Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Plot heatmap of polytomy density over space and time #162

Open
duncanMR opened this issue Apr 29, 2024 · 0 comments
Open

Plot heatmap of polytomy density over space and time #162

duncanMR opened this issue Apr 29, 2024 · 0 comments

Comments

@duncanMR
Copy link
Contributor

Given our interest in how polytomies affect tsdate performance, it would be very helpful to be able to create a heatmap of polytomy density in bins across space and time. This would be particularly useful in conjuction with the mutations plot, since we can test whether the dense bands in mutation times correlate with regions of high polytomy density.

We briefly discussed the implementation of this plot in the tsdate meeting last week: @jeromekelleher had an idea for how to iterate through the trees and keep track of node arity in time bins. Nate Pope pointed out that this algorithm is similar to the coalescent rate calculator, so we might be able to repurpose that code.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant