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fix(scripts): count Venn overlap by distinct variant key #99

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Merged
ameynert merged 1 commit into from
Jun 3, 2026
Merged

fix(scripts): count Venn overlap by distinct variant key #99

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20 changes: 13 additions & 7 deletions scripts/compare_divref_gnomad.R
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Original file line number Diff line number Diff line change
Expand Up @@ -100,13 +100,19 @@ divref_in_gnomad %>% write_tsv(paste0(opts$output_base, ".divref_in_gnomad.tsv")

# Plot: Venn diagram of DivRef vs gnomAD variant overlap ----

n_both <- nrow(divref_in_gnomad)
n_divref_only <- nrow(divref_not_in_gnomad)
n_gnomad_only <- nrow(gnomad) - n_both

log_info(nrow(divref_in_gnomad), " DivRef variants found in gnomAD")
log_info(nrow(divref_not_in_gnomad), " DivRef variants not found in gnomAD")
log_info(n_gnomad_only, "gnomAD variants not found in DivRef")
# Count by distinct variant key, not by joined-row count: a duplicate `variant` in the gnomAD
# table would otherwise inflate the overlap and could push n_gnomad_only negative (which euler()
# rejects). On clean inputs these equal the row counts. The joined frames above are still used for
# the per-variant AF-difference plots.
divref_keys <- unique(divref$variants)
gnomad_keys <- unique(gnomad$variant)
n_both <- length(intersect(divref_keys, gnomad_keys))
n_divref_only <- length(setdiff(divref_keys, gnomad_keys))
n_gnomad_only <- length(setdiff(gnomad_keys, divref_keys))

log_info(n_both, " DivRef variants found in gnomAD")
log_info(n_divref_only, " DivRef variants not found in gnomAD")
log_info(n_gnomad_only, " gnomAD variants not found in DivRef")

venn_counts <- c(n_divref_only, n_gnomad_only, n_both)
names(venn_counts) <- c("DivRef 1.1", opts$gnomad_label, paste0("DivRef 1.1&", opts$gnomad_label))
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