info

Solution

Here's some ways I think we can make an improved 2D genome/mutation viewer. For now let's ignore the case where we need to show mutation frequencies – we can focus on the use case where we just need to show the characteristic mutations for a lineage like B.1.1.7

• The should have a switch between showing either genes or proteins. It's not that helpful to have both shown at the same time and it just makes things more confusing. We should probably default to proteins since that level is more relevant when looking at AA mutations
• The genome organization itself is pretty limiting. To elaborate:
  • We shouldn't force ourselves to make the visual gene/protein sizes proportional to their actual size in bases. For example, in the outbreak.info example, some of the genes are so small that they can't even be labelled. And then there's so little mutations in ORF1ab that the space dedicated to it is wasted
  • We don't even have to be faithful to the order of the genes. It's useful for people to find their gene of interest, but that's only if they have memorized the order of genes (I forget the order after Spike). It might even be more useful to have the genes/proteins in alphabetical order instead.
  • If we start to ignore the order of the genes, then we don't have to display them in a linear/circular connected layout anymore. We could move to a list-like layout, for example
• Mutation information should show both the reference and alternate bases/residues. We should also have a place to show the canonical "news article" name, i.e., E484K, so that they are easily recognizable