Skip to content

fix: apply negative tree branch length correction iteratively #45

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.

Sign up for GitHub

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

Merged
ahmig merged 1 commit into from
May 2, 2026
Merged

fix: apply negative tree branch length correction iteratively #45

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 7 additions & 5 deletions workflow/scripts/report/allele_freq_tree_data.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,11 +19,13 @@ fix_negative_edge_length <- function(nj.tree) {
) %>%
as.data.table()
colnames(edge_infos) <- c("from", "to", "length")
nega_froms <- edge_infos[length < 0, sort(unique(from))]
for (nega_from in nega_froms) {
minus_length <- edge_infos[from == nega_from, ][order(length)][1, length]
edge_infos[from == nega_from, length := length - minus_length]
edge_infos[to == nega_from, length := length + minus_length]
while (any(edge_infos$length < 0)) {
nega_froms <- edge_infos[length < 0, sort(unique(from))]
for (nega_from in nega_froms) {
minus_length <- edge_infos[from == nega_from, ][order(length)][1, length]
edge_infos[from == nega_from, length := length - minus_length]
edge_infos[to == nega_from, length := length + minus_length]
}
}
nj.tree$edge.length <- edge_infos$length
nj.tree
Expand Down
Loading