categorise mutations #1449
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categorise mutations #1449
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This is in preparation for a forthcoming commit which will need this information to decide whether a mutation is homoplasic.
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jameshadfield
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These changes were motivated by issue #1444 [1] where separating mutations into categories can aid both QC and biological interpretation. I chose to use "mutations" to refer to mutations observed on a branch and "changes" to refer to the collection of mutations between a tip and the root. The categories are not necessarily disjoint, as a mutation back to the root will also be a homoplasy or a unique mutation. Note that changes between a tip sequence and the root aren't grouped into homoplasies, as a single change (A→C) may be the result of multiple mutations (e.g. A→B→C) and thus we would need to check the tip state of each position which is difficult with the current code. On-hover panels are left unchanged in this commit. [1] #1444
Previously we displayed the mutations on the branch leading to the tip, which was inconsistent with the information shown when clicking on a tip. Showing a summary of counts is a good compromise between visual space and conveying all the information. Note that hovering on the branch leading to the tip still shows the mutations leading to the tip, if that info is desired.
Grouping nucleotide mutations (as per previous commits) while hovering on branches is really helpful for understanding the tree. The penalty is the use of more space, and so I've chosen to not group AA mutations here; one can shift+click on the branch to see these grouped if needed.
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Description of proposed changes
See #1444 for context & commit messages for further info. Or just look at the examples 😉
Testing
Unit tests added, as well as interactive testing
Examples
Branch Hover
I've grouped nucleotide mutations on branch hover, as I find it super useful for exploring the tree to see if mutations are homoplasic or reversions to the root (i.e. potentially backfilled). In the interest of keeping the size of the info-box manageable, I've kept the AA mutations unchanged.
Branch (shift+)click
Branches group mutations into unique vs homoplasies vs gaps vs Ns. They also report which are reversions to the root. Gaps and Ns are grouped into intervals.
Tip hover
When hovering over tips we no longer report the mutations on the branch leading to the tip, rather we report a summary of changes w.r.t the root. If you want to see the mutations on the branch leading to the tip, then you can still hover on the branch to see them.
Tip click
When clicking on a tip we list those changes between the root and this sample:
Questions
Further work
I purposefully didn't spend a huge amount of time tweaking the aesthetics of the changes here, as I plan to incorporate the nextclade / CoVariants badges shortly.